Updating DESCRIPTION, perf_profile, roxygen2 to version: 8.1.1, plus …

DESCRIPTION

@@ -82,4 +82,4 @@ Suggests:
 Encoding: UTF-8
 Language: en-GB
 Config/testthat/edition: 3
-Config/roxygen2/version: 8.1.0
+Config/roxygen2/version: 8.1.1

docs/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,38 @@
+# NA
+
+## Instructions & checklist for PR author
+
+### Description of changes
+
+\[Add descriptions of changes made\]
+
+### Refactor instructions
+
+Replaced `x <- eval(parse(text = x.name), envir = parent.frame())` with
+`x <- .loadServersideObject(x)`
+
+If necessary, check the class of the object using `.checkClass()`
+
+### Testing instructions
+
+Writen server-side unit tests for unhappy flow
+
+Run `devtools::test(filter = "smk-|disc|arg")` and check it passes
+
+Run `devtools::check(args = '--no-tests')` and check it passes (we run
+tests separately to skip performance checks)
+
+Run
+[`devtools::build()`](https://devtools.r-lib.org/reference/build.html)
+and check it builds without errors
+
+## Instructions & checklist for PR reviewers
+
+Run `devtools::test(filter = "smk-|disc|arg")` and check it passes
+
+Run `devtools::check(args = '--no-tests')` and check it passes (we run
+tests separately to skip performance checks)
+
+Run
+[`devtools::build()`](https://devtools.r-lib.org/reference/build.html)
+and check it builds without errors

docs/authors.md

@@ -37,12 +37,12 @@
 Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui
 L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A,
 Escribà-Montagut X, Wheater S (????). *dsBase: 'DataSHIELD' Server Side
-Base Functions*. R package version 6.3.6.9000.
+Base Functions*. R package version 7.0.0.9000.
 
     @Manual{,
       title = {dsBase: 'DataSHIELD' Server Side Base Functions},
       author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
-      note = {R package version 6.3.6.9000},
+      note = {R package version 7.0.0.9000},
     }
 
 Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J,

docs/llms.txt

@@ -127,11 +127,11 @@ analysis platform.” *Bioinformatics Advances*, *5*(1), 1-21.
 - [`asIntegerDS()`](asIntegerDS.md) : Coerces an R object into class
   integer
 
-- [`asListDS()`](asListDS.md) : asListDS a serverside aggregate function
+- [`asListDS()`](asListDS.md) : asListDS a serverside assign function
   called by ds.asList
 
 - [`asLogicalDS()`](asLogicalDS.md) : Coerces an R object into class
-  numeric
+  logical
 
 - [`asMatrixDS()`](asMatrixDS.md) : Coerces an R object into a matrix
 
@@ -213,6 +213,9 @@ analysis platform.” *Bioinformatics Advances*, *5*(1), 1-21.
 - [`elsplineDS()`](elsplineDS.md) : Basis for a piecewise linear spline
   with meaningful coefficients
 
+- [`expDS()`](expDS.md) : Computes the exponential values of the input
+  variable
+
 - [`extractQuantilesDS1()`](extractQuantilesDS1.md) : Secure ranking of
   "V2BR" (vector to be ranked) across all sources and use of these ranks
   to estimate global quantiles across all studies
@@ -317,6 +320,9 @@ analysis platform.” *Bioinformatics Advances*, *5*(1), 1-21.
 - [`lmerSLMADS2()`](lmerSLMADS2.md) : Fitting linear mixed effect
   models - serverside function
 
+- [`logDS()`](logDS.md) : Computes the logarithm values of the input
+  variable
+
 - [`lsDS()`](lsDS.md) : lists all objects on a serverside environment
 
 - [`lsplineDS()`](lsplineDS.md) : Basis for a piecewise linear spline

docs/pkgdown.yml

@@ -1,5 +1,5 @@
-pandoc: 3.1.3
-pkgdown: 2.2.0
+pandoc: 3.7.0.2
+pkgdown: 2.2.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2026-07-06T11:51Z
+last_built: 2026-10-14T12:49Z

docs/reference/BooleDS.md

@@ -58,3 +58,5 @@ The function converts the input vector into Boolean indicators.
 ## Author
 
 DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands

docs/reference/absDS.md

@@ -28,3 +28,5 @@ vector.
 ## Author
 
 Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands