From 65d59040e868ce1071bb363b041f745beca5f904 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Sat, 11 Apr 2026 12:43:20 +0200
Subject: [PATCH 01/12] refactor: move checks to serverside

---
 R/corDS.R          |  7 +++++--
 R/corTestDS.R      |  6 ++++--
 R/covDS.R          |  7 +++++--
 R/kurtosisDS1.R    |  5 +++--
 R/kurtosisDS2.R    |  5 +++--
 R/meanDS.R         |  7 +++++--
 R/meanSdGpDS.R     | 17 +++++++++++------
 R/quantileMeanDS.R | 17 ++++++++++-------
 R/skewnessDS1.R    |  5 +++--
 R/skewnessDS2.R    |  5 +++--
 R/varDS.R          |  7 +++++--
 11 files changed, 57 insertions(+), 31 deletions(-)

diff --git a/R/corDS.R b/R/corDS.R
index abc73145..0c3a84a0 100644
--- a/R/corDS.R
+++ b/R/corDS.R
@@ -27,9 +27,12 @@ corDS <- function(x=NULL, y=NULL){
   nfilter.glm <- as.numeric(thr$nfilter.glm)
   #############################################################
   
-  x.val <- eval(parse(text=x), envir = parent.frame())
+  x.val <- .loadServersideObject(x)
+  .checkClass(obj = x.val, obj_name = x, permitted_classes = c("numeric", "integer", "matrix", "data.frame"))
+
   if (!is.null(y)){
-    y.val <- eval(parse(text=y), envir = parent.frame())
+    y.val <- .loadServersideObject(y)
+    .checkClass(obj = y.val, obj_name = y, permitted_classes = c("numeric", "integer", "matrix", "data.frame"))
   }
   else{
     y.val <- NULL
diff --git a/R/corTestDS.R b/R/corTestDS.R
index ef5aac33..521cbb55 100644
--- a/R/corTestDS.R
+++ b/R/corTestDS.R
@@ -17,8 +17,10 @@
 #'
 corTestDS <- function(x, y, method, exact, conf.level){
 
-  x.var <- eval(parse(text=x), envir = parent.frame())
-  y.var <- eval(parse(text=y), envir = parent.frame())
+  x.var <- .loadServersideObject(x)
+  .checkClass(obj = x.var, obj_name = x, permitted_classes = c("numeric", "integer"))
+  y.var <- .loadServersideObject(y)
+  .checkClass(obj = y.var, obj_name = y, permitted_classes = c("numeric", "integer"))
   
   # get the number of pairwise complete cases
   n <- sum(stats::complete.cases(x.var, y.var))
diff --git a/R/covDS.R b/R/covDS.R
index 9f645b62..15e43830 100644
--- a/R/covDS.R
+++ b/R/covDS.R
@@ -36,9 +36,12 @@ covDS <- function(x=NULL, y=NULL, use=NULL){
   #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
   
-  x.val <- eval(parse(text=x), envir = parent.frame())
+  x.val <- .loadServersideObject(x)
+  .checkClass(obj = x.val, obj_name = x, permitted_classes = c("numeric", "integer", "matrix", "data.frame"))
+
   if (!is.null(y)){
-    y.val <- eval(parse(text=y), envir = parent.frame())
+    y.val <- .loadServersideObject(y)
+    .checkClass(obj = y.val, obj_name = y, permitted_classes = c("numeric", "integer", "matrix", "data.frame"))
   }
   else{
     y.val <- NULL
diff --git a/R/kurtosisDS1.R b/R/kurtosisDS1.R
index 4f3f4e52..435ff6e2 100644
--- a/R/kurtosisDS1.R
+++ b/R/kurtosisDS1.R
@@ -19,8 +19,9 @@ kurtosisDS1 <- function (x, method){
   nfilter.tab <- as.numeric(thr$nfilter.tab)
   #############################################################
   
-  x <- eval(parse(text=x), envir = parent.frame())
-  x <- x[stats::complete.cases(x)]
+  x.val <- .loadServersideObject(x)
+  .checkClass(obj = x.val, obj_name = x, permitted_classes = c("numeric", "integer"))
+  x <- x.val[stats::complete.cases(x.val)]
   
   if(length(x) < nfilter.tab){
     kurtosis.out <- NA
diff --git a/R/kurtosisDS2.R b/R/kurtosisDS2.R
index 1d4e3fec..864ca5aa 100644
--- a/R/kurtosisDS2.R
+++ b/R/kurtosisDS2.R
@@ -23,8 +23,9 @@ kurtosisDS2 <- function(x, global.mean){
   nfilter.tab <- as.numeric(thr$nfilter.tab)
   #############################################################
   
-  x <- eval(parse(text=x), envir = parent.frame())
-  x <- x[stats::complete.cases(x)]
+  x.val <- .loadServersideObject(x)
+  .checkClass(obj = x.val, obj_name = x, permitted_classes = c("numeric", "integer"))
+  x <- x.val[stats::complete.cases(x.val)]
   
   if(length(x) < nfilter.tab){
     sum_quartics.out <- NA
diff --git a/R/meanDS.R b/R/meanDS.R
index 59d1bc4e..8e4f8998 100644
--- a/R/meanDS.R
+++ b/R/meanDS.R
@@ -3,12 +3,12 @@
 #' @description Calculates the mean value.
 #' @details if the length of input vector is less than the set filter
 #' a missing value is returned.
-#' @param xvect a vector
+#' @param x a character string, the name of a numeric or integer vector
 #' @return a numeric, the statistical mean
 #' @author Gaye A, Burton PR
 #' @export
 #'
-meanDS <- function(xvect){
+meanDS <- function(x){
 
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
@@ -19,6 +19,9 @@ meanDS <- function(xvect){
   #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
 
+  xvect <- .loadServersideObject(x)
+  .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer"))
+
   out.mean <- mean(xvect, na.rm=TRUE)
   out.numNa <- length(which(is.na(xvect)))
   out.totN <- length(xvect)
diff --git a/R/meanSdGpDS.R b/R/meanSdGpDS.R
index 41fdb721..2375250e 100644
--- a/R/meanSdGpDS.R
+++ b/R/meanSdGpDS.R
@@ -3,17 +3,17 @@
 #' @description Server-side function called by ds.meanSdGp 
 #' @details Computes the mean and standard deviation across groups defined by one
 #' factor
-#' @param X a client-side supplied character string identifying the variable for which
+#' @param x a client-side supplied character string identifying the variable for which
 #' means/SDs are to be calculated
-#' @param INDEX a client-side supplied character string identifying the factor across
+#' @param index a client-side supplied character string identifying the factor across
 #' which means/SDs are to be calculated
 #' @author Burton PR
-#' 
+#'
 #' @return List with results from the group statistics
 #' @export
 #'
-meanSdGpDS <- function (X, INDEX){
-  
+meanSdGpDS <- function (x, index){
+
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
   thr <- dsBase::listDisclosureSettingsDS()
@@ -23,9 +23,14 @@ meanSdGpDS <- function (X, INDEX){
   #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
 
+  X <- .loadServersideObject(x)
+  .checkClass(obj = X, obj_name = x, permitted_classes = c("numeric", "integer"))
+  INDEX <- .loadServersideObject(index)
+  .checkClass(obj = INDEX, obj_name = index, permitted_classes = c("factor", "character", "integer"))
+
   FUN.mean <- function(x) {mean(x,na.rm=TRUE)}
   FUN.var <- function(x)  {stats::var(x,na.rm=TRUE)}
-  
+
   #Strip missings from both X and INDEX
   analysis.matrix<-cbind(X,INDEX)
   
diff --git a/R/quantileMeanDS.R b/R/quantileMeanDS.R
index 79fe3a96..199aee81 100644
--- a/R/quantileMeanDS.R
+++ b/R/quantileMeanDS.R
@@ -2,18 +2,21 @@
 #' @title Generates quantiles and mean information without maximum and minimum
 #' @description the probabilities 5%, 10%, 25%, 50%, 75%, 90%, 95% and the mean
 #' are used to compute the corresponding quantiles.
-#' @param xvect a numerical vector
-#' @return a numeric vector that represents the sample quantiles 
+#' @param x a character string, the name of a numeric or integer vector
+#' @return a numeric vector that represents the sample quantiles
 #' @export
 #' @author Burton, P.; Gaye, A.
-#' 
-quantileMeanDS <- function (xvect) {
-  
+#'
+quantileMeanDS <- function (x) {
+
+  xvect <- .loadServersideObject(x)
+  .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer"))
+
   # check if the input vector is valid (i.e. meets DataSHIELD criteria)
   check <- isValidDS(xvect)
-  
+
   if(check){
-    # if the input vector is valid 
+    # if the input vector is valid
     qq <- stats::quantile(xvect,c(0.05,0.1,0.25,0.5,0.75,0.9,0.95), na.rm=TRUE)
     mm <- mean(xvect,na.rm=TRUE)
     quantile.obj <- c(qq, mm)
diff --git a/R/skewnessDS1.R b/R/skewnessDS1.R
index 19f95dfc..41b5b98e 100644
--- a/R/skewnessDS1.R
+++ b/R/skewnessDS1.R
@@ -19,8 +19,9 @@ skewnessDS1 <- function(x, method){
   nfilter.tab <- as.numeric(thr$nfilter.tab)
   #############################################################
   
-  x <- eval(parse(text=x), envir = parent.frame())
-  x <- x[stats::complete.cases(x)]
+  x.val <- .loadServersideObject(x)
+  .checkClass(obj = x.val, obj_name = x, permitted_classes = c("numeric", "integer"))
+  x <- x.val[stats::complete.cases(x.val)]
   
   if(length(x) < nfilter.tab){
     skewness.out <- NA
diff --git a/R/skewnessDS2.R b/R/skewnessDS2.R
index 8d1cb484..3d7224ef 100644
--- a/R/skewnessDS2.R
+++ b/R/skewnessDS2.R
@@ -23,8 +23,9 @@ skewnessDS2 <- function(x, global.mean){
   nfilter.tab <- as.numeric(thr$nfilter.tab)
   #############################################################
   
-  x <- eval(parse(text=x), envir = parent.frame())
-  x <- x[stats::complete.cases(x)]
+  x.val <- .loadServersideObject(x)
+  .checkClass(obj = x.val, obj_name = x, permitted_classes = c("numeric", "integer"))
+  x <- x.val[stats::complete.cases(x.val)]
   
   if(length(x) < nfilter.tab){
     sum_cubes.out <- NA
diff --git a/R/varDS.R b/R/varDS.R
index 390a9589..c508ba40 100644
--- a/R/varDS.R
+++ b/R/varDS.R
@@ -3,7 +3,7 @@
 #' @description Calculates the variance.
 #' @details if the length of input vector is less than the set filter
 #' a missing value is returned.
-#' @param xvect a vector
+#' @param x a character string, the name of a numeric or integer vector
 #' @return a list, with the sum of the input variable, the sum of squares of the input variable,
 #' the number of missing values, the number of valid values, the number of total length of the
 #' variable, and a study message indicating whether the number of valid is less than the
@@ -11,7 +11,7 @@
 #' @author Amadou Gaye, Demetris Avraam, for DataSHIELD Development Team
 #' @export
 #'
-varDS <- function(xvect){
+varDS <- function(x){
 
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
@@ -22,6 +22,9 @@ varDS <- function(xvect){
   #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
 
+  xvect <- .loadServersideObject(x)
+  .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer"))
+
   out.sum <- sum(xvect, na.rm=TRUE)
   out.sumSquares <- sum(xvect^2, na.rm=TRUE)
   out.numNa <- length(which(is.na(xvect)))

From 073bedc21bf6ddccfddb3916220e938c0ebaf9ca Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Sat, 11 Apr 2026 12:43:28 +0200
Subject: [PATCH 02/12] test: update unit tests

---
 tests/testthat/test-smk-corDS.R          | 10 ++++
 tests/testthat/test-smk-corTestDS.R      | 10 ++++
 tests/testthat/test-smk-covDS.R          | 10 ++++
 tests/testthat/test-smk-kurtosisDS1.R    |  9 ++++
 tests/testthat/test-smk-kurtosisDS2.R    |  9 ++++
 tests/testthat/test-smk-meanDS.R         | 15 ++++--
 tests/testthat/test-smk-meanSdGpDS.R     | 62 ++++++++++++++++++++++++
 tests/testthat/test-smk-quantileMeanDS.R | 13 ++++-
 tests/testthat/test-smk-skewnessDS1.R    |  9 ++++
 tests/testthat/test-smk-skewnessDS2.R    |  9 ++++
 tests/testthat/test-smk-varDS.R          | 15 ++++--
 11 files changed, 163 insertions(+), 8 deletions(-)
 create mode 100644 tests/testthat/test-smk-meanSdGpDS.R

diff --git a/tests/testthat/test-smk-corDS.R b/tests/testthat/test-smk-corDS.R
index bdc3607c..034a4b00 100644
--- a/tests/testthat/test-smk-corDS.R
+++ b/tests/testthat/test-smk-corDS.R
@@ -718,6 +718,16 @@ test_that("simple corDS, casewise, some", {
     expect_equal(res$sums.of.squares[4], 58.0)
 })
 
+test_that("corDS throws error when object does not exist", {
+    expect_error(corDS("nonexistent_x", "nonexistent_y"), regexp = "does not exist")
+})
+
+test_that("corDS throws error when object is of invalid type", {
+    bad_input <- list(a = 1:3, b = 4:6)
+    y <- c(1.0, 2.0, 3.0)
+    expect_error(corDS("bad_input", "y"), regexp = "must be of type")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-corTestDS.R b/tests/testthat/test-smk-corTestDS.R
index b500a085..2dbee274 100644
--- a/tests/testthat/test-smk-corTestDS.R
+++ b/tests/testthat/test-smk-corTestDS.R
@@ -602,6 +602,16 @@ test_that("simple corTestDS, some, with na, spearman", {
     expect_equal(res$`Correlation test`$data.name[[1]], "x.var and y.var")
 })
 
+test_that("corTestDS throws error when object does not exist", {
+    expect_error(corTestDS("nonexistent_x", "nonexistent_y", "pearson", NULL, 0.95), regexp = "does not exist")
+})
+
+test_that("corTestDS throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    y <- c(1.0, 2.0, 3.0)
+    expect_error(corTestDS("bad_input", "y", "pearson", NULL, 0.95), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-covDS.R b/tests/testthat/test-smk-covDS.R
index ce731938..64710a72 100644
--- a/tests/testthat/test-smk-covDS.R
+++ b/tests/testthat/test-smk-covDS.R
@@ -232,6 +232,16 @@ test_that("numeric covDS, pairwise.complete", {
     expect_true(is.na(res$errorMessage))
 })
 
+test_that("covDS throws error when object does not exist", {
+    expect_error(covDS("nonexistent_x", "nonexistent_y", "pairwise.complete"), regexp = "does not exist")
+})
+
+test_that("covDS throws error when object is of invalid type", {
+    bad_input <- list(a = 1:3, b = 4:6)
+    y <- c(1.0, 2.0, 3.0)
+    expect_error(covDS("bad_input", "y", "pairwise.complete"), regexp = "must be of type")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-kurtosisDS1.R b/tests/testthat/test-smk-kurtosisDS1.R
index fe939107..53d9e277 100644
--- a/tests/testthat/test-smk-kurtosisDS1.R
+++ b/tests/testthat/test-smk-kurtosisDS1.R
@@ -69,6 +69,15 @@ test_that("simple kurtosisDS1, method 3", {
     expect_equal(res$ValidityMessage, "VALID ANALYSIS")
 })
 
