Merging with v6.3.3-dev plus document update

Author: StuartWheater

.Rbuildignore

@@ -9,3 +9,4 @@
 ^pkgdown$
 ^\.circleci$
 ^\.circleci/config\.yml$
+^\.github$

.circleci/config.yml

@@ -25,6 +25,7 @@ jobs:
               sudo apt-get install -y libxml2-dev
       - run:
           command: |
+              echo "options(Ncpus=4)" >> ~/.Rprofile
               sudo Rscript -e "install.packages('RANN', dependencies=TRUE)"
               sudo Rscript -e "install.packages('stringr', dependencies=TRUE)"
               sudo Rscript -e "install.packages('lme4', dependencies=TRUE)"

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -1,9 +1,47 @@
 Package: dsBase
-Title: DataSHIELD Server Site Base Functions
-Description: DataSHIELD Server Site Base Functions.
-Version: 6.4.0.9000
-Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
-Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
+Title: 'DataSHIELD' Server Site Base Functions
+Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows
+    you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
+    been designed to only share non disclosive summary statistics, with built in automated output
+    checking based on statistical disclosure control. With data sites setting the threshold values for
+    the automated output checks.
+Version: 6.4.0-9000
+Authors@R: c(person(given = "Paul",
+                    family = "Burton",
+                    role = c("aut")),
+             person(given = "Rebecca",
+                    family = "Wilson",
+                    role = c("aut")),
+             person(given = "Olly",
+                    family = "Butters",
+                    role = c("aut")),
+             person(given = "Patricia",
+                    family = "Ryser-Welch",
+                    role = c("aut")),
+             person(given = "Alex",
+                    family = "Westerberg",
+                    role = c("aut")),
+             person(given = "Leire",
+                    family = "Abarrategui",
+                    role = c("aut")),
+             person(given = "Roberto",
+                    family = "Villegas-Diaz",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-5036-8661")),
+             person(given = "Demetris",
+                    family = "Avraam",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-8908-2441")),
+             person(given = "Yannick",
+                    family = "Marcon",
+                    role = c("aut"),
+                    email = "yannick.marcon@obiba.org",
+                    comment = c(ORCID = "0000-0003-0138-2023")),
+             person(given = "Stuart",
+                    family = "Wheater",
+                    role = c("aut", "cre"),
+                    email = "stuart.wheater@arjuna.com",
+                    comment = c(ORCID = "0009-0003-2419-1964")))
 License: GPL-3
 Depends: 
     R (>= 4.0.0)
@@ -25,178 +63,5 @@ Imports:
     tidyverse
 Suggests:
     testthat
-AggregateMethods:
-    asFactorDS1,
-    asListDS,
-    aucDS,
-    boxPlotGGDS,
-    checkNegValueDS,
-    classDS,
-    colnamesDS,
-    corTestDS,
-    corDS,
-    covDS,
-    dataFrameSubsetDS1,
-    densityGridDS,
-    extractQuantilesDS1,
-    extractQuantilesDS2,
-    dimDS,
-    gamlssDS,
-    glmDS1,
-    glmDS2,
-    glmerSLMADS2,
-    glmPredictDS.ag,
-    glmSLMADS1,
-    glmSLMADS2,
-    glmSummaryDS.ag,
-    heatmapPlotDS,
-    hetcorDS,
-    histogramDS1,
-    histogramDS2,
-    isNaDS,
-    isValidDS,
-    kurtosisDS1,
-    kurtosisDS2,
-    lengthDS,
-    levelsDS,
-    lexisDS1,
-    listDisclosureSettingsDS,
-    lmerSLMADS2,
-    lsDS,
-    matrixDetDS1,
-    meanDS,
-    meanSdGpDS,
-    messageDS,
-    metadataDS,
-    miceDS,
-    minMaxRandDS,
-    namesDS,
-    numNaDS,
-    quantileMeanDS,
-    rangeDS,
-    ranksSecureDS1,
-    ranksSecureDS3,
-    rmDS,
-    scatterPlotDS,
-    scoreVectDS,
-    setSeedDS,
-    skewnessDS1,
-    skewnessDS2,
-    table1DDS,
-    table2DDS,
-    tableDS,
-    tableDS2,
-    tapplyDS,
-    testObjExistsDS,
-    varDS,
-    exists=base::exists,
-    is.character=base::is.character,
-    is.factor=base::is.factor,
-    is.list=base::is.list,
-    is.null=base::is.null,
-    is.numeric=base::is.numeric,
-    NROW=base::NROW,
-    t.test=stats::t.test
-AssignMethods:
-    absDS,
-    asCharacterDS,
-    asDataMatrixDS,
-    asFactorDS2,
-    asFactorSimpleDS,
-    asIntegerDS,
-    asListDS,
-    asLogicalDS,
-    asMatrixDS,
-    asNumericDS,
-    blackBoxDS,
-    blackBoxRanksDS,
-    BooleDS,
-    boxPlotGG_data_TreatmentDS,
-    boxPlotGG_data_Treatment_numericDS,
-    bp_standardsDS,
-    cbindDS,
-    cDS,
-    changeRefGroupDS,
-    completeCasesDS,
-    dataFrameDS,
-    dataFrameFillDS,
-    dataFrameSortDS,
-    dataFrameSubsetDS2,
-    dmtC2SDS,
-    elsplineDS,
-    glmerSLMADS.assign,
-    glmPredictDS.as,
-    glmSLMADS.assign,
-    glmSummaryDS.as,
-    getWGSRDS,
-    igb_standardsDS,
-    listDS,
-    lexisDS2,
-    lexisDS3,
-    lmerSLMADS.assign,
-    lsplineDS,
-    matrixDetDS2,
-    matrixDiagDS,
-    matrixDimnamesDS,
-    matrixDS,
-    matrixInvertDS,
-    matrixMultDS,
-    matrixTransposeDS,
-    mergeDS,
-    nsDS,
-    qlsplineDS,
-    ranksSecureDS2,
-    ranksSecureDS4,
-    ranksSecureDS5,
-    rbindDS,
-    rBinomDS,
-    recodeLevelsDS,
-    recodeValuesDS,
-    repDS,
-    replaceNaDS,
-    reShapeDS,
-    rNormDS,
-    rowColCalcDS,
-    rPoisDS,
-    rUnifDS,
-    sampleDS,
-    seqDS,
-    sqrtDS,
-    tableDS.assign,
-    tapplyDS.assign,
-    uniqueDS,
-    unListDS,
-    vectorDS,
-    as.character=base::as.character,
-    as.null=base::as.null,
-    as.numeric=base::as.numeric,
-    attach=base::attach,
-    c=dsBase::vectorDS,
-    complete.cases=stats::complete.cases,
-    list=base::list,
-    exp=base::exp,
-    log=base::log,
-    sqrt=base::sqrt,
-    abs=base::abs,
-    sin=base::sin,
-    cos=base::cos,
-    tan=base::tan,
-    asin=base::asin,
-    acos=base::acos,
-    atan=base::atan,
-    sum=base::sum,
-    unlist=base::unlist
-Options:
-    datashield.privacyLevel=5,
-    default.datashield.privacyControlLevel="banana",
-    default.nfilter.glm=0.33,
-    default.nfilter.kNN=3,
-    default.nfilter.string=80,
-    default.nfilter.subset=3,
-    default.nfilter.stringShort=20,
-    default.nfilter.tab=3,
-    default.nfilter.noise=0.25,
-    default.nfilter.levels.density=0.33,
-    default.nfilter.levels.max=40
 RoxygenNote: 7.3.2
 Encoding: UTF-8

