Skip to content

docs: updated server references to include Armadillo #714

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
StuartWheater merged 2 commits into from
Oct 13, 2026
Merged

docs: updated server references to include Armadillo #714

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
eb5b3bb
docs: updated server references to include Armadillo
timcadman Sep 25, 2026
f7e40e7
docs: update examples to include armadillo
timcadman Oct 13, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 11 additions & 11 deletions R/ds.Boole.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,29 +44,29 @@
#' \dontrun{
#'
#' ## Version 6, for version 5 see the Wiki
#' # Connecting to the Opal servers
#' # 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$build()
#'
#' # Log onto the remote Opal training servers
#' # Log onto the remote Armadillo/Opal training servers
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Generating Boolean indicators
Expand Down
22 changes: 11 additions & 11 deletions R/ds.abs.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,29 +22,29 @@
#' @examples
#' \dontrun{
#'
#' # Connecting to the Opal servers
#' # Connecting to the Armadillo/Opal servers
#'
#' require('DSI')
#' require('DSMolgenisArmadillo')
#' require('DSOpal')
#' require('dsBaseClient')
#'
#' armadillo_url <- "http://192.168.56.100:8080/"
#' token <- armadillo.get_credentials(armadillo_url)
#' builder <- DSI::newDSLoginBuilder()
#' builder$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$build()
#'
#' # Log onto the remote Opal training servers
#' # Log onto the remote Armadillo/Opal training servers
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Example 1: Generate a normally distributed variable with zero mean and variance equal
Expand Down
22 changes: 11 additions & 11 deletions R/ds.asCharacter.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,33 +18,33 @@
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
#'
#' # connecting to the Opal servers
#' # connecting to the Armadillo/Opal servers
#'
#' require('DSI')
#' require('DSMolgenisArmadillo')
#' require('DSOpal')
#' require('dsBaseClient')
#'
#' armadillo_url <- "http://192.168.56.100:8080/"
#' token <- armadillo.get_credentials(armadillo_url)
#' builder <- DSI::newDSLoginBuilder()
#' builder$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$build()
#'
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Converting the R object into a class character
#' ds.asCharacter(x.name = "D$LAB_TSC",
#' newobj = "char.obj",
#' datasources = connections[1]) #only the first Opal server is used ("study1")
#' datasources = connections[1]) #only the first server is used ("study1")
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
Expand Down
22 changes: 11 additions & 11 deletions R/ds.asDataMatrix.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,33 +17,33 @@
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
#'
#' # connecting to the Opal servers
#' # 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")
#'
#' # 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 server is used ("study1")
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
Expand Down
26 changes: 13 additions & 13 deletions R/ds.asFactor.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -140,28 +140,28 @@
#' \dontrun{
#'
#' ## Version 6, for version 5 see Wiki
#' # Connecting to the Opal servers
#' # 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 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$PM_BMI_CATEGORICAL",
Expand All @@ -170,14 +170,14 @@
#' #from all studies is created
#' fixed.dummy.vars = TRUE, #create a matrix of dummy variables
#' baseline.level = 1,
#' datasources = connections)#all the Opal servers are used, in this case 3
#' datasources = connections)#all the servers are used, in this case 2
#' #(see above the connection to the servers)
#' ds.asFactor(input.var.name = "D$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 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)
Expand Down
22 changes: 11 additions & 11 deletions R/ds.asInteger.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,33 +31,33 @@
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
#'
#' # connecting to the Opal servers
#' # 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")
#'
#' # Converting the R object into an integer
#' ds.asInteger(x.name = "D$LAB_TSC",
#' newobj = "int.obj",
#' datasources = connections[1]) #only the first Opal server is used ("study1")
#' datasources = connections[1]) #only the first server is used ("study1")
#' ds.class(x = "int.obj", datasources = connections[1])
#'
#' # Clear the Datashield R sessions and logout
Expand Down
22 changes: 11 additions & 11 deletions R/ds.asList.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,33 +18,33 @@
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
#'
#' # connecting to the Opal servers
#' # connecting to the Armadillo/Opal servers
#'
#' require('DSI')
#' require('DSMolgenisArmadillo')
#' require('DSOpal')
#' require('dsBaseClient')
#'
#' armadillo_url <- "http://192.168.56.100:8080/"
#' token <- armadillo.get_credentials(armadillo_url)
#' builder <- DSI::newDSLoginBuilder()
#' builder$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$build()
#'
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Converting the R object into a List
#' ds.asList(x.name = "D",
#' newobj = "D.asList",
#' datasources = connections[1]) #only the first Opal server is used ("study1")
#' datasources = connections[1]) #only the first server is used ("study1")
#' ds.class(x = "D.asList", datasources = connections[1])
#'
#' # Clear the Datashield R sessions and logout
Expand Down
22 changes: 11 additions & 11 deletions R/ds.asLogical.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,33 +17,33 @@
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
#'
#' # connecting to the Opal servers
#' # connecting to the Armadillo/Opal servers
#'
#' require('DSI')
#' require('DSMolgenisArmadillo')
#' require('DSOpal')
#' require('dsBaseClient')
#'
#' armadillo_url <- "http://192.168.56.100:8080/"
#' token <- armadillo.get_credentials(armadillo_url)
#' builder <- DSI::newDSLoginBuilder()
#' builder$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$build()
#'
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Converting the R object into a logical
#' ds.asLogical(x.name = "D$LAB_TSC",
#' newobj = "logical.obj",
#' datasources =connections[1]) #only the first Opal server is used ("study1")
#' datasources =connections[1]) #only the first server is used ("study1")
#' ds.class(x = "logical.obj", datasources = connections[1])
#'
#' # Clear the Datashield R sessions and logout
Expand Down
Loading
Loading