+test_that("kurtosisDS1 throws error when object does not exist", {
+    expect_error(kurtosisDS1("nonexistent_object", 1), regexp = "does not exist")
+})
+
+test_that("kurtosisDS1 throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(kurtosisDS1("bad_input", 1), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-kurtosisDS2.R b/tests/testthat/test-smk-kurtosisDS2.R
index 8f122a6e..f481b08f 100644
--- a/tests/testthat/test-smk-kurtosisDS2.R
+++ b/tests/testthat/test-smk-kurtosisDS2.R
@@ -40,6 +40,15 @@ test_that("simple kurtosisDS2", {
     expect_equal(res$ValidityMessage, "VALID ANALYSIS")
 })
 
+test_that("kurtosisDS2 throws error when object does not exist", {
+    expect_error(kurtosisDS2("nonexistent_object", 2.5), regexp = "does not exist")
+})
+
+test_that("kurtosisDS2 throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(kurtosisDS2("bad_input", 2.5), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-meanDS.R b/tests/testthat/test-smk-meanDS.R
index e6d81a73..707218f9 100644
--- a/tests/testthat/test-smk-meanDS.R
+++ b/tests/testthat/test-smk-meanDS.R
@@ -25,7 +25,7 @@ set.standard.disclosure.settings()
 test_that("numeric meanDS", {
     input <- c(0.0, 1.0, 2.0, 3.0, 4.0)
 
-    res <- meanDS(input)
+    res <- meanDS("input")
 
     expect_length(res, 5)
     expect_equal(class(res), "list")
@@ -45,7 +45,7 @@ test_that("numeric meanDS", {
 test_that("numeric meanDS, with NA", {
     input <- c(0.0, NA, 2.0, NA, 4.0)
 
-    res <- meanDS(input)
+    res <- meanDS("input")
 
     expect_length(res, 5)
     expect_equal(class(res), "list")
@@ -65,7 +65,7 @@ test_that("numeric meanDS, with NA", {
 test_that("numeric meanDS, with all NA", {
     input <- c(NA, NA, NA, NA, NA)
     
-    res <- meanDS(input)
+    res <- meanDS("input")
     
     expect_length(res, 5)
     expect_equal(class(res), "list")
@@ -81,6 +81,15 @@ test_that("numeric meanDS, with all NA", {
     expect_equal(res$ValidityMessage, "VALID ANALYSIS")
 })
 
+test_that("meanDS throws error when object does not exist", {
+    expect_error(meanDS("nonexistent_object"), regexp = "does not exist")
+})
+
+test_that("meanDS throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(meanDS("bad_input"), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-meanSdGpDS.R b/tests/testthat/test-smk-meanSdGpDS.R
new file mode 100644
index 00000000..44a00ee2
--- /dev/null
+++ b/tests/testthat/test-smk-meanSdGpDS.R
@@ -0,0 +1,62 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+# context("meanSdGpDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("meanSdGpDS::smk::numeric by factor")
+test_that("simple meanSdGpDS, numeric by factor", {
+    x_var <- c(1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0)
+    index_var <- as.factor(c("A", "A", "A", "A", "A", "B", "B", "B", "B", "B"))
+
+    res <- meanSdGpDS("x_var", "index_var")
+
+    expect_equal(class(res), "list")
+    expect_true(res$Table_valid)
+    expect_equal(res$Nvalid, 10)
+    expect_equal(res$Nmissing, 0)
+    expect_equal(res$Ntotal, 10)
+    expect_equal(res$Mean_gp[["A"]], 3.0)
+    expect_equal(res$Mean_gp[["B"]], 8.0)
+})
+
+test_that("meanSdGpDS throws error when X does not exist", {
+    index_var <- as.factor(c("A", "A", "B", "B"))
+    expect_error(meanSdGpDS("nonexistent_x", "index_var"), regexp = "does not exist")
+})
+
+test_that("meanSdGpDS throws error when INDEX does not exist", {
+    x_var <- c(1.0, 2.0, 3.0, 4.0)
+    expect_error(meanSdGpDS("x_var", "nonexistent_index"), regexp = "does not exist")
+})
+
+test_that("meanSdGpDS throws error when X is not numeric or integer", {
+    bad_x <- c("a", "b", "c", "d")
+    index_var <- as.factor(c("A", "A", "B", "B"))
+    expect_error(meanSdGpDS("bad_x", "index_var"), regexp = "must be of type numeric or integer")
+})
+
+#
+# Done
+#
+
+# context("meanSdGpDS::smk::shutdown")
+
+# context("meanSdGpDS::smk::done")
\ No newline at end of file
diff --git a/tests/testthat/test-smk-quantileMeanDS.R b/tests/testthat/test-smk-quantileMeanDS.R
index 33eb0c6f..f585cea3 100644
--- a/tests/testthat/test-smk-quantileMeanDS.R
+++ b/tests/testthat/test-smk-quantileMeanDS.R
@@ -23,7 +23,7 @@
 test_that("numeric quantileMeanDS", {
     input <- c(0.0, 1.0, 2.0, 3.0, 4.0)
 
-    res <- quantileMeanDS(input)
+    res <- quantileMeanDS("input")
 
     expect_length(res, 8)
     expect_equal(class(res), "numeric")
@@ -54,7 +54,7 @@ test_that("numeric quantileMeanDS", {
 test_that("numeric quantileMeanDS, with NA", {
     input <- c(0.0, NA, 2.0, NA, 4.0)
 
-    res <- quantileMeanDS(input)
+    res <- quantileMeanDS("input")
 
     expect_length(res, 8)
     expect_equal(class(res), "numeric")
@@ -81,6 +81,15 @@ test_that("numeric quantileMeanDS, with NA", {
     expect_equal(res.names[[8]], "Mean")
 })
 
+test_that("quantileMeanDS throws error when object does not exist", {
+    expect_error(quantileMeanDS("nonexistent_object"), regexp = "does not exist")
+})
+
+test_that("quantileMeanDS throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(quantileMeanDS("bad_input"), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-skewnessDS1.R b/tests/testthat/test-smk-skewnessDS1.R
index 562c3f65..48093a37 100644
--- a/tests/testthat/test-smk-skewnessDS1.R
+++ b/tests/testthat/test-smk-skewnessDS1.R
@@ -69,6 +69,15 @@ test_that("simple skewnessDS1, method 3", {
     expect_equal(res$ValidityMessage, "VALID ANALYSIS")
 })
 
+test_that("skewnessDS1 throws error when object does not exist", {
+    expect_error(skewnessDS1("nonexistent_object", 1), regexp = "does not exist")
+})
+
+test_that("skewnessDS1 throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(skewnessDS1("bad_input", 1), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-skewnessDS2.R b/tests/testthat/test-smk-skewnessDS2.R
index 9e59061d..3c32f2e8 100644
--- a/tests/testthat/test-smk-skewnessDS2.R
+++ b/tests/testthat/test-smk-skewnessDS2.R
@@ -40,6 +40,15 @@ test_that("simple skewnessDS2", {
     expect_equal(res$ValidityMessage, "VALID ANALYSIS")
 })
 
+test_that("skewnessDS2 throws error when object does not exist", {
+    expect_error(skewnessDS2("nonexistent_object", 2.5), regexp = "does not exist")
+})
+
+test_that("skewnessDS2 throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(skewnessDS2("bad_input", 2.5), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-varDS.R b/tests/testthat/test-smk-varDS.R
index 517b8d8f..b6049bb1 100644
--- a/tests/testthat/test-smk-varDS.R
+++ b/tests/testthat/test-smk-varDS.R
@@ -25,7 +25,7 @@ set.standard.disclosure.settings()
 test_that("numeric varDS", {
     input <- c(0.0, 1.0, 2.0, 3.0, 4.0)
 
-    res <- varDS(input)
+    res <- varDS("input")
 
     expect_length(res, 6)
     expect_equal(class(res), "list")
@@ -47,7 +47,7 @@ test_that("numeric varDS", {
 test_that("numeric varDS, with NA", {
     input <- c(0.0, NA, 2.0, NA, 4.0)
 
-    res <- varDS(input)
+    res <- varDS("input")
 
     expect_length(res, 6)
     expect_equal(class(res), "list")
@@ -69,7 +69,7 @@ test_that("numeric varDS, with NA", {
 test_that("numeric varDS, with all NA", {
     input <- c(NA, NA, NA, NA, NA)
     
-    res <- varDS(input)
+    res <- varDS("input")
     
     expect_length(res, 6)
     expect_equal(class(res), "list")
@@ -87,6 +87,15 @@ test_that("numeric varDS, with all NA", {
     expect_equal(res$ValidityMessage, "VALID ANALYSIS")
 })
 
+test_that("varDS throws error when object does not exist", {
+    expect_error(varDS("nonexistent_object"), regexp = "does not exist")
+})
+
+test_that("varDS throws error when object is not numeric or integer", {
+    bad_input <- c("a", "b", "c")
+    expect_error(varDS("bad_input"), regexp = "must be of type numeric or integer")
+})
+
 #
 # Done
 #

From 7870e5b2d8b9630ef608bd5b0aec544134e3930f Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Sat, 11 Apr 2026 13:20:57 +0200
Subject: [PATCH 03/12] fixed unit tests

---
 tests/testthat/test-disc-meanDS.R    | 2 +-
 tests/testthat/test-disc-varDS.R     | 2 +-
 tests/testthat/test-perf-meanDS.R    | 4 ++--
 tests/testthat/test-perf-varDS.R     | 4 ++--
 tests/testthat/test-smk-meanDS.R     | 4 ++--
 tests/testthat/test-smk-meanSdGpDS.R | 4 ++--
 tests/testthat/test-smk-varDS.R      | 8 ++++----
 7 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/tests/testthat/test-disc-meanDS.R b/tests/testthat/test-disc-meanDS.R
index 22864733..41e3d9f9 100644
--- a/tests/testthat/test-disc-meanDS.R
+++ b/tests/testthat/test-disc-meanDS.R
@@ -25,7 +25,7 @@ set.standard.disclosure.settings()
 test_that("numeric meanDS, with below nfilter.tab values", {
     input <- c(NA, NA, 2.0, NA, 4.0)
     
-    expect_error(meanDS(input), "FAILED: Nvalid less than nfilter.tab", fixed = TRUE)
+    expect_error(meanDS("input"), "FAILED: Nvalid less than nfilter.tab", fixed = TRUE)
 })
 
 #
diff --git a/tests/testthat/test-disc-varDS.R b/tests/testthat/test-disc-varDS.R
index 3b60a771..28c8983d 100644
--- a/tests/testthat/test-disc-varDS.R
+++ b/tests/testthat/test-disc-varDS.R
@@ -25,7 +25,7 @@ set.standard.disclosure.settings()
 test_that("numeric varDS, with below nfilter.tab values", {
     input <- c(NA, NA, 2.0, NA, 4.0)
 
-    expect_error(varDS(input), "FAILED: Nvalid less than nfilter.tab", fixed = TRUE)
+    expect_error(varDS("input"), "FAILED: Nvalid less than nfilter.tab", fixed = TRUE)
 })
 
 #
diff --git a/tests/testthat/test-perf-meanDS.R b/tests/testthat/test-perf-meanDS.R
index 59266cb2..648ff3d3 100644
--- a/tests/testthat/test-perf-meanDS.R
+++ b/tests/testthat/test-perf-meanDS.R
@@ -36,7 +36,7 @@ test_that("numeric meanDS - performance", {
     .current.time <- .start.time
 
     while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
-        meanDS(input)
+        meanDS("input")
 
         .count <- .count + 1
         .current.time <- Sys.time()
@@ -71,7 +71,7 @@ test_that("numeric meanDS, with NA - performance", {
     .current.time <- .start.time
 
     while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
-        meanDS(input)
+        meanDS("input")
 
         .count <- .count + 1
         .current.time <- Sys.time()
diff --git a/tests/testthat/test-perf-varDS.R b/tests/testthat/test-perf-varDS.R
index 10fff94a..7abe84f6 100644
--- a/tests/testthat/test-perf-varDS.R
+++ b/tests/testthat/test-perf-varDS.R
@@ -36,7 +36,7 @@ test_that("numeric varDS - performance", {
     .current.time <- .start.time
 
     while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
-        varDS(input)
+        varDS("input")
 
         .count <- .count + 1
         .current.time <- Sys.time()
@@ -71,7 +71,7 @@ test_that("numeric varDS, with NA - performance", {
     .current.time <- .start.time
 
     while (difftime(.current.time, .start.time, units = "secs")[[1]] < .durationSec) {
-        varDS(input)
+        varDS("input")
 
         .count <- .count + 1
         .current.time <- Sys.time()
diff --git a/tests/testthat/test-smk-meanDS.R b/tests/testthat/test-smk-meanDS.R
index 707218f9..4a11f514 100644
--- a/tests/testthat/test-smk-meanDS.R
+++ b/tests/testthat/test-smk-meanDS.R
@@ -63,8 +63,8 @@ test_that("numeric meanDS, with NA", {
 
 # context("meanDS::smk::numeric with all NA")
 test_that("numeric meanDS, with all NA", {
-    input <- c(NA, NA, NA, NA, NA)
-    
+    input <- rep(NA_real_, 5)
+
     res <- meanDS("input")
     
     expect_length(res, 5)
diff --git a/tests/testthat/test-smk-meanSdGpDS.R b/tests/testthat/test-smk-meanSdGpDS.R
index 44a00ee2..de3d4ecb 100644
--- a/tests/testthat/test-smk-meanSdGpDS.R
+++ b/tests/testthat/test-smk-meanSdGpDS.R
@@ -33,8 +33,8 @@ test_that("simple meanSdGpDS, numeric by factor", {
     expect_equal(res$Nvalid, 10)
     expect_equal(res$Nmissing, 0)
     expect_equal(res$Ntotal, 10)
-    expect_equal(res$Mean_gp[["A"]], 3.0)
-    expect_equal(res$Mean_gp[["B"]], 8.0)
+    expect_equal(as.numeric(res$Mean_gp)[1], 3.0)
+    expect_equal(as.numeric(res$Mean_gp)[2], 8.0)
 })
 
 test_that("meanSdGpDS throws error when X does not exist", {
diff --git a/tests/testthat/test-smk-varDS.R b/tests/testthat/test-smk-varDS.R
index b6049bb1..bfe5ce2e 100644
--- a/tests/testthat/test-smk-varDS.R
+++ b/tests/testthat/test-smk-varDS.R
@@ -67,13 +67,13 @@ test_that("numeric varDS, with NA", {
 
 # context("varDS::smk::numeric with all NA")
 test_that("numeric varDS, with all NA", {
-    input <- c(NA, NA, NA, NA, NA)
-    
+    input <- rep(NA_real_, 5)
+
     res <- varDS("input")
-    
+
     expect_length(res, 6)
     expect_equal(class(res), "list")
-    expect_equal(class(res$Sum), "integer")
+    expect_equal(class(res$Sum), "numeric")
     expect_equal(res$Sum, 0)
     expect_equal(class(res$SumOfSquares), "numeric")
     expect_equal(res$SumOfSquares, 0)

From 3c9432e9d20fc80ed3e8eb7213aabddd7572e952 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Sat, 11 Apr 2026 13:21:09 +0200
Subject: [PATCH 04/12] updated authorship

---
 R/corDS.R             | 1 +
 R/corTestDS.R         | 1 +
 R/covDS.R             | 1 +
 R/kurtosisDS1.R       | 1 +
 R/kurtosisDS2.R       | 1 +
 R/meanDS.R            | 1 +
 R/meanSdGpDS.R        | 1 +
 R/quantileMeanDS.R    | 1 +
 R/skewnessDS1.R       | 1 +
 R/skewnessDS2.R       | 1 +
 R/varDS.R             | 1 +
 man/corDS.Rd          | 2 ++
 man/corTestDS.Rd      | 2 ++
 man/covDS.Rd          | 2 ++
 man/kurtosisDS1.Rd    | 2 ++
 man/kurtosisDS2.Rd    | 2 ++
 man/meanDS.Rd         | 6 ++++--
 man/meanSdGpDS.Rd     | 8 +++++---
 man/quantileMeanDS.Rd | 6 ++++--
 man/skewnessDS1.Rd    | 2 ++
 man/skewnessDS2.Rd    | 2 ++
 man/varDS.Rd          | 6 ++++--
 22 files changed, 42 insertions(+), 9 deletions(-)

diff --git a/R/corDS.R b/R/corDS.R
index 0c3a84a0..dc5a3986 100644
--- a/R/corDS.R
+++ b/R/corDS.R
@@ -16,6 +16,7 @@
 #' by the 'nfilter.glm'). The second disclosure control checks that none of them is dichotomous with a
 #' level having fewer counts than the pre-specified 'nfilter.tab' threshold.
 #' @author Paul Burton, and Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 corDS <- function(x=NULL, y=NULL){
diff --git a/R/corTestDS.R b/R/corTestDS.R
index 521cbb55..0b533e5d 100644
--- a/R/corTestDS.R
+++ b/R/corTestDS.R
@@ -13,6 +13,7 @@
 #' 4 complete pairs of observations.
 #' @return the results of the correlation test.
 #' @author Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 corTestDS <- function(x, y, method, exact, conf.level){
diff --git a/R/covDS.R b/R/covDS.R
index 15e43830..90207905 100644
--- a/R/covDS.R
+++ b/R/covDS.R
@@ -23,6 +23,7 @@
 #' counts than the pre-specified 'nfilter.tab' threshold. If any of the input variables do not pass the disclosure
 #' controls then all the output values are replaced with NAs.
 #' @author Amadou Gaye, Paul Burton, and Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 covDS <- function(x=NULL, y=NULL, use=NULL){
diff --git a/R/kurtosisDS1.R b/R/kurtosisDS1.R
index 435ff6e2..d3419f65 100644
--- a/R/kurtosisDS1.R
+++ b/R/kurtosisDS1.R
@@ -9,6 +9,7 @@
 #' @return a list including the kurtosis of the input numeric variable, the number of valid observations and
 #' the study-side validity message.
 #' @author Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 kurtosisDS1 <- function (x, method){
diff --git a/R/kurtosisDS2.R b/R/kurtosisDS2.R
index 864ca5aa..791e4f52 100644
--- a/R/kurtosisDS2.R
+++ b/R/kurtosisDS2.R
@@ -13,6 +13,7 @@
 #' indicating indicating a valid analysis if the number of valid observations are above the protection filter 
 #' nfilter.tab or invalid analysis otherwise.
 #' @author Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 kurtosisDS2 <- function(x, global.mean){
diff --git a/R/meanDS.R b/R/meanDS.R
index 8e4f8998..1cfc60a2 100644
--- a/R/meanDS.R
+++ b/R/meanDS.R
@@ -6,6 +6,7 @@
 #' @param x a character string, the name of a numeric or integer vector
 #' @return a numeric, the statistical mean
 #' @author Gaye A, Burton PR
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 meanDS <- function(x){
diff --git a/R/meanSdGpDS.R b/R/meanSdGpDS.R
index 2375250e..9d9ca432 100644
--- a/R/meanSdGpDS.R
+++ b/R/meanSdGpDS.R
@@ -8,6 +8,7 @@
 #' @param index a client-side supplied character string identifying the factor across
 #' which means/SDs are to be calculated
 #' @author Burton PR
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #'
 #' @return List with results from the group statistics
 #' @export
diff --git a/R/quantileMeanDS.R b/R/quantileMeanDS.R
index 199aee81..f94e430b 100644
--- a/R/quantileMeanDS.R
+++ b/R/quantileMeanDS.R
@@ -6,6 +6,7 @@
 #' @return a numeric vector that represents the sample quantiles
 #' @export
 #' @author Burton, P.; Gaye, A.
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #'
 quantileMeanDS <- function (x) {
 
diff --git a/R/skewnessDS1.R b/R/skewnessDS1.R
index 41b5b98e..a52819df 100644
--- a/R/skewnessDS1.R
+++ b/R/skewnessDS1.R
@@ -9,6 +9,7 @@
 #' @return a list including the skewness of the input numeric variable, the number of valid observations and
 #' the study-side validity message.
 #' @author Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 skewnessDS1 <- function(x, method){
diff --git a/R/skewnessDS2.R b/R/skewnessDS2.R
index 3d7224ef..d73f1791 100644
--- a/R/skewnessDS2.R
+++ b/R/skewnessDS2.R
@@ -13,6 +13,7 @@
 #' indicating indicating a valid analysis if the number of valid observations are above the protection filter 
 #' nfilter.tab or invalid analysis otherwise.
 #' @author Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 skewnessDS2 <- function(x, global.mean){
diff --git a/R/varDS.R b/R/varDS.R
index c508ba40..0e0475b4 100644
--- a/R/varDS.R
+++ b/R/varDS.R
@@ -9,6 +9,7 @@
 #' variable, and a study message indicating whether the number of valid is less than the
 #' disclosure threshold
 #' @author Amadou Gaye, Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 varDS <- function(x){
diff --git a/man/corDS.Rd b/man/corDS.Rd
index 91e0a36d..b3b37363 100644
--- a/man/corDS.Rd
+++ b/man/corDS.Rd
@@ -32,4 +32,6 @@ variables
 }
 \author{
 Paul Burton, and Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/corTestDS.Rd b/man/corTestDS.Rd
index 83c8ecc0..28e7ab01 100644
--- a/man/corTestDS.Rd
+++ b/man/corTestDS.Rd
@@ -32,4 +32,6 @@ The function runs a two-sided correlation test
 }
 \author{
 Demetris Avraam, for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/covDS.Rd b/man/covDS.Rd
index 25b7d527..9600ce75 100644
--- a/man/covDS.Rd
+++ b/man/covDS.Rd
@@ -40,4 +40,6 @@ variables
 }
 \author{
 Amadou Gaye, Paul Burton, and Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/kurtosisDS1.Rd b/man/kurtosisDS1.Rd
index a6029a3d..34098514 100644
--- a/man/kurtosisDS1.Rd
+++ b/man/kurtosisDS1.Rd
@@ -25,4 +25,6 @@ The method is specified by the argument \code{method} in the client-side \code{d
 }
 \author{
 Demetris Avraam, for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/kurtosisDS2.Rd b/man/kurtosisDS2.Rd
index a61f16c4..9a6e1327 100644
--- a/man/kurtosisDS2.Rd
+++ b/man/kurtosisDS2.Rd
@@ -29,4 +29,6 @@ of x across all studies and the number of valid observations of the input variab
 }
 \author{
 Demetris Avraam, for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/meanDS.Rd b/man/meanDS.Rd
index 6802ad58..251d025b 100644
--- a/man/meanDS.Rd
+++ b/man/meanDS.Rd
@@ -4,10 +4,10 @@
 \alias{meanDS}
 \title{Computes statistical mean of a vector}
 \usage{
-meanDS(xvect)
+meanDS(x)
 }
 \arguments{
-\item{xvect}{a vector}
+\item{x}{a character string, the name of a numeric or integer vector}
 }
 \value{
 a numeric, the statistical mean
@@ -21,4 +21,6 @@ a missing value is returned.
 }
 \author{
 Gaye A, Burton PR
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/meanSdGpDS.Rd b/man/meanSdGpDS.Rd
index 0b7cc1d5..031fdb14 100644
--- a/man/meanSdGpDS.Rd
+++ b/man/meanSdGpDS.Rd
@@ -4,13 +4,13 @@
 \alias{meanSdGpDS}
 \title{MeanSdGpDS}
 \usage{
-meanSdGpDS(X, INDEX)
+meanSdGpDS(x, index)
 }
 \arguments{
-\item{X}{a client-side supplied character string identifying the variable for which
+\item{x}{a client-side supplied character string identifying the variable for which
 means/SDs are to be calculated}
 
