From eb5b3bb6d7d069b241dc8e8b3343b996c6d5c81c Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Fri, 25 Sep 2026 17:54:17 +0200 Subject: [PATCH 1/2] docs: updated server references to include Armadillo --- R/ds.Boole.R | 4 ++-- R/ds.abs.R | 4 ++-- R/ds.asCharacter.R | 4 ++-- R/ds.asDataMatrix.R | 4 ++-- R/ds.asFactor.R | 8 ++++---- R/ds.asInteger.R | 4 ++-- R/ds.asList.R | 4 ++-- R/ds.asLogical.R | 4 ++-- R/ds.asMatrix.R | 4 ++-- R/ds.asNumeric.R | 4 ++-- R/ds.assign.R | 4 ++-- R/ds.boxPlot.R | 2 +- R/ds.c.R | 4 ++-- R/ds.cbind.R | 4 ++-- R/ds.changeRefGroup.R | 4 ++-- R/ds.class.R | 4 ++-- R/ds.colnames.R | 4 ++-- R/ds.completeCases.R | 22 +++++++++++----------- R/ds.contourPlot.R | 4 ++-- R/ds.cor.R | 4 ++-- R/ds.corTest.R | 2 +- R/ds.cov.R | 6 +++--- R/ds.dataFrame.R | 6 +++--- R/ds.dataFrameFill.R | 4 ++-- R/ds.dataFrameSort.R | 4 ++-- R/ds.dataFrameSubset.R | 2 +- R/ds.densityGrid.R | 8 ++++---- R/ds.dim.R | 8 ++++---- R/ds.exists.R | 6 +++--- R/ds.exp.R | 6 +++--- R/ds.extractQuantiles.R | 2 +- R/ds.forestplot.R | 2 +- R/ds.getWGSR.R | 4 ++-- R/ds.glm.R | 6 +++--- R/ds.glmSLMA.R | 6 +++--- R/ds.glmerSLMA.R | 6 +++--- R/ds.heatmapPlot.R | 4 ++-- R/ds.histogram.R | 4 ++-- R/ds.isNA.R | 2 +- R/ds.isValid.R | 2 +- R/ds.length.R | 2 +- R/ds.levels.R | 2 +- R/ds.lexis.R | 4 ++-- R/ds.list.R | 2 +- R/ds.listDisclosureSettings.R | 4 ++-- R/ds.listOpals.R | 2 +- R/ds.listServersideFunctions.R | 4 ++-- R/ds.lmerSLMA.R | 4 ++-- R/ds.log.R | 6 +++--- R/ds.look.R | 2 +- R/ds.ls.R | 2 +- R/ds.make.R | 2 +- R/ds.matrix.R | 2 +- R/ds.matrixDet.R | 2 +- R/ds.matrixDet.report.R | 2 +- R/ds.matrixDiag.R | 2 +- R/ds.matrixDimnames.R | 2 +- R/ds.matrixInvert.R | 2 +- R/ds.matrixMult.R | 2 +- R/ds.matrixTranspose.R | 2 +- R/ds.mdPattern.R | 2 +- R/ds.mean.R | 2 +- R/ds.meanByClass.R | 2 +- R/ds.meanSdGp.R | 2 +- R/ds.merge.R | 2 +- R/ds.message.R | 2 +- R/ds.metadata.R | 2 +- R/ds.names.R | 2 +- R/ds.numNA.R | 2 +- R/ds.quantileMean.R | 2 +- R/ds.rBinom.R | 10 +++++----- R/ds.rNorm.R | 10 +++++----- R/ds.rPois.R | 10 +++++----- R/ds.rUnif.R | 10 +++++----- R/ds.rbind.R | 10 +++++----- R/ds.reShape.R | 4 ++-- R/ds.recodeLevels.R | 2 +- R/ds.recodeValues.R | 2 +- R/ds.rep.R | 4 ++-- R/ds.replaceNA.R | 4 ++-- R/ds.rm.R | 2 +- R/ds.rowColCalc.R | 4 ++-- R/ds.sample.R | 8 ++++---- R/ds.scatterPlot.R | 4 ++-- R/ds.seq.R | 4 ++-- R/ds.setSeed.R | 4 ++-- R/ds.skewness.R | 4 ++-- R/ds.sqrt.R | 4 ++-- R/ds.summary.R | 4 ++-- R/ds.tapply.R | 2 +- R/ds.tapply.assign.R | 2 +- R/ds.testObjExists.R | 2 +- R/ds.unList.R | 2 +- R/ds.unique.R | 2 +- R/ds.var.R | 2 +- R/subsetHelper.R | 2 +- man/ds.Boole.Rd | 4 ++-- man/ds.abs.Rd | 4 ++-- man/ds.asCharacter.Rd | 4 ++-- man/ds.asDataMatrix.Rd | 4 ++-- man/ds.asFactor.Rd | 8 ++++---- man/ds.asInteger.Rd | 4 ++-- man/ds.asList.Rd | 4 ++-- man/ds.asLogical.Rd | 4 ++-- man/ds.asMatrix.Rd | 4 ++-- man/ds.asNumeric.Rd | 4 ++-- man/ds.assign.Rd | 4 ++-- man/ds.boxPlot.Rd | 2 +- man/ds.c.Rd | 4 ++-- man/ds.cbind.Rd | 4 ++-- man/ds.changeRefGroup.Rd | 4 ++-- man/ds.class.Rd | 4 ++-- man/ds.colnames.Rd | 4 ++-- man/ds.completeCases.Rd | 22 +++++++++++----------- man/ds.contourPlot.Rd | 4 ++-- man/ds.cor.Rd | 4 ++-- man/ds.corTest.Rd | 2 +- man/ds.cov.Rd | 6 +++--- man/ds.dataFrame.Rd | 6 +++--- man/ds.dataFrameFill.Rd | 4 ++-- man/ds.dataFrameSort.Rd | 4 ++-- man/ds.dataFrameSubset.Rd | 2 +- man/ds.densityGrid.Rd | 8 ++++---- man/ds.dim.Rd | 8 ++++---- man/ds.exists.Rd | 6 +++--- man/ds.exp.Rd | 6 +++--- man/ds.extractQuantiles.Rd | 2 +- man/ds.forestplot.Rd | 2 +- man/ds.getWGSR.Rd | 4 ++-- man/ds.glm.Rd | 6 +++--- man/ds.glmSLMA.Rd | 6 +++--- man/ds.glmerSLMA.Rd | 6 +++--- man/ds.heatmapPlot.Rd | 4 ++-- man/ds.histogram.Rd | 4 ++-- man/ds.isNA.Rd | 2 +- man/ds.isValid.Rd | 2 +- man/ds.length.Rd | 2 +- man/ds.levels.Rd | 2 +- man/ds.lexis.Rd | 4 ++-- man/ds.list.Rd | 2 +- man/ds.listDisclosureSettings.Rd | 4 ++-- man/ds.listOpals.Rd | 2 +- man/ds.listServersideFunctions.Rd | 4 ++-- man/ds.lmerSLMA.Rd | 4 ++-- man/ds.log.Rd | 6 +++--- man/ds.look.Rd | 2 +- man/ds.ls.Rd | 2 +- man/ds.make.Rd | 2 +- man/ds.matrix.Rd | 2 +- man/ds.matrixDet.Rd | 2 +- man/ds.matrixDet.report.Rd | 2 +- man/ds.matrixDiag.Rd | 2 +- man/ds.matrixDimnames.Rd | 2 +- man/ds.matrixInvert.Rd | 2 +- man/ds.matrixMult.Rd | 2 +- man/ds.matrixTranspose.Rd | 2 +- man/ds.mdPattern.Rd | 2 +- man/ds.mean.Rd | 2 +- man/ds.meanByClass.Rd | 2 +- man/ds.meanSdGp.Rd | 2 +- man/ds.merge.Rd | 2 +- man/ds.message.Rd | 2 +- man/ds.metadata.Rd | 2 +- man/ds.names.Rd | 2 +- man/ds.numNA.Rd | 2 +- man/ds.quantileMean.Rd | 2 +- man/ds.rBinom.Rd | 10 +++++----- man/ds.rNorm.Rd | 10 +++++----- man/ds.rPois.Rd | 10 +++++----- man/ds.rUnif.Rd | 10 +++++----- man/ds.rbind.Rd | 10 +++++----- man/ds.reShape.Rd | 4 ++-- man/ds.recodeLevels.Rd | 2 +- man/ds.recodeValues.Rd | 2 +- man/ds.rep.Rd | 4 ++-- man/ds.replaceNA.Rd | 4 ++-- man/ds.rm.Rd | 2 +- man/ds.rowColCalc.Rd | 4 ++-- man/ds.sample.Rd | 8 ++++---- man/ds.scatterPlot.Rd | 4 ++-- man/ds.seq.Rd | 4 ++-- man/ds.setSeed.Rd | 4 ++-- man/ds.skewness.Rd | 4 ++-- man/ds.sqrt.Rd | 4 ++-- man/ds.summary.Rd | 4 ++-- man/ds.tapply.Rd | 2 +- man/ds.tapply.assign.Rd | 2 +- man/ds.testObjExists.Rd | 2 +- man/ds.unList.Rd | 2 +- man/ds.unique.Rd | 2 +- man/ds.var.Rd | 2 +- man/subsetHelper.Rd | 2 +- 192 files changed, 380 insertions(+), 380 deletions(-) diff --git a/R/ds.Boole.R b/R/ds.Boole.R index c435e4c6f..45f6efa5e 100644 --- a/R/ds.Boole.R +++ b/R/ds.Boole.R @@ -44,7 +44,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -66,7 +66,7 @@ #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Generating Boolean indicators diff --git a/R/ds.abs.R b/R/ds.abs.R index cc4523f32..974cbcb4e 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -22,7 +22,7 @@ #' @examples #' \dontrun{ #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -44,7 +44,7 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Generate a normally distributed variable with zero mean and variance equal diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index 623e43dbe..df354f85a 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -18,7 +18,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -44,7 +44,7 @@ #' # Converting the R object into a class character #' ds.asCharacter(x.name = "D$LAB_TSC", #' newobj = "char.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index bdfa9fdd0..5ee86fb34 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -17,7 +17,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -43,7 +43,7 @@ #' # Converting the R object into a matrix #' ds.asDataMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index e6b6e7ce2..f3da4ee44 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -140,7 +140,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -161,7 +161,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", @@ -170,14 +170,14 @@ #' #from all studies is created #' fixed.dummy.vars = TRUE, #create a matrix of dummy variables #' baseline.level = 1, -#' datasources = connections)#all the Opal servers are used, in this case 3 +#' datasources = connections)#all the Armadillo/Opal servers are used, in this case 3 #' #(see above the connection to the servers) #' ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", #' newobj.name = "fact.obj", #' forced.factor.levels = c(2,3), #the variable is split in 2 levels #' fixed.dummy.vars = TRUE, #create a matrix of dummy variables #' baseline.level = 1, -#' datasources = connections[1])#only the first Opal server is used ("study1") +#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index 0e9670df0..d46b73cbb 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -31,7 +31,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -57,7 +57,7 @@ #' # Converting the R object into an integer #' ds.asInteger(x.name = "D$LAB_TSC", #' newobj = "int.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' ds.class(x = "int.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asList.R b/R/ds.asList.R index 83007f5a3..7aa836a8d 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -18,7 +18,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -44,7 +44,7 @@ #' # Converting the R object into a List #' ds.asList(x.name = "D", #' newobj = "D.asList", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' ds.class(x = "D.asList", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R index 85617edcf..c14abc22b 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -17,7 +17,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -43,7 +43,7 @@ #' # Converting the R object into a logical #' ds.asLogical(x.name = "D$LAB_TSC", #' newobj = "logical.obj", -#' datasources =connections[1]) #only the first Opal server is used ("study1") +#' datasources =connections[1]) #only the first Armadillo/Opal server is used ("study1") #' ds.class(x = "logical.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R index f39803773..61cfed2eb 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -20,7 +20,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -46,7 +46,7 @@ #' # Converting the R object into a matrix #' ds.asMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 803a6308d..dada7ab35 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -31,7 +31,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -57,7 +57,7 @@ #' # Converting the R object into a numeric class #' ds.asNumeric(x.name = "D$LAB_TSC", #' newobj = "num.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' ds.class(x = "num.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.assign.R b/R/ds.assign.R index 79c373d5c..736457ad7 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -22,7 +22,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -48,7 +48,7 @@ #' # Assign a variable to a name #' ds.assign(toAssign = "D$LAB_TSC", #' newobj = "labtsc", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index e02aab96a..63d00bb40 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -24,7 +24,7 @@ #' ### Please ensure you have a training Virtual Machine running, #' or that you have a live connection to a server. #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.c.R b/R/ds.c.R index 7be360a44..e48c225e5 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -21,7 +21,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -48,7 +48,7 @@ #' myvect <- c("D$LAB_TSC", "D$LAB_HDL") #' ds.c(x = myvect, #' newobj = "new.vect", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.cbind.R b/R/ds.cbind.R index 0f85ca990..248719385 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -45,7 +45,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -66,7 +66,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Assign the exponent of a numeric variable at each server and cbind it diff --git a/R/ds.changeRefGroup.R b/R/ds.changeRefGroup.R index a06ac1435..1155a0d8d 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -39,7 +39,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -60,7 +60,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Changing the reference group in the server-side diff --git a/R/ds.class.R b/R/ds.class.R index ab6e89378..5123204ee 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -17,7 +17,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -38,7 +38,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Getting the class of the R objects stored in the server-side diff --git a/R/ds.colnames.R b/R/ds.colnames.R index 06e647284..1ff7f1dbf 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -18,7 +18,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -39,7 +39,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Getting column names of the R objects stored in the server-side diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index 107f70de6..5ca727ab6 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -24,7 +24,7 @@ #' @examples #' \dontrun{ #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -45,23 +45,23 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Select complete cases from different R objects #' -#' ds.completeCases(x1 = "D", #data frames in the Opal servers -#' #(see above the connection to the Opal servers) +#' ds.completeCases(x1 = "D", #data frames in the Armadillo/Opal servers +#' #(see above the connection to the Armadillo/Opal servers) #' newobj = "D.completeCases", # name for the output object -#' # that is stored in the Opal servers -#' datasources = connections) # All Opal servers are used -#' # (see above the connection to the Opal servers) +#' # that is stored in the Armadillo/Opal servers +#' datasources = connections) # All Armadillo/Opal servers are used +#' # (see above the connection to the Armadillo/Opal servers) #' -#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Opal servers -#' #(see above the connection to the Opal servers) +#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Armadillo/Opal servers +#' #(see above the connection to the Armadillo/Opal servers) #' newobj = "LAB_TSC.completeCases", #name for the output variable -#' #that is stored in the Opal servers -#' datasources = connections[2]) #only the second Opal server is used ("study2") +#' #that is stored in the Armadillo/Opal servers +#' datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.contourPlot.R b/R/ds.contourPlot.R index 42084006c..9aad4f04d 100644 --- a/R/ds.contourPlot.R +++ b/R/ds.contourPlot.R @@ -61,7 +61,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -82,7 +82,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Generating contour plots diff --git a/R/ds.cor.R b/R/ds.cor.R index 9c0ef8e1d..d81ca4a75 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -43,7 +43,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -64,7 +64,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Get the correlation matrix of two continuous variables diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 95b59d0c8..3d8e95a39 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -32,7 +32,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.cov.R b/R/ds.cov.R index 0aa75a3d5..6031ac7c2 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -53,7 +53,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -74,7 +74,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Calculate the covariance between two vectors @@ -90,7 +90,7 @@ #' y = 'gender', #' naAction = 'pairwise.complete', #' type = 'combine', -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index ccd671c4d..b1cd63778 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -45,7 +45,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -68,7 +68,7 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Create a new data frame @@ -80,7 +80,7 @@ #' completeCases = TRUE, #only rows with not missing values are selected #' DataSHIELD.checks = FALSE, #' newobj = "df1", -#' datasources = connections[1], #only the first Opal server is used ("study1") +#' datasources = connections[1], #only the first Armadillo/Opal server is used ("study1") #' notify.of.progress = FALSE) #' #' diff --git a/R/ds.dataFrameFill.R b/R/ds.dataFrameFill.R index f4bb080c4..7b385e8ec 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -26,7 +26,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -48,7 +48,7 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Create two data frames with one different column diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index f8fc52f77..96824a25a 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -41,7 +41,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -70,7 +70,7 @@ #' sort.descending = TRUE, #' sort.method = "numeric", #' newobj = "df.sort", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 9792afa48..192211987 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -41,7 +41,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index d617dd731..cd0a59106 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -35,7 +35,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -56,20 +56,20 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Generate the density grid #' # Example1: generate a combined grid density object (default) #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", -#' datasources = connections)#all opal servers are used +#' datasources = connections)#all Armadillo/Opal servers are used #' #' # Example2: generate a grid density object for each study separately #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", #' type="split" -#' datasources = connections[1])#only the first Opal server is used ("study1") +#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") #' #' # Example3: generate a grid density object where the number of intervals is set to 15, for #' each study separately diff --git a/R/ds.dim.R b/R/ds.dim.R index 17c5fb75e..d588906bb 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -37,7 +37,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -64,14 +64,14 @@ #' # Calculate the dimension #' ds.dim(x="D", #' type="combine", #global dimension -#'#' datasources = connections)#all opal servers are used +#'#' datasources = connections)#all Armadillo/Opal servers are used #' ds.dim(x="D", #' type = "both",#separate dimension for each study #' #and the pooled dimension (default) -#'#' datasources = connections)#all opal servers are used +#'#' datasources = connections)#all Armadillo/Opal servers are used #' ds.dim(x="D", #' type="split", #separate dimension for each study -#'#' datasources = connections[1])#only the first opal server is used ("study1") +#'#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.exists.R b/R/ds.exists.R index 6dff8b4c1..7dc128b42 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -25,7 +25,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -50,9 +50,9 @@ #' #' # Check if the object exist in the server-side #' ds.exists(x = "D", -#' datasources = connections) #All opal servers are used +#' datasources = connections) #All Armadillo/Opal servers are used #' ds.exists(x = "D", -#' datasources = connections[1]) #Only the first Opal server is used (study1) +#' datasources = connections[1]) #Only the first Armadillo/Opal server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.exp.R b/R/ds.exp.R index 65102600a..8d8b46f8f 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -21,7 +21,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -43,13 +43,13 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # compute exponential function of the 'PM_BMI_CONTINUOUS' variable #' ds.exp(x = "D$PM_BMI_CONTINUOUS", #' newobj = "exp.PM_BMI_CONTINUOUS", -#' datasources = connections[1]) #only the first Opal server is used (study1) +#' datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.extractQuantiles.R b/R/ds.extractQuantiles.R index 4068f8f3b..579c0980a 100644 --- a/R/ds.extractQuantiles.R +++ b/R/ds.extractQuantiles.R @@ -60,7 +60,7 @@ #' otherwise left behind. These are not usually needed, but could be of value #' if one were investigating a problem with the ranking. FALSE: do not delete #' the residual objects -#' @param extract.datasources specifies the particular opal object(s) to use. +#' @param extract.datasources specifies the particular Armadillo/Opal connection object(s) to use. #' This is set via the argument in ds.ranksSecure. For more details #' see the associated document entitled "secure.global.ranking.docx". Also see #' the header file for ds.ranksSecure. diff --git a/R/ds.forestplot.R b/R/ds.forestplot.R index e1bc21c13..a9d19a24a 100644 --- a/R/ds.forestplot.R +++ b/R/ds.forestplot.R @@ -33,7 +33,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the logistic regression model diff --git a/R/ds.getWGSR.R b/R/ds.getWGSR.R index 803068116..f0ae833f8 100644 --- a/R/ds.getWGSR.R +++ b/R/ds.getWGSR.R @@ -63,7 +63,7 @@ #' @examples #' \dontrun{ #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -85,7 +85,7 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Generate the weight-for-height (wfh) index diff --git a/R/ds.glm.R b/R/ds.glm.R index 24488e226..428fc285f 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -217,7 +217,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -241,7 +241,7 @@ #' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the GLM @@ -297,7 +297,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the logistic regression model diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index ef366e21f..d8e721908 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -267,7 +267,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -291,7 +291,7 @@ #' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the GLM @@ -343,7 +343,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the logistic regression model diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index 0665b24e5..c6d64f464 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -168,7 +168,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -189,7 +189,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Select all rows without missing values @@ -222,7 +222,7 @@ #' table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' diff --git a/R/ds.heatmapPlot.R b/R/ds.heatmapPlot.R index 483124607..9e6d8f183 100644 --- a/R/ds.heatmapPlot.R +++ b/R/ds.heatmapPlot.R @@ -95,7 +95,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -116,7 +116,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Compute the heat map plot diff --git a/R/ds.histogram.R b/R/ds.histogram.R index f9b375dda..e57334e72 100644 --- a/R/ds.histogram.R +++ b/R/ds.histogram.R @@ -91,7 +91,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -112,7 +112,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Compute the histogram diff --git a/R/ds.isNA.R b/R/ds.isNA.R index 80ffcc08a..e2bf6f9e9 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -22,7 +22,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.isValid.R b/R/ds.isValid.R index 266dbca2d..fb264bf87 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -23,7 +23,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.length.R b/R/ds.length.R index d2acd0e79..45a708876 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -28,7 +28,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.levels.R b/R/ds.levels.R index 5dc650b40..9a0e422d7 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -18,7 +18,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.lexis.R b/R/ds.lexis.R index abc019a73..68ff570b6 100644 --- a/R/ds.lexis.R +++ b/R/ds.lexis.R @@ -141,7 +141,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -165,7 +165,7 @@ #' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Example 1: Create the expanded data frame. diff --git a/R/ds.list.R b/R/ds.list.R index ebbf57492..d66fedc02 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -21,7 +21,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.listDisclosureSettings.R b/R/ds.listDisclosureSettings.R index 33c73875c..29fb35125 100644 --- a/R/ds.listDisclosureSettings.R +++ b/R/ds.listDisclosureSettings.R @@ -62,7 +62,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -83,7 +83,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Call to list current disclosure settings in all data repository servers diff --git a/R/ds.listOpals.R b/R/ds.listOpals.R index a07aaa0e6..310baef56 100644 --- a/R/ds.listOpals.R +++ b/R/ds.listOpals.R @@ -3,7 +3,7 @@ #' @description ds.listOpals calls the internal DataSHIELD function getOpals() which identifies #' all Opal objects in the analytic environment. #' @details ds.listOpals calls the internal DataSHIELD function getOpals() which identifies -#' all Opal objects in the analytic environment. If there are no Opal servers in the analytic +#' all Opal objects in the analytic environment. If there are no Armadillo/Opal servers in the analytic #' environment ds.listOpalsIreminds the user that they have to login to a valid set of Opal #' login objects, if they wish to use DataSHIELD. If there is only one set of Opals, ds.listOpals #' copies that one set and names the copy 'default.opals'. This default set will then be used by diff --git a/R/ds.listServersideFunctions.R b/R/ds.listServersideFunctions.R index 97188b288..dae0ff5e5 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -18,7 +18,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -39,7 +39,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # List server-side functions diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index 23192f7a8..5d8f2da4b 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -164,7 +164,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -185,7 +185,7 @@ #' table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' #Log onto the remote Opal training servers +#' #Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Select all rows without missing values diff --git a/R/ds.log.R b/R/ds.log.R index cfa2155f2..2712b6a2d 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -20,7 +20,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -42,7 +42,7 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Calculating the log value of the 'PM_BMI_CONTINUOUS' variable @@ -50,7 +50,7 @@ #' ds.log(x = "D$PM_BMI_CONTINUOUS", #' base = exp(2), #' newobj = "log.PM_BMI_CONTINUOUS", -#' datasources = connections[1]) #only the first Opal server is used (study1) +#' datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.look.R b/R/ds.look.R index 8dffa52f2..e3add192d 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -31,7 +31,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.ls.R b/R/ds.ls.R index ce96c9015..170afbd35 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -67,7 +67,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.make.R b/R/ds.make.R index 044c727a6..b39e78ef1 100644 --- a/R/ds.make.R +++ b/R/ds.make.R @@ -77,7 +77,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrix.R b/R/ds.matrix.R index 5a0ed3150..3ad95c796 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -56,7 +56,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixDet.R b/R/ds.matrixDet.R index 2f4d49606..447ac9cfa 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -25,7 +25,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixDet.report.R b/R/ds.matrixDet.report.R index 4d914d5c3..794873d55 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -24,7 +24,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index 7b78d9bac..a44dda2cf 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -64,7 +64,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixDimnames.R b/R/ds.matrixDimnames.R index be7cb1694..b2c9d9693 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -23,7 +23,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixInvert.R b/R/ds.matrixInvert.R index d92591c41..c072b81dc 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -20,7 +20,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixMult.R b/R/ds.matrixMult.R index 35e9d7111..5e0b18617 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -25,7 +25,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.matrixTranspose.R b/R/ds.matrixTranspose.R index 4de06471a..9d707c57b 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -23,7 +23,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.mdPattern.R b/R/ds.mdPattern.R index af59498e2..3c98e7848 100644 --- a/R/ds.mdPattern.R +++ b/R/ds.mdPattern.R @@ -65,7 +65,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.mean.R b/R/ds.mean.R index ca91ca1dc..c8ca6c14c 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -62,7 +62,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.meanByClass.R b/R/ds.meanByClass.R index 538ef8c81..c87d66496 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -37,7 +37,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.meanSdGp.R b/R/ds.meanSdGp.R index f95cdbb91..b8ecc13ce 100644 --- a/R/ds.meanSdGp.R +++ b/R/ds.meanSdGp.R @@ -75,7 +75,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.merge.R b/R/ds.merge.R index c2d11678f..f8a2e8119 100644 --- a/R/ds.merge.R +++ b/R/ds.merge.R @@ -56,7 +56,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.message.R b/R/ds.message.R index eb88d8b95..4ac1a2998 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -31,7 +31,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.metadata.R b/R/ds.metadata.R index 78ceb43c3..4ddab2ea2 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -17,7 +17,7 @@ #' @examples #' \dontrun{ #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.names.R b/R/ds.names.R index e348f0021..2a11df1a3 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -27,7 +27,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.numNA.R b/R/ds.numNA.R index 444034f71..7d193f9e7 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -20,7 +20,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.quantileMean.R b/R/ds.quantileMean.R index fd8145a66..889e064cc 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -31,7 +31,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index 1759db7d4..0ec1142bd 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -54,7 +54,7 @@ #' @examples #' \dontrun{ #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -77,17 +77,17 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' #Generating the vectors in the Opal servers +#' #Generating the vectors in the Armadillo/Opal servers #' ds.rBinom(samp.size=c(13,20,25), #the length of the vector created in each source is different #' size=c(10,23,5), #Bernoulli trials change in each source #' prob=c(0.6,0.1,0.5), #Probability changes in each source #' newobj="Binom.dist", #' seed.as.integer=45, #' return.full.seed.as.set=FALSE, -#' datasources=connections) #all the Opal servers are used, in this case 3 +#' datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 #' #(see above the connection to the servers) #' #' ds.rBinom(samp.size=15, @@ -96,7 +96,7 @@ #' newobj="Binom.dist", #' seed.as.integer=324, #' return.full.seed.as.set=FALSE, -#' datasources=connections[2]) #only the second Opal server is used ("study2") +#' datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 05bb15d20..00783071c 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -65,7 +65,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -86,10 +86,10 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Opal servers +#' # Generating the vectors in the Armadillo/Opal servers #' #' ds.rNorm(samp.size=c(10,20,45), #the length of the vector created in each source is different #' mean=c(1,6,4), #the mean of the Normal distribution changes in each server @@ -99,7 +99,7 @@ #' return.full.seed.as.set=FALSE, #' force.output.to.k.decimal.places=c(4,5,6), #output random numbers have different #' #decimal quantity in each source -#' datasources=connections) #all the Opal servers are used, in this case 3 +#' datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 #' #(see above the connection to the servers) #' #' ds.rNorm(samp.size=10, @@ -109,7 +109,7 @@ #' seed.as.integer=2345, #' return.full.seed.as.set=FALSE, #' force.output.to.k.decimal.places=1, -#' datasources=connections[2]) #only the second Opal server is used ("study2") +#' datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rPois.R b/R/ds.rPois.R index e6ae42d46..6748c73de 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -53,7 +53,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -76,23 +76,23 @@ #' logindata <- builder$build() -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Opal servers +#' # Generating the vectors in the Armadillo/Opal servers #' ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different #' lambda=c(2,3,4), #different mean per interval (2,3,4) in each source #' newobj="Pois.dist", #' seed.as.integer=1234, #' return.full.seed.as.set=FALSE, -#' datasources=connections) #all the Opal servers are used, in this case 3 +#' datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 #' #(see above the connection to the servers) #' ds.rPois(samp.size=13, #' lambda=5, #' newobj="Pois.dist", #' seed.as.integer=1234, #' return.full.seed.as.set=FALSE, -#' datasources=connections[1]) #only the first Opal server is used ("study1") +#' datasources=connections[1]) #only the first Armadillo/Opal server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index bac2db04b..d6c806b4d 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -72,7 +72,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -94,10 +94,10 @@ #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Opal servers +#' # Generating the vectors in the Armadillo/Opal servers #' #' ds.rUnif(samp.size = c(12,20,4), #the length of the vector created in each source is different #' min = c(0,2,5), #different minumum value of the function in each source @@ -106,7 +106,7 @@ #' seed.as.integer = 234, #' return.full.seed.as.set = FALSE, #' force.output.to.k.decimal.places = c(1,2,3), -#' datasources = connections) #all the Opal servers are used, in this case 3 +#' datasources = connections) #all the Armadillo/Opal servers are used, in this case 3 #' #(see above the connection to the servers) #' #' ds.rUnif(samp.size = 12, @@ -116,7 +116,7 @@ #' seed.as.integer = 12345, #' return.full.seed.as.set = FALSE, #' force.output.to.k.decimal.places = 2, -#' datasources = connections[2]) #only the second Opal server is used ("study2") +#' datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 2943312db..d355d1b48 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -36,7 +36,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -57,19 +57,19 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Combining R objects by rows #' #' #' ds.rbind(x = "D", #data frames in the server-side to be conbined -#' #(see above the connection to the Opal servers) +#' #(see above the connection to the Armadillo/Opal servers) #' DataSHIELD.checks = FALSE, #' force.colnames = NULL, #' newobj = "D.rbind", # name for the output object that is stored in the data servers -#' datasources = connections, # All Opal servers are used -#' #(see above the connection to the Opal servers) +#' datasources = connections, # All Armadillo/Opal servers are used +#' #(see above the connection to the Armadillo/Opal servers) #' notify.of.progress = FALSE) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.reShape.R b/R/ds.reShape.R index 38fa36b5f..9dd1c231f 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -40,7 +40,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -61,7 +61,7 @@ #' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Reshape server-side grouped data diff --git a/R/ds.recodeLevels.R b/R/ds.recodeLevels.R index 32bf30e62..13e1c5031 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -26,7 +26,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index c0a52c3d5..a8f63d85b 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -32,7 +32,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.rep.R b/R/ds.rep.R index 7874045f4..957eb9780 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -31,7 +31,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -52,7 +52,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, #' assign = TRUE, #' symbol = "D") diff --git a/R/ds.replaceNA.R b/R/ds.replaceNA.R index 0596f2da3..0977127fc 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -32,7 +32,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -53,7 +53,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Replace missing values in variable 'LAB_HDL' by the mean value diff --git a/R/ds.rm.R b/R/ds.rm.R index e977afe5c..b61b1d7e1 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -27,7 +27,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.rowColCalc.R b/R/ds.rowColCalc.R index 8d0ec804e..f61ca223a 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -24,7 +24,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -48,7 +48,7 @@ #' logindata <- builder$build() #' myvar <- list("LAB_TSC","LAB_HDL") #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, #' variables = myvar, symbol = "D") #' diff --git a/R/ds.sample.R b/R/ds.sample.R index e52af826c..91e4510f3 100644 --- a/R/ds.sample.R +++ b/R/ds.sample.R @@ -110,14 +110,14 @@ #' For further details see help for \code{sample} in native R. #' @param newobj This a character string providing a name for the output #' data.frame which defaults to 'newobj.sample' if no name is specified. -#' @param datasources specifies the particular opal object(s) to use. If the -#' argument is not specified the default set of opals will be used. The default opals +#' @param datasources specifies the particular Armadillo/Opal connection object(s) to use. If the +#' argument is not specified the default set of Armadillo/Opal servers will be used. The default servers #' are called default.opals and the default can be set using the function #' \code{ds.setDefaultOpals}. If the is to be specified, it should be set without #' inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to -#' apply the function solely to e.g. the second opal server in a set of three, +#' apply the function solely to e.g. the second Armadillo/Opal server in a set of three, #' the argument can be specified as: e.g. datasources=opals.em[2]. -#' If you wish to specify the first and third opal servers in a set you specify: +#' If you wish to specify the first and third Armadillo/Opal servers in a set you specify: #' e.g. datasources=opals.em[c(1,3)] #' @param notify.of.progress specifies if console output should be produce to indicate #' progress. The default value for notify.of.progress is FALSE. diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 4d9c872db..73eb4e74c 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -77,7 +77,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -100,7 +100,7 @@ #' logindata <- builder$build() -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Example 1: generate a scatter plot for each study separately diff --git a/R/ds.seq.R b/R/ds.seq.R index 1bb958368..4d93bd25f 100644 --- a/R/ds.seq.R +++ b/R/ds.seq.R @@ -65,7 +65,7 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -86,7 +86,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Create 3 different sequences diff --git a/R/ds.setSeed.R b/R/ds.setSeed.R index acd73f810..4f27196df 100644 --- a/R/ds.setSeed.R +++ b/R/ds.setSeed.R @@ -46,7 +46,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -67,7 +67,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Generate a pseudorandom number in the server-side diff --git a/R/ds.skewness.R b/R/ds.skewness.R index 22214612c..690fe9d0b 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -1,7 +1,7 @@ #' #' @title Calculates the skewness of a server-side numeric variable #' @description This function calculates the skewness of a numeric variable -#' that is stored on the server-side (Opal server). +#' that is stored on the server-side (Armadillo/Opal server). #' @details This function is similar to the function \code{skewness} in R package \code{e1071}. #' #' The function calculates the skewness of an input variable \code{x} @@ -43,7 +43,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 3aef21937..679728689 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -22,7 +22,7 @@ #' @examples #' \dontrun{ #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -44,7 +44,7 @@ #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Get the square root of LAB_HDL variable diff --git a/R/ds.summary.R b/R/ds.summary.R index 3174023a3..9949b56cb 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -26,7 +26,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') @@ -47,7 +47,7 @@ #' table = "CNSIM.CNSIM3", driver = "OpalDriver") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Calculate the summary of a numeric variable diff --git a/R/ds.tapply.R b/R/ds.tapply.R index 3972bf839..01ce4fc31 100644 --- a/R/ds.tapply.R +++ b/R/ds.tapply.R @@ -77,7 +77,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.tapply.assign.R b/R/ds.tapply.assign.R index 5e2ac52fd..b3fbc18ce 100644 --- a/R/ds.tapply.assign.R +++ b/R/ds.tapply.assign.R @@ -82,7 +82,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.testObjExists.R b/R/ds.testObjExists.R index 5b7e946ae..c03b79ec9 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -21,7 +21,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.unList.R b/R/ds.unList.R index 9af30d6b9..298c795ca 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -28,7 +28,7 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.unique.R b/R/ds.unique.R index dd8e5e532..df6b322a7 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -13,7 +13,7 @@ #' @return \code{ds.unique} returns the vector of unique R objects which are written to the server-side. #' @examples #' \dontrun{ -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/ds.var.R b/R/ds.var.R index fcf204956..fd7202142 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -40,7 +40,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/R/subsetHelper.R b/R/subsetHelper.R index 62648552c..62af5f6a3 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -22,7 +22,7 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') #' require('DSOpal') diff --git a/man/ds.Boole.Rd b/man/ds.Boole.Rd index af451932d..9a9c443ac 100644 --- a/man/ds.Boole.Rd +++ b/man/ds.Boole.Rd @@ -70,7 +70,7 @@ Server function called: \code{BooleDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -91,7 +91,7 @@ Server function called: \code{BooleDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Generating Boolean indicators diff --git a/man/ds.abs.Rd b/man/ds.abs.Rd index 6cd9404d8..735a40c36 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -35,7 +35,7 @@ specified by the user through the argument \code{newobj}, otherwise is named by \examples{ \dontrun{ - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -57,7 +57,7 @@ specified by the user through the argument \code{newobj}, otherwise is named by logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Generate a normally distributed variable with zero mean and variance equal diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index e557c9fc1..b6048a30f 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -32,7 +32,7 @@ Server function called: \code{asCharacterDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -58,7 +58,7 @@ Server function called: \code{asCharacterDS} # Converting the R object into a class character ds.asCharacter(x.name = "D$LAB_TSC", newobj = "char.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index d9e253e6a..80f334c22 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -34,7 +34,7 @@ Server function called: \code{asDataMatrixDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -60,7 +60,7 @@ Server function called: \code{asDataMatrixDS}. # Converting the R object into a matrix ds.asDataMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index 2ca4d1c4e..b88aba82e 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -166,7 +166,7 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -187,7 +187,7 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", @@ -196,14 +196,14 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} #from all studies is created fixed.dummy.vars = TRUE, #create a matrix of dummy variables baseline.level = 1, - datasources = connections)#all the Opal servers are used, in this case 3 + datasources = connections)#all the Armadillo/Opal servers are used, in this case 3 #(see above the connection to the servers) ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", newobj.name = "fact.obj", forced.factor.levels = c(2,3), #the variable is split in 2 levels fixed.dummy.vars = TRUE, #create a matrix of dummy variables baseline.level = 1, - datasources = connections[1])#only the first Opal server is used ("study1") + datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index 0bf7ab473..d97baa4a1 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -47,7 +47,7 @@ Server function called: \code{asIntegerDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -73,7 +73,7 @@ Server function called: \code{asIntegerDS} # Converting the R object into an integer ds.asInteger(x.name = "D$LAB_TSC", newobj = "int.