NAMESPACE

@@ -4,6 +4,7 @@ export(BooleDS)
 export(absDS)
 export(asCharacterDS)
 export(asDataFrameDS)
+export(asDataMatrixDS)
 export(asFactorDS1)
 export(asFactorDS2)
 export(asFactorSimpleDS)

R/BooleDS.R

@@ -16,10 +16,13 @@
 #' the final output variable
 #' should be of class numeric (1/0) or class logical (TRUE/FALSE).
 #' @param na.assign.text A character string taking values 'NA', '1' or '0'. If 'NA'
-#' then any NA values in the input vector remain as NAs in the output vector. If '1' 
-#' or '0' NA values in the input vector are all converted to 1 or 0 respectively.
-#' @return the levels of the input variable.
+#' then any NA values in the
+#' input vector remain as NAs in the output vector. If '1' or '0' NA values in the
+#' input vector are all converted to 1 or 0 respectively.
+#' 
 #' @author DataSHIELD Development Team
+#' 
+#' @return the levels of the input variable.
 #' @export
 #'
 BooleDS <- function(V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL, na.assign.text, numeric.output=TRUE){

R/absDS.R

@@ -6,21 +6,19 @@
 #' @param x a string character, the name of a numeric or integer vector
 #' @return the object specified by the \code{newobj} argument
 #' of \code{ds.abs} (or default name \code{abs.newobj})
-#' which is written to the serverside. The output object is of class numeric 
+#' which is written to the serverside. The output object is of class numeric
 #' or integer.
 #' @author Demetris Avraam for DataSHIELD Development Team
 #' @export
 #'
-absDS <- function(x){
-
-  x.var <- eval(parse(text=x), envir = parent.frame())
+absDS <- function(x) {
+  x.var <- eval(parse(text = x), envir = parent.frame())
 
   # compute the absolute values of x
   out <- abs(x.var)
-  
+
   # assign the outcome to the data servers
   return(out)
-
 }
 # ASSIGN FUNCTION
 # absDS

R/asCharacterDS.R

@@ -1,4 +1,4 @@
-#' 
+#'
 #' @title Coerces an R object into class character
 #' @description this function is based on the native R function \code{as.character}
 #' @details See help for function \code{as.character} in native R
@@ -11,14 +11,12 @@
 #' details see help on the clientside function \code{ds.asCharacter}
 #' @author Amadou Gaye, Paul Burton, Demetris Avraam for DataSHIELD Development Team
 #' @export
-#' 
-asCharacterDS <- function(x.name){
-
-  x <- eval(parse(text=x.name), envir = parent.frame())
+#'
+asCharacterDS <- function(x.name) {
+  x <- eval(parse(text = x.name), envir = parent.frame())
 
   output <- as.character(x)
   return(output)
-  
 }
 # ASSIGN FUNCTION
 # asCharacterDS

R/asDataMatrixDS.R

@@ -11,14 +11,12 @@
 #' details see help on the clientside function \code{ds.asDataMatrix}
 #' @author Tim Cadman
 #' @export
-asDataFrameDS <- function (x.name){
-
-if(is.character(x.name)){
-	x <- eval(parse(text=x.name), envir = parent.frame())
-
-	}else{
-   studysideMessage<-"ERROR: x.name must be specified as a character string"
-   stop(studysideMessage, call. = FALSE)
+asDataMatrixDS <- function(x.name) {
+  if (is.character(x.name)) {
+    x <- eval(parse(text = x.name), envir = parent.frame())
+  } else {
+    studysideMessage <- "ERROR: x.name must be specified as a character string"
+    stop(studysideMessage, call. = FALSE)
   }
 
   output <- data.frame(x)