-\item{INDEX}{a client-side supplied character string identifying the factor across
+\item{index}{a client-side supplied character string identifying the factor across
 which means/SDs are to be calculated}
 }
 \value{
@@ -25,4 +25,6 @@ factor
 }
 \author{
 Burton PR
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/quantileMeanDS.Rd b/man/quantileMeanDS.Rd
index 5781685d..1f453984 100644
--- a/man/quantileMeanDS.Rd
+++ b/man/quantileMeanDS.Rd
@@ -4,10 +4,10 @@
 \alias{quantileMeanDS}
 \title{Generates quantiles and mean information without maximum and minimum}
 \usage{
-quantileMeanDS(xvect)
+quantileMeanDS(x)
 }
 \arguments{
-\item{xvect}{a numerical vector}
+\item{x}{a character string, the name of a numeric or integer vector}
 }
 \value{
 a numeric vector that represents the sample quantiles
@@ -18,4 +18,6 @@ are used to compute the corresponding quantiles.
 }
 \author{
 Burton, P.; Gaye, A.
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/skewnessDS1.Rd b/man/skewnessDS1.Rd
index 76f48fc0..fe2921d7 100644
--- a/man/skewnessDS1.Rd
+++ b/man/skewnessDS1.Rd
@@ -25,4 +25,6 @@ The method is specified by the argument \code{method} in the client-side \code{d
 }
 \author{
 Demetris Avraam, for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/skewnessDS2.Rd b/man/skewnessDS2.Rd
index 4537f001..12646548 100644
--- a/man/skewnessDS2.Rd
+++ b/man/skewnessDS2.Rd
@@ -29,4 +29,6 @@ of x across all studies and the number of valid observations of the input variab
 }
 \author{
 Demetris Avraam, for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/varDS.Rd b/man/varDS.Rd
index 1c485c9b..78c9b05c 100644
--- a/man/varDS.Rd
+++ b/man/varDS.Rd
@@ -4,10 +4,10 @@
 \alias{varDS}
 \title{Computes the variance of vector}
 \usage{
-varDS(xvect)
+varDS(x)
 }
 \arguments{
-\item{xvect}{a vector}
+\item{x}{a character string, the name of a numeric or integer vector}
 }
 \value{
 a list, with the sum of the input variable, the sum of squares of the input variable,
@@ -24,4 +24,6 @@ a missing value is returned.
 }
 \author{
 Amadou Gaye, Demetris Avraam, for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }

From 8c44d302457d17175b4f92f1521f87f39a3d79a5 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 12:50:17 +0200
Subject: [PATCH 05/12] refactor: return class for consistency checking, remove
 ValidityMessage

---
 R/corTestDS.R      |  6 +++---
 R/kurtosisDS1.R    |  7 ++-----
 R/kurtosisDS2.R    | 15 ++++++---------
 R/quantileMeanDS.R |  6 +++---
 R/skewnessDS1.R    |  5 +----
 R/skewnessDS2.R    | 16 ++++++----------
 6 files changed, 21 insertions(+), 34 deletions(-)

diff --git a/R/corTestDS.R b/R/corTestDS.R
index 0b533e5d..547484c8 100644
--- a/R/corTestDS.R
+++ b/R/corTestDS.R
@@ -29,9 +29,9 @@ corTestDS <- function(x, y, method, exact, conf.level){
   # runs a two-sided correlation test
   corTest <- stats::cor.test(x=x.var, y=y.var, method=method, exact=exact, conf.level=conf.level)
 
-  out <- list(n, corTest)
-  names(out) <- c("Number of pairwise complete cases", "Correlation test")
-  
+  out <- list(n, corTest, class = class(x.var))
+  names(out)[1:2] <- c("Number of pairwise complete cases", "Correlation test")
+
   # return the results
   return(out)
 
diff --git a/R/kurtosisDS1.R b/R/kurtosisDS1.R
index d3419f65..9789ae68 100644
--- a/R/kurtosisDS1.R
+++ b/R/kurtosisDS1.R
@@ -34,19 +34,16 @@ kurtosisDS1 <- function (x, method){
     
     if(method==1){
       kurtosis.out <- g2
-      studysideMessage <- "VALID ANALYSIS"
     }
     if(method==2){
       kurtosis.out <- ((length(x) + 1) * g2 + 6) * (length(x) - 1)/((length(x) - 2) * (length(x) - 3))
-      studysideMessage <- "VALID ANALYSIS"
     }
     if(method==3){
       kurtosis.out <- (g2 + 3) * (1 - 1/length(x))^2 - 3
-      studysideMessage <- "VALID ANALYSIS"
     }
   }
-  
-  out.obj <- list(Kurtosis=kurtosis.out, Nvalid=length(x), ValidityMessage=studysideMessage)
+
+  out.obj <- list(Kurtosis=kurtosis.out, Nvalid=length(x), class=class(x.val))
   return(out.obj)
   
 }
diff --git a/R/kurtosisDS2.R b/R/kurtosisDS2.R
index 791e4f52..392641ed 100644
--- a/R/kurtosisDS2.R
+++ b/R/kurtosisDS2.R
@@ -29,16 +29,13 @@ kurtosisDS2 <- function(x, global.mean){
   x <- x.val[stats::complete.cases(x.val)]
   
   if(length(x) < nfilter.tab){
-    sum_quartics.out <- NA
-    sum_squares.out <- NA
-    studysideMessage <- "FAILED: Nvalid less than nfilter.tab"
-  }else{
-    sum_quartics.out <- sum((x - global.mean)^4)
-    sum_squares.out <- sum((x - global.mean)^2)
-    studysideMessage <- "VALID ANALYSIS"
+    stop("FAILED: Nvalid less than nfilter.tab", call. = FALSE)
   }
-  
-  out.obj <- list(Sum.quartics=sum_quartics.out, Sum.squares=sum_squares.out, Nvalid=length(x), ValidityMessage=studysideMessage)
+
+  sum_quartics.out <- sum((x - global.mean)^4)
+  sum_squares.out <- sum((x - global.mean)^2)
+
+  out.obj <- list(Sum.quartics=sum_quartics.out, Sum.squares=sum_squares.out, Nvalid=length(x), class=class(x.val))
   return(out.obj)
   
 }
diff --git a/R/quantileMeanDS.R b/R/quantileMeanDS.R
index f94e430b..26772caf 100644
--- a/R/quantileMeanDS.R
+++ b/R/quantileMeanDS.R
@@ -21,10 +21,10 @@ quantileMeanDS <- function (x) {
     qq <- stats::quantile(xvect,c(0.05,0.1,0.25,0.5,0.75,0.9,0.95), na.rm=TRUE)
     mm <- mean(xvect,na.rm=TRUE)
     quantile.obj <- c(qq, mm)
-    names(quantile.obj) <- c("5%","10%","25%","50%","75%","90%","95%","Mean")    
+    names(quantile.obj) <- c("5%","10%","25%","50%","75%","90%","95%","Mean")
   }else{
     quantile.obj <- NA
   }
-  
-  return(quantile.obj)
+
+  return(list(quantiles = quantile.obj, class = class(xvect)))
 }
diff --git a/R/skewnessDS1.R b/R/skewnessDS1.R
index a52819df..59e13745 100644
--- a/R/skewnessDS1.R
+++ b/R/skewnessDS1.R
@@ -34,19 +34,16 @@ skewnessDS1 <- function(x, method){
     
     if(method==1){
       skewness.out <- g1
-      studysideMessage <- "VALID ANALYSIS"
     }
     if(method==2){
       skewness.out <- g1 * sqrt(length(x)*(length(x)-1))/(length(x)-2)
-      studysideMessage <- "VALID ANALYSIS"
     }
     if(method==3){
       skewness.out <- g1 * ((length(x)-1)/(length(x)))^(3/2)
-      studysideMessage <- "VALID ANALYSIS"
     }
   }
 