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") ds.class(x = "int.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asList.Rd b/man/ds.asList.Rd index 6af6f9607..58b877d0b 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -32,7 +32,7 @@ Server function called: \code{asListDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -58,7 +58,7 @@ Server function called: \code{asListDS} # Converting the R object into a List ds.asList(x.name = "D", newobj = "D.asList", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") ds.class(x = "D.asList", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asLogical.Rd b/man/ds.asLogical.Rd index ec539cc33..ac6051c1c 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -32,7 +32,7 @@ Server function called: \code{asLogicalDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -58,7 +58,7 @@ Server function called: \code{asLogicalDS} # Converting the R object into a logical ds.asLogical(x.name = "D$LAB_TSC", newobj = "logical.obj", - datasources =connections[1]) #only the first Opal server is used ("study1") + datasources =connections[1]) #only the first Armadillo/Opal server is used ("study1") ds.class(x = "logical.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asMatrix.Rd b/man/ds.asMatrix.Rd index 8116ac1d1..b2da4dbab 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -37,7 +37,7 @@ Server function called: \code{asMatrixDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -63,7 +63,7 @@ Server function called: \code{asMatrixDS} # Converting the R object into a matrix ds.asMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 73f03693f..2a4f0f9a2 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -46,7 +46,7 @@ Server function called: \code{asNumericDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -72,7 +72,7 @@ Server function called: \code{asNumericDS} # Converting the R object into a numeric class ds.asNumeric(x.name = "D$LAB_TSC", newobj = "num.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") ds.class(x = "num.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.assign.Rd b/man/ds.assign.Rd index df41057b3..30dd0be67 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -34,7 +34,7 @@ assigned the variable called \code{newobj} on the server-side. \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -60,7 +60,7 @@ assigned the variable called \code{newobj} on the server-side. # Assign a variable to a name ds.assign(toAssign = "D$LAB_TSC", newobj = "labtsc", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.boxPlot.Rd b/man/ds.boxPlot.Rd index 9b73d4868..364680348 100644 --- a/man/ds.boxPlot.Rd +++ b/man/ds.boxPlot.Rd @@ -48,7 +48,7 @@ of grouping using categorical variables on the dataset (only for data frames) ### Please ensure you have a training Virtual Machine running, or that you have a live connection to a server. - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.c.Rd b/man/ds.c.Rd index c0046d463..ac8f4c538 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -38,7 +38,7 @@ Server function called: \code{cDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -65,7 +65,7 @@ Server function called: \code{cDS} myvect <- c("D$LAB_TSC", "D$LAB_HDL") ds.c(x = myvect, newobj = "new.vect", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.cbind.Rd b/man/ds.cbind.Rd index 82ddbd88e..5a01502cd 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -73,7 +73,7 @@ Server function called: \code{cbindDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -94,7 +94,7 @@ Server function called: \code{cbindDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Assign the exponent of a numeric variable at each server and cbind it diff --git a/man/ds.changeRefGroup.Rd b/man/ds.changeRefGroup.Rd index c20f23895..9584829aa 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -54,7 +54,7 @@ Server function called: \code{changeRefGroupDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -75,7 +75,7 @@ Server function called: \code{changeRefGroupDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Changing the reference group in the server-side diff --git a/man/ds.class.Rd b/man/ds.class.Rd index 861eeddc9..88d7a28aa 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -29,7 +29,7 @@ Server function called: \code{classDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -50,7 +50,7 @@ Server function called: \code{classDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting the class of the R objects stored in the server-side diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index 6915dd592..99616f89c 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -30,7 +30,7 @@ Server function called: \code{colnamesDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -51,7 +51,7 @@ Server function called: \code{colnamesDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting column names of the R objects stored in the server-side diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index 8a8f4ea4f..3d17864e5 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -39,7 +39,7 @@ Server function called: \code{completeCasesDS} \examples{ \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -60,23 +60,23 @@ Server function called: \code{completeCasesDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Select complete cases from different R objects - ds.completeCases(x1 = "D", #data frames in the Opal servers - #(see above the connection to the Opal servers) + ds.completeCases(x1 = "D", #data frames in the Armadillo/Opal servers + #(see above the connection to the Armadillo/Opal servers) newobj = "D.completeCases", # name for the output object - # that is stored in the Opal servers - datasources = connections) # All Opal servers are used - # (see above the connection to the Opal servers) + # that is stored in the Armadillo/Opal servers + datasources = connections) # All Armadillo/Opal servers are used + # (see above the connection to the Armadillo/Opal servers) - ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Opal servers - #(see above the connection to the Opal servers) + ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Armadillo/Opal servers + #(see above the connection to the Armadillo/Opal servers) newobj = "LAB_TSC.completeCases", #name for the output variable - #that is stored in the Opal servers - datasources = connections[2]) #only the second Opal server is used ("study2") + #that is stored in the Armadillo/Opal servers + datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.contourPlot.Rd b/man/ds.contourPlot.Rd index 165295642..a4c6826c9 100644 --- a/man/ds.contourPlot.Rd +++ b/man/ds.contourPlot.Rd @@ -93,7 +93,7 @@ Server functions called: \code{heatmapPlotDS}, \code{rangeDS} and \code{densityG \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -114,7 +114,7 @@ Server functions called: \code{heatmapPlotDS}, \code{rangeDS} and \code{densityG table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Generating contour plots diff --git a/man/ds.cor.Rd b/man/ds.cor.Rd index b73297091..290940858 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -65,7 +65,7 @@ Server function called: \code{corDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -86,7 +86,7 @@ Server function called: \code{corDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Get the correlation matrix of two continuous variables diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index 1dbaf49c3..6c4cbad8e 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -60,7 +60,7 @@ Server function called: \code{corTestDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.cov.Rd b/man/ds.cov.Rd index a953b8e4f..00abe3991 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -76,7 +76,7 @@ and the total number of missing values aggregated from all the involved studies, \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -97,7 +97,7 @@ and the total number of missing values aggregated from all the involved studies, table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Calculate the covariance between two vectors @@ -113,7 +113,7 @@ and the total number of missing values aggregated from all the involved studies, y = 'gender', naAction = 'pairwise.complete', type = 'combine', - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 918a50443..1434718a1 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -81,7 +81,7 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -103,7 +103,7 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Create a new data frame @@ -115,7 +115,7 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} completeCases = TRUE, #only rows with not missing values are selected DataSHIELD.checks = FALSE, newobj = "df1", - datasources = connections[1], #only the first Opal server is used ("study1") + datasources = connections[1], #only the first Armadillo/Opal server is used ("study1") notify.of.progress = FALSE) diff --git a/man/ds.dataFrameFill.Rd b/man/ds.dataFrameFill.Rd index e096223e9..76dfdde7f 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -45,7 +45,7 @@ Server function called: \code{dataFrameFillDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -67,7 +67,7 @@ Server function called: \code{dataFrameFillDS} logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Create two data frames with one different column diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index af86a99fc..a4a9fd562 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -66,7 +66,7 @@ Server function called: \code{dataFrameSortDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -95,7 +95,7 @@ Server function called: \code{dataFrameSortDS}. sort.descending = TRUE, sort.method = "numeric", newobj = "df.sort", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index 5d909752c..b3de8bb35 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -75,7 +75,7 @@ Server functions called: \code{dataFrameSubsetDS1} and \code{dataFrameSubsetDS2} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 00fe1e91f..6ebdb373a 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -59,7 +59,7 @@ Server function called: \code{densityGridDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -80,20 +80,20 @@ Server function called: \code{densityGridDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Generate the density grid # Example1: generate a combined grid density object (default) ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", - datasources = connections)#all opal servers are used + datasources = connections)#all Armadillo/Opal servers are used # Example2: generate a grid density object for each study separately ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", type="split" - datasources = connections[1])#only the first Opal server is used ("study1") + datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") # Example3: generate a grid density object where the number of intervals is set to 15, for each study separately diff --git a/man/ds.dim.Rd b/man/ds.dim.Rd index 1fbacddf6..4ea32eeac 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -51,7 +51,7 @@ Server function called: \code{dimDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -78,14 +78,14 @@ Server function called: \code{dimDS} # Calculate the dimension ds.dim(x="D", type="combine", #global dimension -#' datasources = connections)#all opal servers are used +#' datasources = connections)#all Armadillo/Opal servers are used ds.dim(x="D", type = "both",#separate dimension for each study #and the pooled dimension (default) -#' datasources = connections)#all opal servers are used +#' datasources = connections)#all Armadillo/Opal servers are used ds.dim(x="D", type="split", #separate dimension for each study -#' datasources = connections[1])#only the first opal server is used ("study1") +#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.exists.Rd b/man/ds.exists.Rd index 2352a2941..b32b3ed9a 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -35,7 +35,7 @@ Server function called: \code{exists} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -60,9 +60,9 @@ Server function called: \code{exists} # Check if the object exist in the server-side ds.exists(x = "D", - datasources = connections) #All opal servers are used + datasources = connections) #All Armadillo/Opal servers are used ds.exists(x = "D", - datasources = connections[1]) #Only the first Opal server is used (study1) + datasources = connections[1]) #Only the first Armadillo/Opal server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.exp.Rd b/man/ds.exp.Rd index dd10147ab..4959536d2 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -31,7 +31,7 @@ Server function called: \code{expDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -53,13 +53,13 @@ Server function called: \code{expDS}. logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # compute exponential function of the 'PM_BMI_CONTINUOUS' variable ds.exp(x = "D$PM_BMI_CONTINUOUS", newobj = "exp.PM_BMI_CONTINUOUS", - datasources = connections[1]) #only the first Opal server is used (study1) + datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.extractQuantiles.Rd b/man/ds.extractQuantiles.Rd index b5a2ddadf..696f4752c 100644 --- a/man/ds.extractQuantiles.Rd +++ b/man/ds.extractQuantiles.Rd @@ -56,7 +56,7 @@ otherwise left behind. These are not usually needed, but could be of value if one were investigating a problem with the ranking. FALSE: do not delete the residual objects} -\item{extract.datasources}{specifies the particular opal object(s) to use. +\item{extract.datasources}{specifies the particular Armadillo/Opal connection object(s) to use. This is set via the argument in ds.ranksSecure. For more details see the associated document entitled "secure.global.ranking.docx". Also see the header file for ds.ranksSecure.} diff --git a/man/ds.forestplot.Rd b/man/ds.forestplot.Rd index 66606601d..a962d4c42 100644 --- a/man/ds.forestplot.Rd +++ b/man/ds.forestplot.Rd @@ -45,7 +45,7 @@ DataSHIELD table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the logistic regression model diff --git a/man/ds.getWGSR.Rd b/man/ds.getWGSR.Rd index c5a8c9323..3c8aef4a9 100644 --- a/man/ds.getWGSR.Rd +++ b/man/ds.getWGSR.Rd @@ -90,7 +90,7 @@ data. \examples{ \dontrun{ - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -112,7 +112,7 @@ data. logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Generate the weight-for-height (wfh) index diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index f3a872c12..c0b80e155 100644 --- a/man/ds.glm.Rd +++ b/man/ds.glm.Rd @@ -261,7 +261,7 @@ Server functions called: \code{glmDS1} and \code{glmDS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -285,7 +285,7 @@ Server functions called: \code{glmDS1} and \code{glmDS2} table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the GLM @@ -341,7 +341,7 @@ Server functions called: \code{glmDS1} and \code{glmDS2} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the logistic regression model diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index 4ad3ab0fa..fa5f1b65d 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -329,7 +329,7 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -353,7 +353,7 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the GLM @@ -405,7 +405,7 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the logistic regression model diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index 3af0a7480..5d27d845f 100644 --- a/man/ds.glmerSLMA.Rd +++ b/man/ds.glmerSLMA.Rd @@ -231,7 +231,7 @@ Server function called: \code{glmerSLMADS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -252,7 +252,7 @@ Server function called: \code{glmerSLMADS2} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Select all rows without missing values @@ -285,7 +285,7 @@ Server function called: \code{glmerSLMADS2} table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.heatmapPlot.Rd b/man/ds.heatmapPlot.Rd index 8d1403218..695cf59d0 100644 --- a/man/ds.heatmapPlot.Rd +++ b/man/ds.heatmapPlot.Rd @@ -127,7 +127,7 @@ Server function called: \code{heatmapPlotDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -148,7 +148,7 @@ Server function called: \code{heatmapPlotDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Compute the heat map plot diff --git a/man/ds.histogram.Rd b/man/ds.histogram.Rd index 181e8ef66..995d1bed3 100644 --- a/man/ds.histogram.Rd +++ b/man/ds.histogram.Rd @@ -121,7 +121,7 @@ Server function called: \code{histogramDS2} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -142,7 +142,7 @@ Server function called: \code{histogramDS2} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Compute the histogram diff --git a/man/ds.isNA.Rd b/man/ds.isNA.Rd index 5afec642e..7f9df15d9 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -36,7 +36,7 @@ Server function called: \code{isNaDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.isValid.Rd b/man/ds.isValid.Rd index eb4f4cd95..9d1fa0ae0 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -37,7 +37,7 @@ Server function called: \code{isValidDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.length.Rd b/man/ds.length.Rd index 72add8698..97f4c9a82 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -47,7 +47,7 @@ Server function called: \code{lengthDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.levels.Rd b/man/ds.levels.Rd index da714bf57..cbae2c24c 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -29,7 +29,7 @@ Server function called: \code{levelsDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.lexis.Rd b/man/ds.lexis.Rd index 45c0afc39..9980be35e 100644 --- a/man/ds.lexis.Rd +++ b/man/ds.lexis.Rd @@ -166,7 +166,7 @@ Server functions called: \code{lexisDS1}, \code{lexisDS2} and \code{lexisDS3} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -190,7 +190,7 @@ Server functions called: \code{lexisDS1}, \code{lexisDS2} and \code{lexisDS3} table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Example 1: Create the expanded data frame. diff --git a/man/ds.list.Rd b/man/ds.list.Rd index 424d10233..f0494920a 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -40,7 +40,7 @@ Server function called: \code{listDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.listDisclosureSettings.Rd b/man/ds.listDisclosureSettings.Rd index 23ab83fd7..bd5ab8e13 100644 --- a/man/ds.listDisclosureSettings.Rd +++ b/man/ds.listDisclosureSettings.Rd @@ -75,7 +75,7 @@ Server function called: \code{listDisclosureSettingsDS} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -95,7 +95,7 @@ Server function called: \code{listDisclosureSettingsDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Call to list current disclosure settings in all data repository servers diff --git a/man/ds.listOpals.Rd b/man/ds.listOpals.Rd index 2ad3784f0..c06b47ca9 100644 --- a/man/ds.listOpals.Rd +++ b/man/ds.listOpals.Rd @@ -16,7 +16,7 @@ all Opal objects in the analytic environment. } \details{ ds.listOpals calls the internal DataSHIELD function getOpals() which identifies -all Opal objects in the analytic environment. If there are no Opal servers in the analytic +all Opal objects in the analytic environment. If there are no Armadillo/Opal servers in the analytic environment ds.listOpalsIreminds the user that they have to login to a valid set of Opal login objects, if they wish to use DataSHIELD. If there is only one set of Opals, ds.listOpals copies that one set and names the copy 'default.opals'. This default set will then be used by diff --git a/man/ds.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index 70d9ba5d1..a6553b57b 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -33,7 +33,7 @@ This function does not call any server-side function. \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -54,7 +54,7 @@ This function does not call any server-side function. table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # List server-side functions diff --git a/man/ds.lmerSLMA.Rd b/man/ds.lmerSLMA.Rd index 197e10933..d8ad7e32a 100644 --- a/man/ds.lmerSLMA.Rd +++ b/man/ds.lmerSLMA.Rd @@ -223,7 +223,7 @@ Server function called: \code{lmerSLMADS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -244,7 +244,7 @@ Server function called: \code{lmerSLMADS2} table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") logindata <- builder$build() - #Log onto the remote Opal training servers + #Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Select all rows without missing values diff --git a/man/ds.log.Rd b/man/ds.log.Rd index a48ee6aae..c1371f188 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -34,7 +34,7 @@ Server function called: \code{logDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -56,7 +56,7 @@ Server function called: \code{logDS} logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Calculating the log value of the 'PM_BMI_CONTINUOUS' variable @@ -64,7 +64,7 @@ Server function called: \code{logDS} ds.log(x = "D$PM_BMI_CONTINUOUS", base = exp(2), newobj = "log.PM_BMI_CONTINUOUS", - datasources = connections[1]) #only the first Opal server is used (study1) + datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.look.Rd b/man/ds.look.Rd index 3cecb4627..7998c50f3 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -45,7 +45,7 @@ The function is a wrapper for the DSI package function \code{datashield.aggregat ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index ae54bd5cd..c4a135bb3 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -87,7 +87,7 @@ Server function called: \code{lsDS}. ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.make.Rd b/man/ds.make.Rd index 5b361b83e..889fcaff1 100644 --- a/man/ds.make.Rd +++ b/man/ds.make.Rd @@ -88,7 +88,7 @@ The \code{ds.make} function is a wrapper for the DSI package function \code{data ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrix.Rd b/man/ds.matrix.Rd index c005e7ad0..2472f4377 100644 --- a/man/ds.matrix.Rd +++ b/man/ds.matrix.Rd @@ -84,7 +84,7 @@ Server function called: \code{matrixDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixDet.Rd b/man/ds.matrixDet.Rd index 6870ae605..6cd6e586e 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -40,7 +40,7 @@ Server function called: \code{matrixDetDS2} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixDet.report.Rd b/man/ds.matrixDet.report.Rd index c9f039f08..13ad32c8c 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -38,7 +38,7 @@ Server function called: \code{matrixDetDS1} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index ab9385f11..514615d10 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -87,7 +87,7 @@ Server function called: \code{matrixDiagDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index 86311432c..7612f332e 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -44,7 +44,7 @@ Server function called: \code{matrixDimnamesDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixInvert.Rd b/man/ds.matrixInvert.Rd index 6159b4f35..6c7d48a27 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -35,7 +35,7 @@ Server function called: \code{matrixInvertDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixMult.Rd b/man/ds.matrixMult.Rd index e43c83d4a..9fa8f818b 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -40,7 +40,7 @@ Server function called: \code{matrixMultDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.matrixTranspose.Rd b/man/ds.matrixTranspose.Rd index 55fcd239d..6f5975412 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -37,7 +37,7 @@ Server function called: \code{matrixTransposeDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.mdPattern.Rd b/man/ds.mdPattern.Rd index b1bacc0b1..b03e6fcba 100644 --- a/man/ds.mdPattern.Rd +++ b/man/ds.mdPattern.Rd @@ -78,7 +78,7 @@ for disclosure control: \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.mean.Rd b/man/ds.mean.Rd index 9c7d7e786..8061295e1 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -80,7 +80,7 @@ Server function called: \code{meanDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.meanByClass.Rd b/man/ds.meanByClass.Rd index f60ba7a45..8684b73fb 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -55,7 +55,7 @@ parameter \code{datasources}. ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.meanSdGp.Rd b/man/ds.meanSdGp.Rd index 11501f722..79a47fe2a 100644 --- a/man/ds.meanSdGp.Rd +++ b/man/ds.meanSdGp.Rd @@ -93,7 +93,7 @@ Server function called: \code{meanSdGpDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.merge.Rd b/man/ds.merge.Rd index a99b07321..54b653a6a 100644 --- a/man/ds.merge.Rd +++ b/man/ds.merge.Rd @@ -93,7 +93,7 @@ Server function called: \code{mergeDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.message.Rd b/man/ds.message.Rd index ab1dff8d6..1ca6ecdbd 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -45,7 +45,7 @@ Server function called: \code{messageDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.metadata.Rd b/man/ds.metadata.Rd index 0e704042b..0fb365fdf 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -28,7 +28,7 @@ which are non-disclosive. \examples{ \dontrun{ - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.names.Rd b/man/ds.names.Rd index 984e25967..bc5eba7ea 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -38,7 +38,7 @@ is formally of class "glm" and "ls" but responds TRUE to is.list(), ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.numNA.Rd b/man/ds.numNA.Rd index bae29ca8b..4015741e1 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -33,7 +33,7 @@ Server function called: \code{numNaDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.quantileMean.Rd b/man/ds.quantileMean.Rd index 01cb36df4..443f921e7 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -49,7 +49,7 @@ Server functions called: \code{quantileMeanDS}, \code{length} and \code{numNaDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.rBinom.Rd b/man/ds.rBinom.Rd index 7642073ad..36b288512 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -82,7 +82,7 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. \examples{ \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -104,17 +104,17 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - #Generating the vectors in the Opal servers + #Generating the vectors in the Armadillo/Opal servers ds.rBinom(samp.size=c(13,20,25), #the length of the vector created in each source is different size=c(10,23,5), #Bernoulli trials change in each source prob=c(0.6,0.1,0.5), #Probability changes in each source newobj="Binom.dist", seed.as.integer=45, return.full.seed.as.set=FALSE, - datasources=connections) #all the Opal servers are used, in this case 3 + datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 #(see above the connection to the servers) ds.rBinom(samp.size=15, @@ -123,7 +123,7 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. newobj="Binom.dist", seed.as.integer=324, return.full.seed.as.set=FALSE, - datasources=connections[2]) #only the second Opal server is used ("study2") + datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rNorm.Rd b/man/ds.rNorm.Rd index c278d757b..592e662db 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -95,7 +95,7 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -116,10 +116,10 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Opal servers + # Generating the vectors in the Armadillo/Opal servers ds.rNorm(samp.size=c(10,20,45), #the length of the vector created in each source is different mean=c(1,6,4), #the mean of the Normal distribution changes in each server @@ -129,7 +129,7 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. return.full.seed.as.set=FALSE, force.output.to.k.decimal.places=c(4,5,6), #output random numbers have different #decimal quantity in each source - datasources=connections) #all the Opal servers are used, in this case 3 + datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 #(see above the connection to the servers) ds.rNorm(samp.size=10, @@ -139,7 +139,7 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. seed.as.integer=2345, return.full.seed.as.set=FALSE, force.output.to.k.decimal.places=1, - datasources=connections[2]) #only the second Opal server is used ("study2") + datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rPois.Rd b/man/ds.rPois.Rd index dc216bd81..5ccde0c9a 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -78,7 +78,7 @@ Server functions called: \code{rPoisDS} and \code{setSeedDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -98,23 +98,23 @@ Server functions called: \code{rPoisDS} and \code{setSeedDS}. user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Opal servers + # Generating the vectors in the Armadillo/Opal servers ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different lambda=c(2,3,4), #different mean per interval (2,3,4) in each source newobj="Pois.dist", seed.as.integer=1234, return.full.seed.as.set=FALSE, - datasources=connections) #all the Opal servers are used, in this case 3 + datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 #(see above the connection to the servers) ds.rPois(samp.size=13, lambda=5, newobj="Pois.dist", seed.as.integer=1234, return.full.seed.as.set=FALSE, - datasources=connections[1]) #only the first Opal server is used ("study1") + datasources=connections[1]) #only the first Armadillo/Opal server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rUnif.Rd b/man/ds.rUnif.Rd index 622c44370..322031988 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -101,7 +101,7 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -122,10 +122,10 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Opal servers + # Generating the vectors in the Armadillo/Opal servers ds.rUnif(samp.size = c(12,20,4), #the length of the vector created in each source is different min = c(0,2,5), #different minumum value of the function in each source @@ -134,7 +134,7 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. seed.as.integer = 234, return.full.seed.as.set = FALSE, force.output.to.k.decimal.places = c(1,2,3), - datasources = connections) #all the Opal servers are used, in this case 3 + datasources = connections) #all the Armadillo/Opal servers are used, in this case 3 #(see above the connection to the servers) ds.rUnif(samp.size = 12, @@ -144,7 +144,7 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. seed.as.integer = 12345, return.full.seed.as.set = FALSE, force.output.to.k.decimal.places = 2, - datasources = connections[2]) #only the second Opal server is used ("study2") + datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rbind.Rd b/man/ds.rbind.Rd index 48315a37e..41db4af63 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -63,7 +63,7 @@ Server functions called: \code{rbindDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -84,19 +84,19 @@ Server functions called: \code{rbindDS}. table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Combining R objects by rows ds.rbind(x = "D", #data frames in the server-side to be conbined - #(see above the connection to the Opal servers) + #(see above the connection to the Armadillo/Opal servers) DataSHIELD.checks = FALSE, force.colnames = NULL, newobj = "D.rbind", # name for the output object that is stored in the data servers - datasources = connections, # All Opal servers are used - #(see above the connection to the Opal servers) + datasources = connections, # All Armadillo/Opal servers are used + #(see above the connection to the Armadillo/Opal servers) notify.of.progress = FALSE) # Clear the Datashield R sessions and logout diff --git a/man/ds.reShape.Rd b/man/ds.reShape.Rd index 7b032112c..cb71c527e 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -73,7 +73,7 @@ Server function called: \code{reShapeDS} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -94,7 +94,7 @@ Server function called: \code{reShapeDS} table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Reshape server-side grouped data diff --git a/man/ds.recodeLevels.Rd b/man/ds.recodeLevels.Rd index 4fbf3402c..a58bd21fc 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -44,7 +44,7 @@ Server function called: \code{levels()} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index 8dd60bb33..cc39ce199 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -59,7 +59,7 @@ Server function called: \code{recodeValuesDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.rep.Rd b/man/ds.rep.Rd index caf7e9b45..70138e9b8 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -66,7 +66,7 @@ Server function called: \code{repDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -87,7 +87,7 @@ Server function called: \code{repDS}. table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.replaceNA.Rd b/man/ds.replaceNA.Rd index f73a3ab50..20de1a686 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -46,7 +46,7 @@ Server function called: \code{replaceNaDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -67,7 +67,7 @@ Server function called: \code{replaceNaDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Replace missing values in variable 'LAB_HDL' by the mean value diff --git a/man/ds.rm.Rd b/man/ds.rm.Rd index a63786217..595fd64c0 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -42,7 +42,7 @@ Server function called: \code{rmDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.rowColCalc.Rd b/man/ds.rowColCalc.Rd index 678184728..0ef4eb792 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -39,7 +39,7 @@ Server functions called: \code{classDS}, \code{dimDS} and \code{colnamesDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -61,7 +61,7 @@ Server functions called: \code{classDS}, \code{dimDS} and \code{colnamesDS} logindata <- builder$build() myvar <- list("LAB_TSC","LAB_HDL") - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, variables = myvar, symbol = "D") diff --git a/man/ds.sample.Rd b/man/ds.sample.Rd index 2f801edcc..a70520dc8 100644 --- a/man/ds.sample.Rd +++ b/man/ds.sample.Rd @@ -75,14 +75,14 @@ For further details see help for \code{sample} in native R.} \item{newobj}{This a character string providing a name for the output data.frame which defaults to 'newobj.sample' if no name is specified.} -\item{datasources}{specifies the particular opal object(s) to use. If the -argument is not specified the default set of opals will be used. The default opals +\item{datasources}{specifies the particular Armadillo/Opal connection object(s) to use. If the +argument is not specified the default set of Armadillo/Opal servers will be used. The default servers are called default.opals and the default can be set using the function \code{ds.setDefaultOpals}. If the is to be specified, it should be set without inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to -apply the function solely to e.g. the second opal server in a set of three, +apply the function solely to e.g. the second Armadillo/Opal server in a set of three, the argument can be specified as: e.g. datasources=opals.em[2]. -If you wish to specify the first and third opal servers in a set you specify: +If you wish to specify the first and third Armadillo/Opal servers in a set you specify: e.g. datasources=opals.em[c(1,3)]} \item{notify.of.progress}{specifies if console output should be produce to indicate diff --git a/man/ds.scatterPlot.Rd b/man/ds.scatterPlot.Rd index 984cd329f..12ea7e2c1 100644 --- a/man/ds.scatterPlot.Rd +++ b/man/ds.scatterPlot.Rd @@ -107,7 +107,7 @@ Server function called: \code{scatterPlotDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -127,7 +127,7 @@ Server function called: \code{scatterPlotDS} user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Example 1: generate a scatter plot for each study separately diff --git a/man/ds.seq.Rd b/man/ds.seq.Rd index 5ce615454..42c312bb4 100644 --- a/man/ds.seq.Rd +++ b/man/ds.seq.Rd @@ -92,7 +92,7 @@ Server function called: \code{seqDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -113,7 +113,7 @@ Server function called: \code{seqDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Create 3 different sequences diff --git a/man/ds.setSeed.Rd b/man/ds.setSeed.Rd index c8b52a69d..df50e17e6 100644 --- a/man/ds.setSeed.Rd +++ b/man/ds.setSeed.Rd @@ -60,7 +60,7 @@ Server function called: \code{setSeedDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -81,7 +81,7 @@ Server function called: \code{setSeedDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Generate a pseudorandom number in the server-side diff --git a/man/ds.skewness.Rd b/man/ds.skewness.Rd index cb74c7219..9a9087488 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -36,7 +36,7 @@ and the number of valid observations. } \description{ This function calculates the skewness of a numeric variable -that is stored on the server-side (Opal server). +that is stored on the server-side (Armadillo/Opal server). } \details{ This function is similar to the function \code{skewness} in R package \code{e1071}. @@ -65,7 +65,7 @@ Server functions called: \code{skewnessDS1} and \code{skewnessDS2} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index 95b5432cd..e92fa5df5 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -35,7 +35,7 @@ specified by the user through the argument \code{newobj}, otherwise is named by \examples{ \dontrun{ - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -57,7 +57,7 @@ specified by the user through the argument \code{newobj}, otherwise is named by logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Get the square root of LAB_HDL variable diff --git a/man/ds.summary.Rd b/man/ds.summary.Rd index 3e8da4f98..141ac0541 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -38,7 +38,7 @@ server functions called: \code{isValidDS}, \code{dimDS} and \code{colnamesDS} ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') @@ -59,7 +59,7 @@ server functions called: \code{isValidDS}, \code{dimDS} and \code{colnamesDS} table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Calculate the summary of a numeric variable diff --git a/man/ds.tapply.Rd b/man/ds.tapply.Rd index 5c764c2bb..f5656ec76 100644 --- a/man/ds.tapply.Rd +++ b/man/ds.tapply.Rd @@ -100,7 +100,7 @@ Server function called: \code{tapplyDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.tapply.assign.Rd b/man/ds.tapply.assign.Rd index 908a15554..232fee8ff 100644 --- a/man/ds.tapply.assign.Rd +++ b/man/ds.tapply.assign.Rd @@ -105,7 +105,7 @@ Server function called: \code{ds.tapply.assign} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.testObjExists.Rd b/man/ds.testObjExists.Rd index ae0fb40d1..a48097c48 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -36,7 +36,7 @@ Server function called: \code{testObjExistsDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.unList.Rd b/man/ds.unList.Rd index 41f1665a2..7926ea7e3 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -43,7 +43,7 @@ Server function called: \code{unListDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index 18d77005a..145bfdee3 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -29,7 +29,7 @@ Server function called: \code{uniqueDS} } \examples{ \dontrun{ - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/ds.var.Rd b/man/ds.var.Rd index 86a89fd90..4ea17d6ac 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -60,7 +60,7 @@ Server function called: \code{varDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') diff --git a/man/subsetHelper.Rd b/man/subsetHelper.Rd index 6922ec94b..674dd8480 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -38,7 +38,7 @@ Server function called: \code{dimDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') require('DSOpal') From f7e40e7c815f1941e311b4154137ed4118b5332c Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Tue, 13 Oct 2026 11:51:56 +0200 Subject: [PATCH 2/2] docs: update examples to include armadillo --- R/ds.Boole.R | 18 ++++++++-------- R/ds.abs.R | 18 ++++++++-------- R/ds.asCharacter.R | 20 ++++++++--------- R/ds.asDataMatrix.R | 20 ++++++++--------- R/ds.asFactor.R | 22 +++++++++---------- R/ds.asInteger.R | 20 ++++++++--------- R/ds.asList.R | 20 ++++++++--------- R/ds.asLogical.R | 20 ++++++++--------- R/ds.asMatrix.R | 20 ++++++++--------- R/ds.asNumeric.R | 20 ++++++++--------- R/ds.assign.R | 20 ++++++++--------- R/ds.boxPlot.R | 18 ++++++++-------- R/ds.c.R | 20 ++++++++--------- R/ds.cbind.R | 18 ++++++++-------- R/ds.changeRefGroup.R | 18 ++++++++-------- R/ds.class.R | 18 ++++++++-------- R/ds.colnames.R | 18 ++++++++-------- R/ds.completeCases.R | 36 +++++++++++++++---------------- R/ds.contourPlot.R | 18 ++++++++-------- R/ds.cor.R | 18 ++++++++-------- R/ds.corTest.R | 18 ++++++++-------- R/ds.cov.R | 20 ++++++++--------- R/ds.dataFrame.R | 20 ++++++++--------- R/ds.dataFrameFill.R | 18 ++++++++-------- R/ds.dataFrameSort.R | 20 ++++++++--------- R/ds.dataFrameSubset.R | 18 ++++++++-------- R/ds.densityGrid.R | 22 +++++++++---------- R/ds.dim.R | 24 ++++++++++----------- R/ds.dmtC2S.R | 10 ++++----- R/ds.exists.R | 22 +++++++++---------- R/ds.exp.R | 20 ++++++++--------- R/ds.extractQuantiles.R | 2 +- R/ds.forestplot.R | 17 +++++++-------- R/ds.getWGSR.R | 18 ++++++++-------- R/ds.glm.R | 33 +++++++++++++--------------- R/ds.glmPredict.R | 10 ++++----- R/ds.glmSLMA.R | 33 +++++++++++++--------------- R/ds.glmSummary.R | 10 ++++----- R/ds.glmerSLMA.R | 33 +++++++++++++--------------- R/ds.heatmapPlot.R | 18 ++++++++-------- R/ds.histogram.R | 18 ++++++++-------- R/ds.isNA.R | 18 ++++++++-------- R/ds.isValid.R | 18 ++++++++-------- R/ds.length.R | 18 ++++++++-------- R/ds.levels.R | 18 ++++++++-------- R/ds.lexis.R | 18 ++++++++-------- R/ds.list.R | 18 ++++++++-------- R/ds.listDisclosureSettings.R | 18 ++++++++-------- R/ds.listServersideFunctions.R | 18 ++++++++-------- R/ds.lmerSLMA.R | 18 ++++++++-------- R/ds.log.R | 20 ++++++++--------- R/ds.look.R | 18 ++++++++-------- R/ds.ls.R | 18 ++++++++-------- R/ds.make.R | 18 ++++++++-------- R/ds.matrix.R | 18 ++++++++-------- R/ds.matrixDet.R | 18 ++++++++-------- R/ds.matrixDet.report.R | 18 ++++++++-------- R/ds.matrixDiag.R | 18 ++++++++-------- R/ds.matrixDimnames.R | 18 ++++++++-------- R/ds.matrixInvert.R | 18 ++++++++-------- R/ds.matrixMult.R | 18 ++++++++-------- R/ds.matrixTranspose.R | 18 ++++++++-------- R/ds.mdPattern.R | 14 +++++++----- R/ds.mean.R | 18 ++++++++-------- R/ds.meanByClass.R | 18 ++++++++-------- R/ds.meanSdGp.R | 18 ++++++++-------- R/ds.merge.R | 18 ++++++++-------- R/ds.message.R | 18 ++++++++-------- R/ds.metadata.R | 18 ++++++++-------- R/ds.names.R | 18 ++++++++-------- R/ds.numNA.R | 18 ++++++++-------- R/ds.quantileMean.R | 18 ++++++++-------- R/ds.rBinom.R | 30 +++++++++++++------------- R/ds.rNorm.R | 32 +++++++++++++-------------- R/ds.rPois.R | 28 ++++++++++++------------ R/ds.rUnif.R | 32 +++++++++++++-------------- R/ds.rbind.R | 24 ++++++++++----------- R/ds.reShape.R | 18 ++++++++-------- R/ds.recodeLevels.R | 18 ++++++++-------- R/ds.recodeValues.R | 18 ++++++++-------- R/ds.rep.R | 18 ++++++++-------- R/ds.replaceNA.R | 22 +++++++++---------- R/ds.rm.R | 18 ++++++++-------- R/ds.rowColCalc.R | 18 ++++++++-------- R/ds.sample.R | 20 ++++++++--------- R/ds.scatterPlot.R | 18 ++++++++-------- R/ds.seq.R | 18 ++++++++-------- R/ds.setSeed.R | 18 ++++++++-------- R/ds.skewness.R | 20 ++++++++--------- R/ds.sqrt.R | 18 ++++++++-------- R/ds.summary.R | 18 ++++++++-------- R/ds.tapply.R | 18 ++++++++-------- R/ds.tapply.assign.R | 18 ++++++++-------- R/ds.testObjExists.R | 18 ++++++++-------- R/ds.unList.R | 18 ++++++++-------- R/ds.unique.R | 18 ++++++++-------- R/ds.var.R | 18 ++++++++-------- R/subsetHelper.R | 18 ++++++++-------- man/ds.Boole.Rd | 18 ++++++++-------- man/ds.abs.Rd | 18 ++++++++-------- man/ds.asCharacter.Rd | 20 ++++++++--------- man/ds.asDataMatrix.Rd | 20 ++++++++--------- man/ds.asFactor.Rd | 22 +++++++++---------- man/ds.asInteger.Rd | 20 ++++++++--------- man/ds.asList.Rd | 20 ++++++++--------- man/ds.asLogical.Rd | 20 ++++++++--------- man/ds.asMatrix.Rd | 20 ++++++++--------- man/ds.asNumeric.Rd | 20 ++++++++--------- man/ds.assign.Rd | 20 ++++++++--------- man/ds.boxPlot.Rd | 18 ++++++++-------- man/ds.c.Rd | 20 ++++++++--------- man/ds.cbind.Rd | 18 ++++++++-------- man/ds.changeRefGroup.Rd | 18 ++++++++-------- man/ds.class.Rd | 18 ++++++++-------- man/ds.colnames.Rd | 18 ++++++++-------- man/ds.completeCases.Rd | 36 +++++++++++++++---------------- man/ds.contourPlot.Rd | 18 ++++++++-------- man/ds.cor.Rd | 18 ++++++++-------- man/ds.corTest.Rd | 18 ++++++++-------- man/ds.cov.Rd | 20 ++++++++--------- man/ds.dataFrame.Rd | 20 ++++++++--------- man/ds.dataFrameFill.Rd | 18 ++++++++-------- man/ds.dataFrameSort.Rd | 20 ++++++++--------- man/ds.dataFrameSubset.Rd | 18 ++++++++-------- man/ds.densityGrid.Rd | 22 +++++++++---------- man/ds.dim.Rd | 24 ++++++++++----------- man/ds.dmtC2S.Rd | 10 ++++----- man/ds.exists.Rd | 22 +++++++++---------- man/ds.exp.Rd | 20 ++++++++--------- man/ds.extractQuantiles.Rd | 2 +- man/ds.forestplot.Rd | 17 +++++++-------- man/ds.getWGSR.Rd | 18 ++++++++-------- man/ds.glm.Rd | 33 +++++++++++++--------------- man/ds.glmPredict.Rd | 10 ++++----- man/ds.glmSLMA.Rd | 33 +++++++++++++--------------- man/ds.glmSummary.Rd | 10 ++++----- man/ds.glmerSLMA.Rd | 33 +++++++++++++--------------- man/ds.heatmapPlot.Rd | 18 ++++++++-------- man/ds.histogram.Rd | 18 ++++++++-------- man/ds.isNA.Rd | 18 ++++++++-------- man/ds.isValid.Rd | 18 ++++++++-------- man/ds.length.Rd | 18 ++++++++-------- man/ds.levels.Rd | 18 ++++++++-------- man/ds.lexis.Rd | 18 ++++++++-------- man/ds.list.Rd | 18 ++++++++-------- man/ds.listDisclosureSettings.Rd | 18 ++++++++-------- man/ds.listServersideFunctions.Rd | 18 ++++++++-------- man/ds.lmerSLMA.Rd | 18 ++++++++-------- man/ds.log.Rd | 20 ++++++++--------- man/ds.look.Rd | 18 ++++++++-------- man/ds.ls.Rd | 18 ++++++++-------- man/ds.make.Rd | 18 ++++++++-------- man/ds.matrix.Rd | 18 ++++++++-------- man/ds.matrixDet.Rd | 18 ++++++++-------- man/ds.matrixDet.report.Rd | 18 ++++++++-------- man/ds.matrixDiag.Rd | 18 ++++++++-------- man/ds.matrixDimnames.Rd | 18 ++++++++-------- man/ds.matrixInvert.Rd | 18 ++++++++-------- man/ds.matrixMult.Rd | 18 ++++++++-------- man/ds.matrixTranspose.Rd | 18 ++++++++-------- man/ds.mdPattern.Rd | 14 +++++++----- man/ds.mean.Rd | 18 ++++++++-------- man/ds.meanByClass.Rd | 18 ++++++++-------- man/ds.meanSdGp.Rd | 18 ++++++++-------- man/ds.merge.Rd | 18 ++++++++-------- man/ds.message.Rd | 18 ++++++++-------- man/ds.metadata.Rd | 18 ++++++++-------- man/ds.names.Rd | 18 ++++++++-------- man/ds.numNA.Rd | 18 ++++++++-------- man/ds.quantileMean.Rd | 18 ++++++++-------- man/ds.rBinom.Rd | 30 +++++++++++++------------- man/ds.rNorm.Rd | 32 +++++++++++++-------------- man/ds.rPois.Rd | 28 ++++++++++++------------ man/ds.rUnif.Rd | 32 +++++++++++++-------------- man/ds.rbind.Rd | 24 ++++++++++----------- man/ds.reShape.Rd | 18 ++++++++-------- man/ds.recodeLevels.Rd | 18 ++++++++-------- man/ds.recodeValues.Rd | 18 ++++++++-------- man/ds.rep.Rd | 18 ++++++++-------- man/ds.replaceNA.Rd | 22 +++++++++---------- man/ds.rm.Rd | 18 ++++++++-------- man/ds.rowColCalc.Rd | 18 ++++++++-------- man/ds.sample.Rd | 20 ++++++++--------- man/ds.scatterPlot.Rd | 18 ++++++++-------- man/ds.seq.Rd | 18 ++++++++-------- man/ds.setSeed.Rd | 18 ++++++++-------- man/ds.skewness.Rd | 20 ++++++++--------- man/ds.sqrt.Rd | 18 ++++++++-------- man/ds.summary.Rd | 18 ++++++++-------- man/ds.tapply.Rd | 18 ++++++++-------- man/ds.tapply.assign.Rd | 18 ++++++++-------- man/ds.testObjExists.Rd | 18 ++++++++-------- man/ds.unList.Rd | 18 ++++++++-------- man/ds.unique.Rd | 18 ++++++++-------- man/ds.var.Rd | 18 ++++++++-------- man/subsetHelper.Rd | 18 ++++++++-------- 196 files changed, 1886 insertions(+), 1898 deletions(-) diff --git a/R/ds.Boole.R b/R/ds.Boole.R index 45f6efa5e..881ebbb74 100644 --- a/R/ds.Boole.R +++ b/R/ds.Boole.R @@ -47,22 +47,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' diff --git a/R/ds.abs.R b/R/ds.abs.R index 974cbcb4e..625591a84 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -25,22 +25,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index df354f85a..700b90b12 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -21,22 +21,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -44,7 +44,7 @@ #' # Converting the R object into a class character #' ds.asCharacter(x.name = "D$LAB_TSC", #' newobj = "char.obj", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index 5ee86fb34..9126b9fc0 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -20,22 +20,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -43,7 +43,7 @@ #' # Converting the R object into a matrix #' ds.asDataMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index f3da4ee44..a8ae29f48 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -143,22 +143,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -170,14 +170,14 @@ #' #from all studies is created #' fixed.dummy.vars = TRUE, #create a matrix of dummy variables #' baseline.level = 1, -#' datasources = connections)#all the Armadillo/Opal servers are used, in this case 3 +#' datasources = connections)#all the servers are used, in this case 2 #' #(see above the connection to the servers) #' ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", #' newobj.name = "fact.obj", #' forced.factor.levels = c(2,3), #the variable is split in 2 levels #' fixed.dummy.vars = TRUE, #create a matrix of dummy variables #' baseline.level = 1, -#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1])#only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index d46b73cbb..bd5eb2921 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -34,22 +34,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -57,7 +57,7 @@ #' # Converting the R object into an integer #' ds.asInteger(x.name = "D$LAB_TSC", #' newobj = "int.obj", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' ds.class(x = "int.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asList.R b/R/ds.asList.R index 7aa836a8d..fb3fbdbc6 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -21,22 +21,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -44,7 +44,7 @@ #' # Converting the R object into a List #' ds.asList(x.name = "D", #' newobj = "D.asList", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' ds.class(x = "D.asList", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R index c14abc22b..89dfb2556 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -20,22 +20,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -43,7 +43,7 @@ #' # Converting the R object into a logical #' ds.asLogical(x.name = "D$LAB_TSC", #' newobj = "logical.obj", -#' datasources =connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources =connections[1]) #only the first server is used ("study1") #' ds.class(x = "logical.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R index 61cfed2eb..1c97dbf1b 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -23,22 +23,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -46,7 +46,7 @@ #' # Converting the R object into a matrix #' ds.asMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index dada7ab35..980a71176 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -34,22 +34,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -57,7 +57,7 @@ #' # Converting the R object into a numeric class #' ds.asNumeric(x.name = "D$LAB_TSC", #' newobj = "num.obj", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' ds.class(x = "num.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.assign.R b/R/ds.assign.R index 736457ad7..c646e3785 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -25,22 +25,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -48,7 +48,7 @@ #' # Assign a variable to a name #' ds.assign(toAssign = "D$LAB_TSC", #' newobj = "labtsc", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index 63d00bb40..cb51d601f 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -27,22 +27,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, diff --git a/R/ds.c.R b/R/ds.c.R index e48c225e5..8a9284139 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -24,22 +24,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -48,7 +48,7 @@ #' myvect <- c("D$LAB_TSC", "D$LAB_HDL") #' ds.c(x = myvect, #' newobj = "new.vect", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.cbind.R b/R/ds.cbind.R index 248719385..1af1737a1 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -48,22 +48,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.changeRefGroup.R b/R/ds.changeRefGroup.R index 1155a0d8d..ae06bd6b8 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -42,22 +42,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.class.R b/R/ds.class.R index 5123204ee..299950a47 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -20,22 +20,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.colnames.R b/R/ds.colnames.R index 1ff7f1dbf..571574217 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -21,22 +21,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index 5ca727ab6..1a3d3f5aa 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -27,22 +27,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -50,18 +50,18 @@ #' #' # Select complete cases from different R objects #' -#' ds.completeCases(x1 = "D", #data frames in the Armadillo/Opal servers -#' #(see above the connection to the Armadillo/Opal servers) +#' ds.completeCases(x1 = "D", #data frames in the servers +#' #(see above the connection to the servers) #' newobj = "D.completeCases", # name for the output object -#' # that is stored in the Armadillo/Opal servers -#' datasources = connections) # All Armadillo/Opal servers are used -#' # (see above the connection to the Armadillo/Opal servers) +#' # that is stored in the servers +#' datasources = connections) # All servers are used +#' # (see above the connection to the servers) #' -#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Armadillo/Opal servers -#' #(see above the connection to the Armadillo/Opal servers) +#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the servers +#' #(see above the connection to the servers) #' newobj = "LAB_TSC.completeCases", #name for the output variable -#' #that is stored in the Armadillo/Opal servers -#' datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") +#' #that is stored in the servers +#' datasources = connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.contourPlot.R b/R/ds.contourPlot.R index 9aad4f04d..94dfa21b0 100644 --- a/R/ds.contourPlot.R +++ b/R/ds.contourPlot.R @@ -64,22 +64,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.cor.R b/R/ds.cor.R index d81ca4a75..8d068beb9 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -46,22 +46,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 3d8e95a39..78c802168 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -35,22 +35,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.cov.R b/R/ds.cov.R index 6031ac7c2..1fdf57f20 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -56,22 +56,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -90,7 +90,7 @@ #' y = 'gender', #' naAction = 'pairwise.complete', #' type = 'combine', -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index b1cd63778..c06322a50 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -48,23 +48,23 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' @@ -80,7 +80,7 @@ #' completeCases = TRUE, #only rows with not missing values are selected #' DataSHIELD.checks = FALSE, #' newobj = "df1", -#' datasources = connections[1], #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1], #only the first server is used ("study1") #' notify.of.progress = FALSE) #' #' diff --git a/R/ds.dataFrameFill.R b/R/ds.dataFrameFill.R index 7b385e8ec..59caf5b0a 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -29,22 +29,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index 96824a25a..3e41eccdd 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -44,22 +44,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -70,7 +70,7 @@ #' sort.descending = TRUE, #' sort.method = "numeric", #' newobj = "df.sort", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 192211987..c6603c41c 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -44,22 +44,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index cd0a59106..e2dcae6c1 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -38,22 +38,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -63,13 +63,13 @@ #' # Example1: generate a combined grid density object (default) #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", -#' datasources = connections)#all Armadillo/Opal servers are used +#' datasources = connections)#all servers are used #' #' # Example2: generate a grid density object for each study separately #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", #' type="split" -#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1])#only the first server is used ("study1") #' #' # Example3: generate a grid density object where the number of intervals is set to 15, for #' each study separately diff --git a/R/ds.dim.R b/R/ds.dim.R index d588906bb..6778a646c 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -40,22 +40,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -64,14 +64,14 @@ #' # Calculate the dimension #' ds.dim(x="D", #' type="combine", #global dimension -#'#' datasources = connections)#all Armadillo/Opal servers are used +#'#' datasources = connections)#all servers are used #' ds.dim(x="D", #' type = "both",#separate dimension for each study #' #and the pooled dimension (default) -#'#' datasources = connections)#all Armadillo/Opal servers are used +#'#' datasources = connections)#all servers are used #' ds.dim(x="D", #' type="split", #separate dimension for each study -#'#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") +#'#' datasources = connections[1])#only the first server is used ("study1") #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dmtC2S.R b/R/ds.dmtC2S.R index 3c032b711..96d059e61 100644 --- a/R/ds.dmtC2S.R +++ b/R/ds.dmtC2S.R @@ -22,17 +22,17 @@ #' the name of the copied DMT defaults to "dmt.copied.C2S". #' @param datasources specifies the particular 'connection object(s)' to use. #' e.g. if you have several data sets in the sources you are working with -#' called opals.a, opals.w2, and connection.xyz, you can choose which of +#' called connections.a, connections.w2, and connection.xyz, you can choose which of #' these to work with. The call 'datashield.connections_find()' lists all of #' the different datasets available and if one of these is called 'default.connections' #' that will be the dataset used by default if no other dataset is specified. If you #' wish to change the connections you wish to use by default the call -#' datashield.connections_default('opals.a') will set 'default.connections' -#' to be 'opals.a' and so in the absence of specific instructions to the contrary +#' datashield.connections_default('connections.a') will set 'default.connections' +#' to be 'connections.a' and so in the absence of specific instructions to the contrary #' (e.g. by specifying a particular dataset to be used via the -#' argument) all subsequent function calls will be to the datasets held in opals.a. +#' argument) all subsequent function calls will be to the datasets held in connections.a. #' If the argument is specified, it should be set without -#' inverted commas: e.g. datasources=opals.a or datasources=default.connections. +#' inverted commas: e.g. datasources=connections.a or datasources=default.connections. #' The argument also allows you to apply a function solely to a subset #' of the studies/sources you are working with. For example, the second source #' in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/R/ds.exists.R b/R/ds.exists.R index 7dc128b42..24c5bfa26 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -28,31 +28,31 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Check if the object exist in the server-side #' ds.exists(x = "D", -#' datasources = connections) #All Armadillo/Opal servers are used +#' datasources = connections) #All servers are used #' ds.exists(x = "D", -#' datasources = connections[1]) #Only the first Armadillo/Opal server is used (study1) +#' datasources = connections[1]) #Only the first server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.exp.R b/R/ds.exp.R index 8d8b46f8f..c23fbaba4 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -24,22 +24,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' @@ -49,7 +49,7 @@ #' # compute exponential function of the 'PM_BMI_CONTINUOUS' variable #' ds.exp(x = "D$PM_BMI_CONTINUOUS", #' newobj = "exp.PM_BMI_CONTINUOUS", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) +#' datasources = connections[1]) #only the first server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.extractQuantiles.R b/R/ds.extractQuantiles.R index 579c0980a..68900f8f3 100644 --- a/R/ds.extractQuantiles.R +++ b/R/ds.extractQuantiles.R @@ -60,7 +60,7 @@ #' otherwise left behind. These are not usually needed, but could be of value #' if one were investigating a problem with the ranking. FALSE: do not delete #' the residual objects -#' @param extract.datasources specifies the particular Armadillo/Opal connection object(s) to use. +#' @param extract.datasources specifies the particular connection object(s) to use. #' This is set via the argument in ds.ranksSecure. For more details #' see the associated document entitled "secure.global.ranking.docx". Also see #' the header file for ds.ranksSecure. diff --git a/R/ds.forestplot.R b/R/ds.forestplot.R index a9d19a24a..d71fafdb1 100644 --- a/R/ds.forestplot.R +++ b/R/ds.forestplot.R @@ -18,19 +18,18 @@ #' \dontrun{ #' # Run a logistic regression #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.getWGSR.R b/R/ds.getWGSR.R index f0ae833f8..f7fa79e36 100644 --- a/R/ds.getWGSR.R +++ b/R/ds.getWGSR.R @@ -66,22 +66,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "ANTHRO.anthro1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/anthro/anthro1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "ANTHRO.anthro2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "ANTHRO.anthro3", driver = "OpalDriver") +#' table = "ANTHRO.anthro2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' diff --git a/R/ds.glm.R b/R/ds.glm.R index 428fc285f..d69377950 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -220,25 +220,25 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' #' # Example 1: Fitting GLM for survival analysis #' # For this analysis we need to load survival data from the server #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -284,17 +284,14 @@ #' #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.glmPredict.R b/R/ds.glmPredict.R index e881bb541..e7e0c02ac 100644 --- a/R/ds.glmPredict.R +++ b/R/ds.glmPredict.R @@ -84,17 +84,17 @@ #' object on the serverside defaults to the name "predict_glm". #' @param datasources specifies the particular 'connection object(s)' to use. #' e.g. if you have several data sets in the sources you are working with -#' called opals.a, opals.w2, and connection.xyz, you can choose which of +#' called connections.a, connections.w2, and connection.xyz, you can choose which of #' these to work with. The call 'datashield.connections_find()' lists all of #' the different datasets available and if one of these is called 'default.connections' #' that will be the dataset used by default if no other dataset is specified. If you #' wish to change the connections you wish to use by default the call -#' datashield.connections_default('opals.a') will set 'default.connections' -#' to be 'opals.a' and so in the absence of specific instructions to the contrary +#' datashield.connections_default('connections.a') will set 'default.connections' +#' to be 'connections.a' and so in the absence of specific instructions to the contrary #' (e.g. by specifying a particular dataset to be used via the -#' argument) all subsequent function calls will be to the datasets held in opals.a. +#' argument) all subsequent function calls will be to the datasets held in connections.a. #' If the argument is specified, it should be set without -#' inverted commas: e.g. datasources=opals.a or datasources=default.connections. +#' inverted commas: e.g. datasources=connections.a or datasources=default.connections. #' The argument also allows you to apply a function solely to a subset #' of the studies/sources you are working with. For example, the second source #' in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index d8e721908..b86271248 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -270,25 +270,25 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' #' # Example 1: Fitting GLM for survival analysis #' # For this analysis we need to load survival data from the server #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -330,17 +330,14 @@ #' #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.glmSummary.R b/R/ds.glmSummary.R index 5a80b7fce..22ae6a965 100644 --- a/R/ds.glmSummary.R +++ b/R/ds.glmSummary.R @@ -41,17 +41,17 @@ #' object on the serverside defaults to "summary_glm.newobj". #' @param datasources specifies the particular 'connection object(s)' to use. #' e.g. if you have several data sets in the sources you are working with -#' called opals.a, opals.w2, and connection.xyz, you can choose which of +#' called connections.a, connections.w2, and connection.xyz, you can choose which of #' these to work with. The call 'datashield.connections_find()' lists all of #' the different datasets available and if one of these is called 'default.connections' #' that will be the dataset used by default if no other dataset is specified. If you #' wish to change the connections you wish to use by default the call -#' datashield.connections_default('opals.a') will set 'default.connections' -#' to be 'opals.a' and so in the absence of specific instructions to the contrary +#' datashield.connections_default('connections.a') will set 'default.connections' +#' to be 'connections.a' and so in the absence of specific instructions to the contrary #' (e.g. by specifying a particular dataset to be used via the -#' argument) all subsequent function calls will be to the datasets held in opals.a. +#' argument) all subsequent function calls will be to the datasets held in connections.a. #' If the argument is specified, it should be set without -#' inverted commas: e.g. datasources=opals.a or datasources=default.connections. +#' inverted commas: e.g. datasources=connections.a or datasources=default.connections. #' The argument also allows you to apply a function solely to a subset #' of the studies/sources you are working with. For example, the second source #' in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index c6d64f464..ed254a081 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -171,22 +171,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -209,17 +209,14 @@ #' #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") +#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.heatmapPlot.R b/R/ds.heatmapPlot.R index 9e6d8f183..33d402aa4 100644 --- a/R/ds.heatmapPlot.R +++ b/R/ds.heatmapPlot.R @@ -98,22 +98,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.histogram.R b/R/ds.histogram.R index e57334e72..d0f4a7f31 100644 --- a/R/ds.histogram.R +++ b/R/ds.histogram.R @@ -94,22 +94,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.isNA.R b/R/ds.isNA.R index e2bf6f9e9..63ef26586 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -25,22 +25,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.isValid.R b/R/ds.isValid.R index fb264bf87..da48891ca 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -26,22 +26,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.length.R b/R/ds.length.R index 45a708876..5db7d1e37 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -31,22 +31,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.levels.R b/R/ds.levels.R index 9a0e422d7..337a27591 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -21,22 +21,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.lexis.R b/R/ds.lexis.R index 68ff570b6..5f4610d46 100644 --- a/R/ds.lexis.R +++ b/R/ds.lexis.R @@ -144,25 +144,25 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' #' # Example 1: Fitting GLM for survival analysis #' # For this analysis we need to load survival data from the server #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.list.R b/R/ds.list.R index d66fedc02..3ec7707b8 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -24,22 +24,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.listDisclosureSettings.R b/R/ds.listDisclosureSettings.R index 29fb35125..04851def6 100644 --- a/R/ds.listDisclosureSettings.R +++ b/R/ds.listDisclosureSettings.R @@ -65,22 +65,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.listServersideFunctions.R b/R/ds.listServersideFunctions.R index dae0ff5e5..2df6630c0 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -21,22 +21,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index 5d8f2da4b..3f0f5cfc0 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -167,22 +167,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") +#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' #Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.log.R b/R/ds.log.R index 2712b6a2d..ca2364619 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -23,22 +23,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' @@ -50,7 +50,7 @@ #' ds.log(x = "D$PM_BMI_CONTINUOUS", #' base = exp(2), #' newobj = "log.PM_BMI_CONTINUOUS", -#' datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) +#' datasources = connections[1]) #only the first server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.look.R b/R/ds.look.R index e3add192d..c1d005bd0 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -34,22 +34,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.ls.R b/R/ds.ls.R index 170afbd35..7377d59ec 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -70,22 +70,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.make.R b/R/ds.make.R index b39e78ef1..80b22885a 100644 --- a/R/ds.make.R +++ b/R/ds.make.R @@ -80,22 +80,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrix.R b/R/ds.matrix.R index 3ad95c796..5813ebe09 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -59,22 +59,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDet.R b/R/ds.matrixDet.R index 447ac9cfa..97bcbff36 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -28,22 +28,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDet.report.R b/R/ds.matrixDet.report.R index 794873d55..e2b8061cc 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -27,22 +27,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index a44dda2cf..4e03f1d01 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -67,22 +67,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDimnames.R b/R/ds.matrixDimnames.R index b2c9d9693..b5db1fee1 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -26,22 +26,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixInvert.R b/R/ds.matrixInvert.R index c072b81dc..a8902aac9 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -23,22 +23,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixMult.R b/R/ds.matrixMult.R index 5e0b18617..bdef9abe2 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -28,22 +28,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixTranspose.R b/R/ds.matrixTranspose.R index 9d707c57b..9286bb286 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -26,22 +26,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.mdPattern.R b/R/ds.mdPattern.R index 3c98e7848..37823071d 100644 --- a/R/ds.mdPattern.R +++ b/R/ds.mdPattern.R @@ -68,18 +68,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.mean.R b/R/ds.mean.R index c8ca6c14c..501c37733 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -65,22 +65,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.meanByClass.R b/R/ds.meanByClass.R index c87d66496..6940c5484 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -40,22 +40,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' diff --git a/R/ds.meanSdGp.R b/R/ds.meanSdGp.R index b8ecc13ce..9232eeb7a 100644 --- a/R/ds.meanSdGp.R +++ b/R/ds.meanSdGp.R @@ -78,22 +78,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.merge.R b/R/ds.merge.R index f8a2e8119..2eae96207 100644 --- a/R/ds.merge.R +++ b/R/ds.merge.R @@ -59,22 +59,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.message.R b/R/ds.message.R index 4ac1a2998..361c9be63 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -34,22 +34,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.metadata.R b/R/ds.metadata.R index 4ddab2ea2..2e080f017 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -20,22 +20,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.names.R b/R/ds.names.R index 2a11df1a3..1466ce8d3 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -30,22 +30,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.numNA.R b/R/ds.numNA.R index 7d193f9e7..b5ad89dce 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -23,22 +23,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.quantileMean.R b/R/ds.quantileMean.R index 889e064cc..4f037f1f7 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -34,22 +34,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index 0ec1142bd..35b8a3ad2 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -57,37 +57,37 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' #Generating the vectors in the Armadillo/Opal servers -#' ds.rBinom(samp.size=c(13,20,25), #the length of the vector created in each source is different -#' size=c(10,23,5), #Bernoulli trials change in each source -#' prob=c(0.6,0.1,0.5), #Probability changes in each source +#' #Generating the vectors in the servers +#' ds.rBinom(samp.size=c(13,20), #the length of the vector created in each source is different +#' size=c(10,23), #Bernoulli trials change in each source +#' prob=c(0.6,0.1), #Probability changes in each source #' newobj="Binom.dist", #' seed.as.integer=45, #' return.full.seed.as.set=FALSE, -#' datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 +#' datasources=connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' #' ds.rBinom(samp.size=15, @@ -96,7 +96,7 @@ #' newobj="Binom.dist", #' seed.as.integer=324, #' return.full.seed.as.set=FALSE, -#' datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") +#' datasources=connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 00783071c..d2e035b8b 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -68,38 +68,38 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Armadillo/Opal servers +#' # Generating the vectors in the servers #' -#' ds.rNorm(samp.size=c(10,20,45), #the length of the vector created in each source is different -#' mean=c(1,6,4), #the mean of the Normal distribution changes in each server -#' sd=c(1,4,3), #the sd of the Normal distribution changes in each server +#' ds.rNorm(samp.size=c(10,20), #the length of the vector created in each source is different +#' mean=c(1,6), #the mean of the Normal distribution changes in each server +#' sd=c(1,4), #the sd of the Normal distribution changes in each server #' newobj="Norm.dist", #' seed.as.integer=2345, #' return.full.seed.as.set=FALSE, -#' force.output.to.k.decimal.places=c(4,5,6), #output random numbers have different +#' force.output.to.k.decimal.places=c(4,5), #output random numbers have different #' #decimal quantity in each source -#' datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 +#' datasources=connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' #' ds.rNorm(samp.size=10, @@ -109,7 +109,7 @@ #' seed.as.integer=2345, #' return.full.seed.as.set=FALSE, #' force.output.to.k.decimal.places=1, -#' datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") +#' datasources=connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rPois.R b/R/ds.rPois.R index 6748c73de..c4d56448d 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -56,43 +56,43 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Armadillo/Opal servers -#' ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different -#' lambda=c(2,3,4), #different mean per interval (2,3,4) in each source +#' # Generating the vectors in the servers +#' ds.rPois(samp.size=c(13,20), #the length of the vector created in each source is different +#' lambda=c(2,3), #different mean per interval (2,3) in each source #' newobj="Pois.dist", #' seed.as.integer=1234, #' return.full.seed.as.set=FALSE, -#' datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 +#' datasources=connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' ds.rPois(samp.size=13, #' lambda=5, #' newobj="Pois.dist", #' seed.as.integer=1234, #' return.full.seed.as.set=FALSE, -#' datasources=connections[1]) #only the first Armadillo/Opal server is used ("study1") +#' datasources=connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index d6c806b4d..e09ed4910 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -75,38 +75,38 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Armadillo/Opal servers +#' # Generating the vectors in the servers #' -#' ds.rUnif(samp.size = c(12,20,4), #the length of the vector created in each source is different -#' min = c(0,2,5), #different minumum value of the function in each source -#' max = c(2,5,9), #different maximum value of the function in each source +#' ds.rUnif(samp.size = c(12,20), #the length of the vector created in each source is different +#' min = c(0,2), #different minumum value of the function in each source +#' max = c(2,5), #different maximum value of the function in each source #' newobj = "Unif.dist", #' seed.as.integer = 234, #' return.full.seed.as.set = FALSE, -#' force.output.to.k.decimal.places = c(1,2,3), -#' datasources = connections) #all the Armadillo/Opal servers are used, in this case 3 +#' force.output.to.k.decimal.places = c(1,2), +#' datasources = connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' #' ds.rUnif(samp.size = 12, @@ -116,7 +116,7 @@ #' seed.as.integer = 12345, #' return.full.seed.as.set = FALSE, #' force.output.to.k.decimal.places = 2, -#' datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") +#' datasources = connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rbind.R b/R/ds.rbind.R index d355d1b48..995b719e2 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -39,22 +39,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -64,12 +64,12 @@ #' #' #' ds.rbind(x = "D", #data frames in the server-side to be conbined -#' #(see above the connection to the Armadillo/Opal servers) +#' #(see above the connection to the servers) #' DataSHIELD.checks = FALSE, #' force.colnames = NULL, #' newobj = "D.rbind", # name for the output object that is stored in the data servers -#' datasources = connections, # All Armadillo/Opal servers are used -#' #(see above the connection to the Armadillo/Opal servers) +#' datasources = connections, # All servers are used +#' #(see above the connection to the servers) #' notify.of.progress = FALSE) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.reShape.R b/R/ds.reShape.R index 9dd1c231f..209734f2f 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -43,22 +43,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.recodeLevels.R b/R/ds.recodeLevels.R index 13e1c5031..3d85a4535 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -29,22 +29,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index a8f63d85b..81c352fbd 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -35,22 +35,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.rep.R b/R/ds.rep.R index 957eb9780..72c9177a5 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -34,22 +34,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.replaceNA.R b/R/ds.replaceNA.R index 0977127fc..1ec2d3a9f 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -35,22 +35,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers @@ -66,7 +66,7 @@ #' #' # Replace the missing values using the mean for each study #' ds.replaceNA(x = "D$LAB_HDL", -#' forNA = list(mean[[1]][1], mean[[1]][2], mean[[1]][3]), +#' forNA = list(mean[[1]][1], mean[[1]][2]), #' newobj = "HDL.noNA", #' datasources = connections) #' @@ -79,7 +79,7 @@ #' #' # Replace the missing values with 999s #' ds.replaceNA(x = "D$PM_BMI_CATEGORICAL", -#' forNA = c(999,999,999), +#' forNA = c(999,999), #' newobj = "bmi999") #' #' # Check if the NAs have been replaced correctly diff --git a/R/ds.rm.R b/R/ds.rm.R index b61b1d7e1..652e9e58d 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -30,22 +30,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.rowColCalc.R b/R/ds.rowColCalc.R index f61ca223a..7aecbba04 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -27,23 +27,23 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' myvar <- list("LAB_TSC","LAB_HDL") diff --git a/R/ds.sample.R b/R/ds.sample.R index 91e4510f3..9128a9e18 100644 --- a/R/ds.sample.R +++ b/R/ds.sample.R @@ -92,7 +92,7 @@ #' If you want to use the same starting seed in all studies but do not wish it to #' be 0, you can specify a non-zero scalar value for and then #' use the argument to generate the random number vectors one source at -#' a time (e.g. ,datasources=default.opals[2] to generate the random vector in source 2). +#' a time (e.g. ,datasources=default.connections[2] to generate the random vector in source 2). #' As an example, if the value is 78326 then the seed #' in each source will be set at 78326*1 = 78326 because the vector of datasources #' being used in each call to the function will always be of length 1 and so the @@ -110,15 +110,15 @@ #' For further details see help for \code{sample} in native R. #' @param newobj This a character string providing a name for the output #' data.frame which defaults to 'newobj.sample' if no name is specified. -#' @param datasources specifies the particular Armadillo/Opal connection object(s) to use. If the -#' argument is not specified the default set of Armadillo/Opal servers will be used. The default servers -#' are called default.opals and the default can be set using the function -#' \code{ds.setDefaultOpals}. If the is to be specified, it should be set without -#' inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to -#' apply the function solely to e.g. the second Armadillo/Opal server in a set of three, -#' the argument can be specified as: e.g. datasources=opals.em[2]. -#' If you wish to specify the first and third Armadillo/Opal servers in a set you specify: -#' e.g. datasources=opals.em[c(1,3)] +#' @param datasources specifies the particular connection object(s) to use. If the +#' argument is not specified the default set of servers will be used. The default servers +#' are called default.connections and the default can be set using the function +#' \code{DSI::datashield.connections_default}. If the is to be specified, it should be set without +#' inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to +#' apply the function solely to e.g. the second server in a set of three, +#' the argument can be specified as: e.g. datasources=connections.em[2]. +#' If you wish to specify the first and third servers in a set you specify: +#' e.g. datasources=connections.em[c(1,3)] #' @param notify.of.progress specifies if console output should be produce to indicate #' progress. The default value for notify.of.progress is FALSE. #' @return the object specified by the argument (or default name diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 73eb4e74c..6a76d7986 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -80,23 +80,23 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() diff --git a/R/ds.seq.R b/R/ds.seq.R index 4d93bd25f..13fc644a4 100644 --- a/R/ds.seq.R +++ b/R/ds.seq.R @@ -68,22 +68,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.setSeed.R b/R/ds.setSeed.R index 4f27196df..5192f7536 100644 --- a/R/ds.setSeed.R +++ b/R/ds.setSeed.R @@ -49,22 +49,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.skewness.R b/R/ds.skewness.R index 690fe9d0b..52f0c87a9 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -1,7 +1,7 @@ #' #' @title Calculates the skewness of a server-side numeric variable #' @description This function calculates the skewness of a numeric variable -#' that is stored on the server-side (Armadillo/Opal server). +#' that is stored on the server-side (server). #' @details This function is similar to the function \code{skewness} in R package \code{e1071}. #' #' The function calculates the skewness of an input variable \code{x} @@ -46,22 +46,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 679728689..76a7538ec 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -25,22 +25,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' diff --git a/R/ds.summary.R b/R/ds.summary.R index 9949b56cb..bac5cb62b 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -29,22 +29,22 @@ #' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' # Log onto the remote Armadillo/Opal training servers diff --git a/R/ds.tapply.R b/R/ds.tapply.R index 01ce4fc31..5342c3323 100644 --- a/R/ds.tapply.R +++ b/R/ds.tapply.R @@ -80,22 +80,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.tapply.assign.R b/R/ds.tapply.assign.R index b3fbc18ce..14722a942 100644 --- a/R/ds.tapply.assign.R +++ b/R/ds.tapply.assign.R @@ -85,22 +85,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.testObjExists.R b/R/ds.testObjExists.R index c03b79ec9..e12799df2 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -24,22 +24,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.unList.R b/R/ds.unList.R index 298c795ca..6f98fdddc 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -31,22 +31,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.unique.R b/R/ds.unique.R index df6b322a7..07ceced2f 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -16,22 +16,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.var.R b/R/ds.var.R index fd7202142..4247e024b 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -43,22 +43,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/subsetHelper.R b/R/subsetHelper.R index 62af5f6a3..2400c0778 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -25,22 +25,22 @@ #' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.Boole.Rd b/man/ds.Boole.Rd index 9a9c443ac..33d69fd31 100644 --- a/man/ds.Boole.Rd +++ b/man/ds.Boole.Rd @@ -73,22 +73,22 @@ Server function called: \code{BooleDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.abs.Rd b/man/ds.abs.Rd index 735a40c36..a89aea27b 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -38,22 +38,22 @@ specified by the user through the argument \code{newobj}, otherwise is named by # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index b6048a30f..19b2c55dd 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -35,22 +35,22 @@ Server function called: \code{asCharacterDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -58,7 +58,7 @@ Server function called: \code{asCharacterDS} # Converting the R object into a class character ds.asCharacter(x.name = "D$LAB_TSC", newobj = "char.obj", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index 80f334c22..08d1bad35 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -37,22 +37,22 @@ Server function called: \code{asDataMatrixDS}. # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -60,7 +60,7 @@ Server function called: \code{asDataMatrixDS}. # Converting the R object into a matrix ds.asDataMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index b88aba82e..43212e9b6 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -169,22 +169,22 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -196,14 +196,14 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} #from all studies is created fixed.dummy.vars = TRUE, #create a matrix of dummy variables baseline.level = 1, - datasources = connections)#all the Armadillo/Opal servers are used, in this case 3 + datasources = connections)#all the servers are used, in this case 2 #(see above the connection to the servers) ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", newobj.name = "fact.obj", forced.factor.levels = c(2,3), #the variable is split in 2 levels fixed.dummy.vars = TRUE, #create a matrix of dummy variables baseline.level = 1, - datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") + datasources = connections[1])#only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index d97baa4a1..7a9cabe01 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -50,22 +50,22 @@ Server function called: \code{asIntegerDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -73,7 +73,7 @@ Server function called: \code{asIntegerDS} # Converting the R object into an integer ds.asInteger(x.name = "D$LAB_TSC", newobj = "int.obj", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") ds.class(x = "int.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asList.Rd b/man/ds.asList.Rd index 58b877d0b..7b88cf6f2 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -35,22 +35,22 @@ Server function called: \code{asListDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -58,7 +58,7 @@ Server function called: \code{asListDS} # Converting the R object into a List ds.asList(x.name = "D", newobj = "D.asList", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") ds.class(x = "D.asList", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asLogical.Rd b/man/ds.asLogical.Rd index ac6051c1c..4d91cde51 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -35,22 +35,22 @@ Server function called: \code{asLogicalDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -58,7 +58,7 @@ Server function called: \code{asLogicalDS} # Converting the R object into a logical ds.asLogical(x.name = "D$LAB_TSC", newobj = "logical.obj", - datasources =connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources =connections[1]) #only the first server is used ("study1") ds.class(x = "logical.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asMatrix.Rd b/man/ds.asMatrix.Rd index b2da4dbab..55006e5a7 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -40,22 +40,22 @@ Server function called: \code{asMatrixDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -63,7 +63,7 @@ Server function called: \code{asMatrixDS} # Converting the R object into a matrix ds.asMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 2a4f0f9a2..7acb2e773 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -49,22 +49,22 @@ Server function called: \code{asNumericDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -72,7 +72,7 @@ Server function called: \code{asNumericDS} # Converting the R object into a numeric class ds.asNumeric(x.name = "D$LAB_TSC", newobj = "num.obj", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") ds.class(x = "num.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.assign.Rd b/man/ds.assign.Rd index 30dd0be67..f66a184fe 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -37,22 +37,22 @@ assigned the variable called \code{newobj} on the server-side. # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -60,7 +60,7 @@ assigned the variable called \code{newobj} on the server-side. # Assign a variable to a name ds.assign(toAssign = "D$LAB_TSC", newobj = "labtsc", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.boxPlot.Rd b/man/ds.boxPlot.Rd index 364680348..3f3cb16eb 100644 --- a/man/ds.boxPlot.Rd +++ b/man/ds.boxPlot.Rd @@ -51,22 +51,22 @@ of grouping using categorical variables on the dataset (only for data frames) # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, diff --git a/man/ds.c.Rd b/man/ds.c.Rd index ac8f4c538..76bd4fa58 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -41,22 +41,22 @@ Server function called: \code{cDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -65,7 +65,7 @@ Server function called: \code{cDS} myvect <- c("D$LAB_TSC", "D$LAB_HDL") ds.c(x = myvect, newobj = "new.vect", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.cbind.Rd b/man/ds.cbind.Rd index 5a01502cd..50b900ef0 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -76,22 +76,22 @@ Server function called: \code{cbindDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.changeRefGroup.Rd b/man/ds.changeRefGroup.Rd index 9584829aa..43f16ac0e 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -57,22 +57,22 @@ Server function called: \code{changeRefGroupDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.class.Rd b/man/ds.class.Rd index 88d7a28aa..3d911fdd0 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -32,22 +32,22 @@ Server function called: \code{classDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index 99616f89c..f089838da 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -33,22 +33,22 @@ Server function called: \code{colnamesDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index 3d17864e5..686b4730e 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -42,22 +42,22 @@ Server function called: \code{completeCasesDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -65,18 +65,18 @@ Server function called: \code{completeCasesDS} # Select complete cases from different R objects - ds.completeCases(x1 = "D", #data frames in the Armadillo/Opal servers - #(see above the connection to the Armadillo/Opal servers) + ds.completeCases(x1 = "D", #data frames in the servers + #(see above the connection to the servers) newobj = "D.completeCases", # name for the output object - # that is stored in the Armadillo/Opal servers - datasources = connections) # All Armadillo/Opal servers are used - # (see above the connection to the Armadillo/Opal servers) + # that is stored in the servers + datasources = connections) # All servers are used + # (see above the connection to the servers) - ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Armadillo/Opal servers - #(see above the connection to the Armadillo/Opal servers) + ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the servers + #(see above the connection to the servers) newobj = "LAB_TSC.completeCases", #name for the output variable - #that is stored in the Armadillo/Opal servers - datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") + #that is stored in the servers + datasources = connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.contourPlot.Rd b/man/ds.contourPlot.Rd index a4c6826c9..1ad94a2d7 100644 --- a/man/ds.contourPlot.Rd +++ b/man/ds.contourPlot.Rd @@ -96,22 +96,22 @@ Server functions called: \code{heatmapPlotDS}, \code{rangeDS} and \code{densityG # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.cor.Rd b/man/ds.cor.Rd index 290940858..90fa8af74 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -68,22 +68,22 @@ Server function called: \code{corDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index 6c4cbad8e..25495438e 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -63,22 +63,22 @@ Server function called: \code{corTestDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.cov.Rd b/man/ds.cov.Rd index 00abe3991..75cf1a988 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -79,22 +79,22 @@ and the total number of missing values aggregated from all the involved studies, # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -113,7 +113,7 @@ and the total number of missing values aggregated from all the involved studies, y = 'gender', naAction = 'pairwise.complete', type = 'combine', - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 1434718a1..6feb1a749 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -84,22 +84,22 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() @@ -115,7 +115,7 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} completeCases = TRUE, #only rows with not missing values are selected DataSHIELD.checks = FALSE, newobj = "df1", - datasources = connections[1], #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1], #only the first server is used ("study1") notify.of.progress = FALSE) diff --git a/man/ds.dataFrameFill.Rd b/man/ds.dataFrameFill.Rd index 76dfdde7f..02adb7851 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -48,22 +48,22 @@ Server function called: \code{dataFrameFillDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index a4a9fd562..3eb2d9e10 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -69,22 +69,22 @@ Server function called: \code{dataFrameSortDS}. # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -95,7 +95,7 @@ Server function called: \code{dataFrameSortDS}. sort.descending = TRUE, sort.method = "numeric", newobj = "df.sort", - datasources = connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index b3de8bb35..628656520 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -78,22 +78,22 @@ Server functions called: \code{dataFrameSubsetDS1} and \code{dataFrameSubsetDS2} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 6ebdb373a..26baa29d4 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -62,22 +62,22 @@ Server function called: \code{densityGridDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -87,13 +87,13 @@ Server function called: \code{densityGridDS} # Example1: generate a combined grid density object (default) ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", - datasources = connections)#all Armadillo/Opal servers are used + datasources = connections)#all servers are used # Example2: generate a grid density object for each study separately ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", type="split" - datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") + datasources = connections[1])#only the first server is used ("study1") # Example3: generate a grid density object where the number of intervals is set to 15, for each study separately diff --git a/man/ds.dim.Rd b/man/ds.dim.Rd index 4ea32eeac..dacda6a6d 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -54,22 +54,22 @@ Server function called: \code{dimDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -78,14 +78,14 @@ Server function called: \code{dimDS} # Calculate the dimension ds.dim(x="D", type="combine", #global dimension -#' datasources = connections)#all Armadillo/Opal servers are used +#' datasources = connections)#all servers are used ds.dim(x="D", type = "both",#separate dimension for each study #and the pooled dimension (default) -#' datasources = connections)#all Armadillo/Opal servers are used +#' datasources = connections)#all servers are used ds.dim(x="D", type="split", #separate dimension for each study -#' datasources = connections[1])#only the first Armadillo/Opal server is used ("study1") +#' datasources = connections[1])#only the first server is used ("study1") # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dmtC2S.Rd b/man/ds.dmtC2S.Rd index bfd673b47..ce991d8da 100644 --- a/man/ds.dmtC2S.Rd +++ b/man/ds.dmtC2S.Rd @@ -16,17 +16,17 @@ the name of the copied DMT defaults to "dmt.copied.C2S".} \item{datasources}{specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with -called opals.a, opals.w2, and connection.xyz, you can choose which of +called connections.a, connections.w2, and connection.xyz, you can choose which of these to work with. The call 'datashield.connections_find()' lists all of the different datasets available and if one of these is called 'default.connections' that will be the dataset used by default if no other dataset is specified. If you wish to change the connections you wish to use by default the call -datashield.connections_default('opals.a') will set 'default.connections' -to be 'opals.a' and so in the absence of specific instructions to the contrary +datashield.connections_default('connections.a') will set 'default.connections' +to be 'connections.a' and so in the absence of specific instructions to the contrary (e.g. by specifying a particular dataset to be used via the -argument) all subsequent function calls will be to the datasets held in opals.a. +argument) all subsequent function calls will be to the datasets held in connections.a. If the argument is specified, it should be set without -inverted commas: e.g. datasources=opals.a or datasources=default.connections. +inverted commas: e.g. datasources=connections.a or datasources=default.connections. The argument also allows you to apply a function solely to a subset of the studies/sources you are working with. For example, the second source in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/man/ds.exists.Rd b/man/ds.exists.Rd index b32b3ed9a..eb9795a02 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -38,31 +38,31 @@ Server function called: \code{exists} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Check if the object exist in the server-side ds.exists(x = "D", - datasources = connections) #All Armadillo/Opal servers are used + datasources = connections) #All servers are used ds.exists(x = "D", - datasources = connections[1]) #Only the first Armadillo/Opal server is used (study1) + datasources = connections[1]) #Only the first server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.exp.Rd b/man/ds.exp.Rd index 4959536d2..cb6b814e7 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -34,22 +34,22 @@ Server function called: \code{expDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() @@ -59,7 +59,7 @@ Server function called: \code{expDS}. # compute exponential function of the 'PM_BMI_CONTINUOUS' variable ds.exp(x = "D$PM_BMI_CONTINUOUS", newobj = "exp.PM_BMI_CONTINUOUS", - datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) + datasources = connections[1]) #only the first server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.extractQuantiles.Rd b/man/ds.extractQuantiles.Rd index 696f4752c..26308f61c 100644 --- a/man/ds.extractQuantiles.Rd +++ b/man/ds.extractQuantiles.Rd @@ -56,7 +56,7 @@ otherwise left behind. These are not usually needed, but could be of value if one were investigating a problem with the ranking. FALSE: do not delete the residual objects} -\item{extract.datasources}{specifies the particular Armadillo/Opal connection object(s) to use. +\item{extract.datasources}{specifies the particular connection object(s) to use. This is set via the argument in ds.ranksSecure. For more details see the associated document entitled "secure.global.ranking.docx". Also see the header file for ds.ranksSecure.} diff --git a/man/ds.forestplot.Rd b/man/ds.forestplot.Rd index a962d4c42..79b2c6dde 100644 --- a/man/ds.forestplot.Rd +++ b/man/ds.forestplot.Rd @@ -30,19 +30,18 @@ DataSHIELD \dontrun{ # Run a logistic regression + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.getWGSR.Rd b/man/ds.getWGSR.Rd index 3c8aef4a9..175725204 100644 --- a/man/ds.getWGSR.Rd +++ b/man/ds.getWGSR.Rd @@ -93,22 +93,22 @@ data. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "ANTHRO.anthro1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/anthro/anthro1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "ANTHRO.anthro2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "ANTHRO.anthro3", driver = "OpalDriver") + table = "ANTHRO.anthro2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index c0b80e155..a15d9f461 100644 --- a/man/ds.glm.Rd +++ b/man/ds.glm.Rd @@ -264,25 +264,25 @@ Server functions called: \code{glmDS1} and \code{glmDS2} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') # Example 1: Fitting GLM for survival analysis # For this analysis we need to load survival data from the server + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -328,17 +328,14 @@ Server functions called: \code{glmDS1} and \code{glmDS2} builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.glmPredict.Rd b/man/ds.glmPredict.Rd index 1904e0fe7..58b1483f6 100644 --- a/man/ds.glmPredict.Rd +++ b/man/ds.glmPredict.Rd @@ -80,17 +80,17 @@ object on the serverside defaults to the name "predict_glm".} \item{datasources}{specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with -called opals.a, opals.w2, and connection.xyz, you can choose which of +called connections.a, connections.w2, and connection.xyz, you can choose which of these to work with. The call 'datashield.connections_find()' lists all of the different datasets available and if one of these is called 'default.connections' that will be the dataset used by default if no other dataset is specified. If you wish to change the connections you wish to use by default the call -datashield.connections_default('opals.a') will set 'default.connections' -to be 'opals.a' and so in the absence of specific instructions to the contrary +datashield.connections_default('connections.a') will set 'default.connections' +to be 'connections.a' and so in the absence of specific instructions to the contrary (e.g. by specifying a particular dataset to be used via the -argument) all subsequent function calls will be to the datasets held in opals.a. +argument) all subsequent function calls will be to the datasets held in connections.a. If the argument is specified, it should be set without -inverted commas: e.g. datasources=opals.a or datasources=default.connections. +inverted commas: e.g. datasources=connections.a or datasources=default.connections. The argument also allows you to apply a function solely to a subset of the studies/sources you are working with. For example, the second source in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index fa5f1b65d..9b3430a6b 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -332,25 +332,25 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') # Example 1: Fitting GLM for survival analysis # For this analysis we need to load survival data from the server + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -392,17 +392,14 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.glmSummary.Rd b/man/ds.glmSummary.Rd index f856c1489..66b93eb6b 100644 --- a/man/ds.glmSummary.Rd +++ b/man/ds.glmSummary.Rd @@ -17,17 +17,17 @@ object on the serverside defaults to "summary_glm.newobj".} \item{datasources}{specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with -called opals.a, opals.w2, and connection.xyz, you can choose which of +called connections.a, connections.w2, and connection.xyz, you can choose which of these to work with. The call 'datashield.connections_find()' lists all of the different datasets available and if one of these is called 'default.connections' that will be the dataset used by default if no other dataset is specified. If you wish to change the connections you wish to use by default the call -datashield.connections_default('opals.a') will set 'default.connections' -to be 'opals.a' and so in the absence of specific instructions to the contrary +datashield.connections_default('connections.a') will set 'default.connections' +to be 'connections.a' and so in the absence of specific instructions to the contrary (e.g. by specifying a particular dataset to be used via the -argument) all subsequent function calls will be to the datasets held in opals.a. +argument) all subsequent function calls will be to the datasets held in connections.a. If the argument is specified, it should be set without -inverted commas: e.g. datasources=opals.a or datasources=default.connections. +inverted commas: e.g. datasources=connections.a or datasources=default.connections. The argument also allows you to apply a function solely to a subset of the studies/sources you are working with. For example, the second source in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index 5d27d845f..968fa6aee 100644 --- a/man/ds.glmerSLMA.Rd +++ b/man/ds.glmerSLMA.Rd @@ -234,22 +234,22 @@ Server function called: \code{glmerSLMADS2} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -272,17 +272,14 @@ Server function called: \code{glmerSLMADS2} builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") + table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.heatmapPlot.Rd b/man/ds.heatmapPlot.Rd index 695cf59d0..56f2157ff 100644 --- a/man/ds.heatmapPlot.Rd +++ b/man/ds.heatmapPlot.Rd @@ -130,22 +130,22 @@ Server function called: \code{heatmapPlotDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.histogram.Rd b/man/ds.histogram.Rd index 995d1bed3..428c062b0 100644 --- a/man/ds.histogram.Rd +++ b/man/ds.histogram.Rd @@ -124,22 +124,22 @@ Server function called: \code{histogramDS2} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.isNA.Rd b/man/ds.isNA.Rd index 7f9df15d9..0bb07cf83 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -39,22 +39,22 @@ Server function called: \code{isNaDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.isValid.Rd b/man/ds.isValid.Rd index 9d1fa0ae0..1ae16a1f2 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -40,22 +40,22 @@ Server function called: \code{isValidDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.length.Rd b/man/ds.length.Rd index 97f4c9a82..e01830739 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -50,22 +50,22 @@ Server function called: \code{lengthDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.levels.Rd b/man/ds.levels.Rd index cbae2c24c..21807efc0 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -32,22 +32,22 @@ Server function called: \code{levelsDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.lexis.Rd b/man/ds.lexis.Rd index 9980be35e..79d19b1fa 100644 --- a/man/ds.lexis.Rd +++ b/man/ds.lexis.Rd @@ -169,25 +169,25 @@ Server functions called: \code{lexisDS1}, \code{lexisDS2} and \code{lexisDS3} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') # Example 1: Fitting GLM for survival analysis # For this analysis we need to load survival data from the server + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.list.Rd b/man/ds.list.Rd index f0494920a..92e8b656c 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -43,22 +43,22 @@ Server function called: \code{listDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.listDisclosureSettings.Rd b/man/ds.listDisclosureSettings.Rd index bd5ab8e13..5ac64a610 100644 --- a/man/ds.listDisclosureSettings.Rd +++ b/man/ds.listDisclosureSettings.Rd @@ -78,21 +78,21 @@ Server function called: \code{listDisclosureSettingsDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index a6553b57b..3706a4fb3 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -36,22 +36,22 @@ This function does not call any server-side function. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.lmerSLMA.Rd b/man/ds.lmerSLMA.Rd index d8ad7e32a..0e7d89ff6 100644 --- a/man/ds.lmerSLMA.Rd +++ b/man/ds.lmerSLMA.Rd @@ -226,22 +226,22 @@ Server function called: \code{lmerSLMADS2} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") + table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() #Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.log.Rd b/man/ds.log.Rd index c1371f188..caa01a93e 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -37,22 +37,22 @@ Server function called: \code{logDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() @@ -64,7 +64,7 @@ Server function called: \code{logDS} ds.log(x = "D$PM_BMI_CONTINUOUS", base = exp(2), newobj = "log.PM_BMI_CONTINUOUS", - datasources = connections[1]) #only the first Armadillo/Opal server is used (study1) + datasources = connections[1]) #only the first server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.look.Rd b/man/ds.look.Rd index 7998c50f3..bacde6f39 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -48,22 +48,22 @@ The function is a wrapper for the DSI package function \code{datashield.aggregat # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index c4a135bb3..9df57306a 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -90,22 +90,22 @@ Server function called: \code{lsDS}. # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.make.Rd b/man/ds.make.Rd index 889fcaff1..f8af3eb6d 100644 --- a/man/ds.make.Rd +++ b/man/ds.make.Rd @@ -91,22 +91,22 @@ The \code{ds.make} function is a wrapper for the DSI package function \code{data # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrix.Rd b/man/ds.matrix.Rd index 2472f4377..260dc286e 100644 --- a/man/ds.matrix.Rd +++ b/man/ds.matrix.Rd @@ -87,22 +87,22 @@ Server function called: \code{matrixDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDet.Rd b/man/ds.matrixDet.Rd index 6cd6e586e..a46acc8ed 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -43,22 +43,22 @@ Server function called: \code{matrixDetDS2} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDet.report.Rd b/man/ds.matrixDet.report.Rd index 13ad32c8c..9a7fe7a0f 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -41,22 +41,22 @@ Server function called: \code{matrixDetDS1} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index 514615d10..f2a4342fd 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -90,22 +90,22 @@ Server function called: \code{matrixDiagDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index 7612f332e..7a9915003 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -47,22 +47,22 @@ Server function called: \code{matrixDimnamesDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixInvert.Rd b/man/ds.matrixInvert.Rd index 6c7d48a27..b73d91dfd 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -38,22 +38,22 @@ Server function called: \code{matrixInvertDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixMult.Rd b/man/ds.matrixMult.Rd index 9fa8f818b..10f4e6585 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -43,22 +43,22 @@ Server function called: \code{matrixMultDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixTranspose.Rd b/man/ds.matrixTranspose.Rd index 6f5975412..bed688b5d 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -40,22 +40,22 @@ Server function called: \code{matrixTransposeDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.mdPattern.Rd b/man/ds.mdPattern.Rd index b03e6fcba..d52730497 100644 --- a/man/ds.mdPattern.Rd +++ b/man/ds.mdPattern.Rd @@ -81,18 +81,22 @@ for disclosure control: # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.mean.Rd b/man/ds.mean.Rd index 8061295e1..2e6cc9f3e 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -83,22 +83,22 @@ Server function called: \code{meanDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.meanByClass.Rd b/man/ds.meanByClass.Rd index 8684b73fb..592de07ce 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -58,22 +58,22 @@ parameter \code{datasources}. # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() diff --git a/man/ds.meanSdGp.Rd b/man/ds.meanSdGp.Rd index 79a47fe2a..768bab717 100644 --- a/man/ds.meanSdGp.Rd +++ b/man/ds.meanSdGp.Rd @@ -96,22 +96,22 @@ Server function called: \code{meanSdGpDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.merge.Rd b/man/ds.merge.Rd index 54b653a6a..15be0af39 100644 --- a/man/ds.merge.Rd +++ b/man/ds.merge.Rd @@ -96,22 +96,22 @@ Server function called: \code{mergeDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.message.Rd b/man/ds.message.Rd index 1ca6ecdbd..9a99f1daa 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -48,22 +48,22 @@ Server function called: \code{messageDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.metadata.Rd b/man/ds.metadata.Rd index 0fb365fdf..e38d0e588 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -31,22 +31,22 @@ which are non-disclosive. # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.names.Rd b/man/ds.names.Rd index bc5eba7ea..9a00feb99 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -41,22 +41,22 @@ is formally of class "glm" and "ls" but responds TRUE to is.list(), # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.numNA.Rd b/man/ds.numNA.Rd index 4015741e1..76abbc4fe 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -36,22 +36,22 @@ Server function called: \code{numNaDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.quantileMean.Rd b/man/ds.quantileMean.Rd index 443f921e7..e703e0d26 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -52,22 +52,22 @@ Server functions called: \code{quantileMeanDS}, \code{length} and \code{numNaDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.rBinom.Rd b/man/ds.rBinom.Rd index 36b288512..a8423c5a0 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -85,36 +85,36 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - #Generating the vectors in the Armadillo/Opal servers - ds.rBinom(samp.size=c(13,20,25), #the length of the vector created in each source is different - size=c(10,23,5), #Bernoulli trials change in each source - prob=c(0.6,0.1,0.5), #Probability changes in each source + #Generating the vectors in the servers + ds.rBinom(samp.size=c(13,20), #the length of the vector created in each source is different + size=c(10,23), #Bernoulli trials change in each source + prob=c(0.6,0.1), #Probability changes in each source newobj="Binom.dist", seed.as.integer=45, return.full.seed.as.set=FALSE, - datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 + datasources=connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rBinom(samp.size=15, @@ -123,7 +123,7 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. newobj="Binom.dist", seed.as.integer=324, return.full.seed.as.set=FALSE, - datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") + datasources=connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rNorm.Rd b/man/ds.rNorm.Rd index 592e662db..c1cd7bc16 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -98,38 +98,38 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Armadillo/Opal servers + # Generating the vectors in the servers - ds.rNorm(samp.size=c(10,20,45), #the length of the vector created in each source is different - mean=c(1,6,4), #the mean of the Normal distribution changes in each server - sd=c(1,4,3), #the sd of the Normal distribution changes in each server + ds.rNorm(samp.size=c(10,20), #the length of the vector created in each source is different + mean=c(1,6), #the mean of the Normal distribution changes in each server + sd=c(1,4), #the sd of the Normal distribution changes in each server newobj="Norm.dist", seed.as.integer=2345, return.full.seed.as.set=FALSE, - force.output.to.k.decimal.places=c(4,5,6), #output random numbers have different + force.output.to.k.decimal.places=c(4,5), #output random numbers have different #decimal quantity in each source - datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 + datasources=connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rNorm(samp.size=10, @@ -139,7 +139,7 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. seed.as.integer=2345, return.full.seed.as.set=FALSE, force.output.to.k.decimal.places=1, - datasources=connections[2]) #only the second Armadillo/Opal server is used ("study2") + datasources=connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rPois.Rd b/man/ds.rPois.Rd index 5ccde0c9a..5a30eee5f 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -81,40 +81,40 @@ Server functions called: \code{rPoisDS} and \code{setSeedDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Armadillo/Opal servers - ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different - lambda=c(2,3,4), #different mean per interval (2,3,4) in each source + # Generating the vectors in the servers + ds.rPois(samp.size=c(13,20), #the length of the vector created in each source is different + lambda=c(2,3), #different mean per interval (2,3) in each source newobj="Pois.dist", seed.as.integer=1234, return.full.seed.as.set=FALSE, - datasources=connections) #all the Armadillo/Opal servers are used, in this case 3 + datasources=connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rPois(samp.size=13, lambda=5, newobj="Pois.dist", seed.as.integer=1234, return.full.seed.as.set=FALSE, - datasources=connections[1]) #only the first Armadillo/Opal server is used ("study1") + datasources=connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rUnif.Rd b/man/ds.rUnif.Rd index 322031988..234c0d9f9 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -104,37 +104,37 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Armadillo/Opal servers + # Generating the vectors in the servers - ds.rUnif(samp.size = c(12,20,4), #the length of the vector created in each source is different - min = c(0,2,5), #different minumum value of the function in each source - max = c(2,5,9), #different maximum value of the function in each source + ds.rUnif(samp.size = c(12,20), #the length of the vector created in each source is different + min = c(0,2), #different minumum value of the function in each source + max = c(2,5), #different maximum value of the function in each source newobj = "Unif.dist", seed.as.integer = 234, return.full.seed.as.set = FALSE, - force.output.to.k.decimal.places = c(1,2,3), - datasources = connections) #all the Armadillo/Opal servers are used, in this case 3 + force.output.to.k.decimal.places = c(1,2), + datasources = connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rUnif(samp.size = 12, @@ -144,7 +144,7 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. seed.as.integer = 12345, return.full.seed.as.set = FALSE, force.output.to.k.decimal.places = 2, - datasources = connections[2]) #only the second Armadillo/Opal server is used ("study2") + datasources = connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rbind.Rd b/man/ds.rbind.Rd index 41db4af63..63eb3b20e 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -66,22 +66,22 @@ Server functions called: \code{rbindDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -91,12 +91,12 @@ Server functions called: \code{rbindDS}. ds.rbind(x = "D", #data frames in the server-side to be conbined - #(see above the connection to the Armadillo/Opal servers) + #(see above the connection to the servers) DataSHIELD.checks = FALSE, force.colnames = NULL, newobj = "D.rbind", # name for the output object that is stored in the data servers - datasources = connections, # All Armadillo/Opal servers are used - #(see above the connection to the Armadillo/Opal servers) + datasources = connections, # All servers are used + #(see above the connection to the servers) notify.of.progress = FALSE) # Clear the Datashield R sessions and logout diff --git a/man/ds.reShape.Rd b/man/ds.reShape.Rd index cb71c527e..fc40cdcba 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -76,22 +76,22 @@ Server function called: \code{reShapeDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.recodeLevels.Rd b/man/ds.recodeLevels.Rd index a58bd21fc..0faa5407d 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -47,22 +47,22 @@ Server function called: \code{levels()} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index cc39ce199..7a602591b 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -62,22 +62,22 @@ Server function called: \code{recodeValuesDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.rep.Rd b/man/ds.rep.Rd index 70138e9b8..8284ffbed 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -69,22 +69,22 @@ Server function called: \code{repDS}. # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.replaceNA.Rd b/man/ds.replaceNA.Rd index 20de1a686..9058b7b0f 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -49,22 +49,22 @@ Server function called: \code{replaceNaDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers @@ -80,7 +80,7 @@ Server function called: \code{replaceNaDS} # Replace the missing values using the mean for each study ds.replaceNA(x = "D$LAB_HDL", - forNA = list(mean[[1]][1], mean[[1]][2], mean[[1]][3]), + forNA = list(mean[[1]][1], mean[[1]][2]), newobj = "HDL.noNA", datasources = connections) @@ -93,7 +93,7 @@ Server function called: \code{replaceNaDS} # Replace the missing values with 999s ds.replaceNA(x = "D$PM_BMI_CATEGORICAL", - forNA = c(999,999,999), + forNA = c(999,999), newobj = "bmi999") # Check if the NAs have been replaced correctly diff --git a/man/ds.rm.Rd b/man/ds.rm.Rd index 595fd64c0..2988826a0 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -45,22 +45,22 @@ Server function called: \code{rmDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.rowColCalc.Rd b/man/ds.rowColCalc.Rd index 0ef4eb792..81fbfdbe7 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -42,22 +42,22 @@ Server functions called: \code{classDS}, \code{dimDS} and \code{colnamesDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() myvar <- list("LAB_TSC","LAB_HDL") diff --git a/man/ds.sample.Rd b/man/ds.sample.Rd index a70520dc8..bd6e893e2 100644 --- a/man/ds.sample.Rd +++ b/man/ds.sample.Rd @@ -53,7 +53,7 @@ If is set as 0 all sources will start with the seed value If you want to use the same starting seed in all studies but do not wish it to be 0, you can specify a non-zero scalar value for and then use the argument to generate the random number vectors one source at -a time (e.g. ,datasources=default.opals[2] to generate the random vector in source 2). +a time (e.g. ,datasources=default.connections[2] to generate the random vector in source 2). As an example, if the value is 78326 then the seed in each source will be set at 78326*1 = 78326 because the vector of datasources being used in each call to the function will always be of length 1 and so the @@ -75,15 +75,15 @@ For further details see help for \code{sample} in native R.} \item{newobj}{This a character string providing a name for the output data.frame which defaults to 'newobj.sample' if no name is specified.} -\item{datasources}{specifies the particular Armadillo/Opal connection object(s) to use. If the -argument is not specified the default set of Armadillo/Opal servers will be used. The default servers -are called default.opals and the default can be set using the function -\code{ds.setDefaultOpals}. If the is to be specified, it should be set without -inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to -apply the function solely to e.g. the second Armadillo/Opal server in a set of three, -the argument can be specified as: e.g. datasources=opals.em[2]. -If you wish to specify the first and third Armadillo/Opal servers in a set you specify: -e.g. datasources=opals.em[c(1,3)]} +\item{datasources}{specifies the particular connection object(s) to use. If the +argument is not specified the default set of servers will be used. The default servers +are called default.connections and the default can be set using the function +\code{DSI::datashield.connections_default}. If the is to be specified, it should be set without +inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to +apply the function solely to e.g. the second server in a set of three, +the argument can be specified as: e.g. datasources=connections.em[2]. +If you wish to specify the first and third servers in a set you specify: +e.g. datasources=connections.em[c(1,3)]} \item{notify.of.progress}{specifies if console output should be produce to indicate progress. The default value for notify.of.progress is FALSE.} diff --git a/man/ds.scatterPlot.Rd b/man/ds.scatterPlot.Rd index 12ea7e2c1..9391dc8e8 100644 --- a/man/ds.scatterPlot.Rd +++ b/man/ds.scatterPlot.Rd @@ -110,22 +110,22 @@ Server function called: \code{scatterPlotDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.seq.Rd b/man/ds.seq.Rd index 42c312bb4..b7ce7a8a4 100644 --- a/man/ds.seq.Rd +++ b/man/ds.seq.Rd @@ -95,22 +95,22 @@ Server function called: \code{seqDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.setSeed.Rd b/man/ds.setSeed.Rd index df50e17e6..b4070a927 100644 --- a/man/ds.setSeed.Rd +++ b/man/ds.setSeed.Rd @@ -63,22 +63,22 @@ Server function called: \code{setSeedDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.skewness.Rd b/man/ds.skewness.Rd index 9a9087488..6bd629be3 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -36,7 +36,7 @@ and the number of valid observations. } \description{ This function calculates the skewness of a numeric variable -that is stored on the server-side (Armadillo/Opal server). +that is stored on the server-side (server). } \details{ This function is similar to the function \code{skewness} in R package \code{e1071}. @@ -68,22 +68,22 @@ Server functions called: \code{skewnessDS1} and \code{skewnessDS2} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index e92fa5df5..767f9894d 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -38,22 +38,22 @@ specified by the user through the argument \code{newobj}, otherwise is named by # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() diff --git a/man/ds.summary.Rd b/man/ds.summary.Rd index 141ac0541..63753c154 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -41,22 +41,22 @@ server functions called: \code{isValidDS}, \code{dimDS} and \code{colnamesDS} # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() # Log onto the remote Armadillo/Opal training servers diff --git a/man/ds.tapply.Rd b/man/ds.tapply.Rd index f5656ec76..bd281d624 100644 --- a/man/ds.tapply.Rd +++ b/man/ds.tapply.Rd @@ -103,22 +103,22 @@ Server function called: \code{tapplyDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.tapply.assign.Rd b/man/ds.tapply.assign.Rd index 232fee8ff..7f09c6ca5 100644 --- a/man/ds.tapply.assign.Rd +++ b/man/ds.tapply.assign.Rd @@ -108,22 +108,22 @@ Server function called: \code{ds.tapply.assign} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.testObjExists.Rd b/man/ds.testObjExists.Rd index a48097c48..47e9406d0 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -39,22 +39,22 @@ Server function called: \code{testObjExistsDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.unList.Rd b/man/ds.unList.Rd index 7926ea7e3..5a36dc26b 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -46,22 +46,22 @@ Server function called: \code{unListDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index 145bfdee3..e1d6e81dd 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -32,22 +32,22 @@ Server function called: \code{uniqueDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.var.Rd b/man/ds.var.Rd index 4ea17d6ac..cfe9272ee 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -63,22 +63,22 @@ Server function called: \code{varDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/subsetHelper.Rd b/man/subsetHelper.Rd index 674dd8480..fb6c9a999 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -41,22 +41,22 @@ Server function called: \code{dimDS} # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")