-  out.obj <- list(Skewness=skewness.out, Nvalid=length(x), ValidityMessage=studysideMessage)
+  out.obj <- list(Skewness=skewness.out, Nvalid=length(x), class=class(x.val))
   return(out.obj)
   
 }
diff --git a/R/skewnessDS2.R b/R/skewnessDS2.R
index d73f1791..dc58ae6c 100644
--- a/R/skewnessDS2.R
+++ b/R/skewnessDS2.R
@@ -29,17 +29,13 @@ skewnessDS2 <- function(x, global.mean){
   x <- x.val[stats::complete.cases(x.val)]
   
   if(length(x) < nfilter.tab){
-    sum_cubes.out <- NA
-    sum_squares.out <- NA
-    studysideMessage <- "FAILED: Nvalid less than nfilter.tab"
-    stop(studysideMessage, call. = FALSE)
-  }else{
-    sum_cubes.out <- sum((x - global.mean)^3)
-    sum_squares.out <- sum((x - global.mean)^2)
-    studysideMessage <- "VALID ANALYSIS"
+    stop("FAILED: Nvalid less than nfilter.tab", call. = FALSE)
   }
-  
-  out.obj <- list(Sum.cubes=sum_cubes.out, Sum.squares=sum_squares.out, Nvalid=length(x), ValidityMessage=studysideMessage)
+
+  sum_cubes.out <- sum((x - global.mean)^3)
+  sum_squares.out <- sum((x - global.mean)^2)
+
+  out.obj <- list(Sum.cubes=sum_cubes.out, Sum.squares=sum_squares.out, Nvalid=length(x), class=class(x.val))
   return(out.obj)
   
 }

From cabc097f99f41d2ff1d19df18bc278febb686adf Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 12:50:28 +0200
Subject: [PATCH 06/12] chore: set privacy level to permissive, fix expDS
 authorship

---
 R/expDS.R       | 2 +-
 inst/DATASHIELD | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/expDS.R b/R/expDS.R
index 3c6b53c3..2ba9e5bb 100644
--- a/R/expDS.R
+++ b/R/expDS.R
@@ -15,7 +15,7 @@ expDS <- function(x) {
   x.var <- .loadServersideObject(x)
   .checkClass(obj = x.var, obj_name = x, permitted_classes = c("numeric", "integer"))
 
-  out <- exp(x.var)
+out <- exp(x.var)
   return(out)
 }
 # ASSIGN FUNCTION
diff --git a/inst/DATASHIELD b/inst/DATASHIELD
index 8753f19d..abcabf73 100644
--- a/inst/DATASHIELD
+++ b/inst/DATASHIELD
@@ -163,7 +163,7 @@ AssignMethods:
     unlist=base::unlist
 Options:
     datashield.privacyLevel=5,
-    default.datashield.privacyControlLevel="banana",
+    default.datashield.privacyControlLevel="permissive",
     default.nfilter.glm=0.33,
     default.nfilter.kNN=3,
     default.nfilter.string=80,

From f8fffa2d2db34e1556d14d708143078e7d336c88 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 14:10:08 +0200
Subject: [PATCH 07/12] refactor: return class for consistency checking, remove
 ValidityMessage

---
 R/meanDS.R     |  5 +----
 R/meanSdGpDS.R | 10 ++++++----
 R/varDS.R      |  9 ++-------
 3 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/R/meanDS.R b/R/meanDS.R
index 1cfc60a2..4fc3269c 100644
--- a/R/meanDS.R
+++ b/R/meanDS.R
@@ -27,14 +27,11 @@ meanDS <- function(x){
   out.numNa <- length(which(is.na(xvect)))
   out.totN <- length(xvect)
   out.validN <- out.totN-out.numNa
-  studysideMessage <- "VALID ANALYSIS"
-
   if((out.validN != 0) && (out.validN < nfilter.tab)){
-    out.mean <- NA
     stop("FAILED: Nvalid less than nfilter.tab", call. = FALSE)
   }
 
-  out.obj <- list(EstimatedMean=out.mean,Nmissing=out.numNa,Nvalid=out.validN,Ntotal=out.totN,ValidityMessage=studysideMessage)
+  out.obj <- list(EstimatedMean=out.mean,Nmissing=out.numNa,Nvalid=out.validN,Ntotal=out.totN,class=class(xvect))
   return(out.obj)
 
 }
diff --git a/R/meanSdGpDS.R b/R/meanSdGpDS.R
index 9d9ca432..eecf0dde 100644
--- a/R/meanSdGpDS.R
+++ b/R/meanSdGpDS.R
@@ -28,6 +28,8 @@ meanSdGpDS <- function (x, index){
   .checkClass(obj = X, obj_name = x, permitted_classes = c("numeric", "integer"))
   INDEX <- .loadServersideObject(index)
   .checkClass(obj = INDEX, obj_name = index, permitted_classes = c("factor", "character", "integer"))
+  x.class <- class(X)
+  index.class <- class(INDEX)
 
   FUN.mean <- function(x) {mean(x,na.rm=TRUE)}
   FUN.var <- function(x)  {stats::var(x,na.rm=TRUE)}
@@ -120,8 +122,8 @@ meanSdGpDS <- function (x, index){
   {
     table.valid<-TRUE
     cell.count.warning<-paste0("All tables valid") 
-    result<-list(table.valid,ansmat.mean,ansmat.sd,ansmat.count,Nvalid,Nmissing,Ntotal,cell.count.warning)
-    names(result)<-list("Table_valid","Mean_gp","StDev_gp", "N_gp","Nvalid","Nmissing","Ntotal","Message")
+    result<-list(table.valid,ansmat.mean,ansmat.sd,ansmat.count,Nvalid,Nmissing,Ntotal,cell.count.warning,x.class,index.class)
+    names(result)<-list("Table_valid","Mean_gp","StDev_gp", "N_gp","Nvalid","Nmissing","Ntotal","Message","class.x","class.index")
     return(result)
   }
   
@@ -129,8 +131,8 @@ meanSdGpDS <- function (x, index){
   {
     table.valid<-FALSE
     cell.count.warning<-paste0("At least one group has between 1 and ", nfilter.tab-1, " observations. Please change groups") 
-    result<-list(table.valid,Nvalid,Nmissing,Ntotal,cell.count.warning)
-    names(result)<-list("Table_valid","Nvalid","Nmissing","Ntotal","Warning")
+    result<-list(table.valid,Nvalid,Nmissing,Ntotal,cell.count.warning,x.class,index.class)
+    names(result)<-list("Table_valid","Nvalid","Nmissing","Ntotal","Warning","class.x","class.index")
     return(result)
   }
   
diff --git a/R/varDS.R b/R/varDS.R
index 0e0475b4..75a21c17 100644
--- a/R/varDS.R
+++ b/R/varDS.R
@@ -31,16 +31,11 @@ varDS <- function(x){
   out.numNa <- length(which(is.na(xvect)))
   out.totN <- length(xvect)
   out.validN <- out.totN-out.numNa
-  studysideMessage <- "VALID ANALYSIS"
-
   if((out.validN != 0) && (out.validN < nfilter.tab)){
-    out.sum <- NA
-    out.sumSquares <- NA
-    studysideMessage <- "FAILED: Nvalid less than nfilter.tab"
-    stop(studysideMessage, call. = FALSE)
+    stop("FAILED: Nvalid less than nfilter.tab", call. = FALSE)
   }
 
-  out.obj <- list(Sum=out.sum,SumOfSquares=out.sumSquares,Nmissing=out.numNa,Nvalid=out.validN,Ntotal=out.totN,ValidityMessage=studysideMessage)
+  out.obj <- list(Sum=out.sum,SumOfSquares=out.sumSquares,Nmissing=out.numNa,Nvalid=out.validN,Ntotal=out.totN,class=class(xvect))
   return(out.obj)
 
 }

From e81a81b3a34634f1360e51ea5c4b83a14960fe7d Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 14:58:01 +0200
Subject: [PATCH 08/12] fix: return class from corDS and covDS for consistency
 checking

---
 R/corDS.R | 2 +-
 R/covDS.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/corDS.R b/R/corDS.R
index dc5a3986..fde5ad3d 100644
--- a/R/corDS.R
+++ b/R/corDS.R
@@ -169,7 +169,7 @@ corDS <- function(x=NULL, y=NULL){
     
   }
   
-  return(list(sums.of.products=sums.of.products, sums=sums, complete.counts=complete.counts, na.counts=na.counts, sums.of.squares=sums.of.squares))
+  return(list(sums.of.products=sums.of.products, sums=sums, complete.counts=complete.counts, na.counts=na.counts, sums.of.squares=sums.of.squares, class=class(x.val)))
   
 }
 # AGGREGATE FUNCTION
diff --git a/R/covDS.R b/R/covDS.R
index 90207905..b15b4a5a 100644
--- a/R/covDS.R
+++ b/R/covDS.R
@@ -302,7 +302,7 @@ covDS <- function(x=NULL, y=NULL, use=NULL){
   
   }
 
-  return(list(sums.of.products=sums.of.products, sums=sums, complete.counts=complete.counts, na.counts=na.counts, errorMessage=errorMessage))
+  return(list(sums.of.products=sums.of.products, sums=sums, complete.counts=complete.counts, na.counts=na.counts, errorMessage=errorMessage, class=class(x.val)))
 
 }
 # AGGREGATE FUNCTION

From 05f68e6aeeac06487d73d073faf4da4d490dd646 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 14:18:33 +0200
Subject: [PATCH 09/12] test: fixed test expectations

---
 tests/testthat/test-smk-cDS.R            | 16 +++----
 tests/testthat/test-smk-corDS.R          |  8 ++--
 tests/testthat/test-smk-corTestDS.R      | 24 +++++-----
 tests/testthat/test-smk-covDS.R          |  4 +-
 tests/testthat/test-smk-kurtosisDS1.R    |  9 ++--
 tests/testthat/test-smk-kurtosisDS2.R    |  3 +-
 tests/testthat/test-smk-listDS.R         |  5 +-
 tests/testthat/test-smk-meanDS.R         |  9 ++--
 tests/testthat/test-smk-quantileMeanDS.R | 58 ++++++++++++++----------
 tests/testthat/test-smk-skewnessDS1.R    |  9 ++--
 tests/testthat/test-smk-skewnessDS2.R    |  3 +-
 tests/testthat/test-smk-varDS.R          |  9 ++--
 12 files changed, 76 insertions(+), 81 deletions(-)

diff --git a/tests/testthat/test-smk-cDS.R b/tests/testthat/test-smk-cDS.R
index 0f9842fc..518d9ac5 100644
--- a/tests/testthat/test-smk-cDS.R
+++ b/tests/testthat/test-smk-cDS.R
@@ -23,9 +23,9 @@ set.standard.disclosure.settings()
 
 # context("cDS::smk::numeric list")
 test_that("numeric list cDS", {
-    input <- list(a=0.0, b=1.0, c=2.0, d=3.0)
+    a <- 0.0; b <- 1.0; c <- 2.0; d <- 3.0
 
-    res <- cDS(input)
+    res <- cDS(c("a", "b", "c", "d"))
 
     expect_length(res, 4)
     expect_equal(class(res), "numeric")
@@ -37,9 +37,9 @@ test_that("numeric list cDS", {
 
 # context("cDS::smk::character list")
 test_that("character list cDS", {
-    input <- list(a="0.0", b="1.0", c="2.0", d="3.0")
+    a <- "0.0"; b <- "1.0"; c <- "2.0"; d <- "3.0"
 
-    res <- cDS(input)
+    res <- cDS(c("a", "b", "c", "d"))
 
     expect_length(res, 4)
     expect_equal(class(res), "character")
@@ -51,9 +51,9 @@ test_that("character list cDS", {
 
 # context("cDS::smk::numeric list small")
 test_that("single numeric list small cDS", {
-    input <- list(a=0, b=1)
+    a <- 0; b <- 1
 
-    res <- cDS(input)
+    res <- cDS(c("a", "b"))
 
     expect_length(res, 2)
     expect_equal(class(res), "logical")
@@ -63,9 +63,7 @@ test_that("single numeric list small cDS", {
 
 # context("cDS::smk::empty list")
 test_that("empty list cDS", {
-    input <- list()
-
-    res <- cDS(input)
+    res <- cDS(character(0))
 
     expect_length(res, 0)
     expect_equal(class(res), "NULL")
diff --git a/tests/testthat/test-smk-corDS.R b/tests/testthat/test-smk-corDS.R
index 034a4b00..e86b6e2c 100644
--- a/tests/testthat/test-smk-corDS.R
+++ b/tests/testthat/test-smk-corDS.R
@@ -378,7 +378,7 @@ test_that("simple corDS, casewise, full", {
     res <- corDS("x", "y")
 
     expect_equal(class(res), "list")
-    expect_length(res, 5)
+    expect_length(res, 6)
 
     if (base::getRversion() < '4.0.0')
     {
@@ -465,7 +465,7 @@ test_that("simple corDS, casewise, neg. full", {
     res <- corDS("x", "y")
 
     expect_equal(class(res), "list")
-    expect_length(res, 5)
+    expect_length(res, 6)
 
     if (base::getRversion() < '4.0.0')
     {
@@ -552,7 +552,7 @@ test_that("simple corDS, casewise, some", {
     res <- corDS("x", "y")
 
     expect_equal(class(res), "list")
-    expect_length(res, 5)
+    expect_length(res, 6)
 
     if (base::getRversion() < '4.0.0')
     {
@@ -640,7 +640,7 @@ test_that("simple corDS, casewise, some", {
     res <- corDS("x", "y")
 
     expect_equal(class(res), "list")
-    expect_length(res, 5)
+    expect_length(res, 6)
 
     if (base::getRversion() < '4.0.0')
     {
diff --git a/tests/testthat/test-smk-corTestDS.R b/tests/testthat/test-smk-corTestDS.R
index 2dbee274..cb54b62f 100644
--- a/tests/testthat/test-smk-corTestDS.R
+++ b/tests/testthat/test-smk-corTestDS.R
@@ -29,7 +29,7 @@ test_that("simple corTestDS, full, without na, pearson", {
     res <- corTestDS("x", "y", "pearson", NULL, 0.95)
 
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
 
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -82,7 +82,7 @@ test_that("simple corTestDS, neg. full, without na, pearson", {
     res <- corTestDS("x", "y", "pearson", NULL, 0.95)
 
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -135,7 +135,7 @@ test_that("simple corTestDS, some, pearson, without na, pearson", {
     res <- corTestDS("x", "y", "pearson", NULL, 0.95)
 
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -189,7 +189,7 @@ test_that("simple corTestDS, some, with na, pearson", {
     res <- corTestDS("x", "y", "pearson", NULL, 0.95)
 
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 3)
@@ -238,7 +238,7 @@ test_that("simple corTestDS, full, without na, kendall", {
     res <- corTestDS("x", "y", "kendall", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -284,7 +284,7 @@ test_that("simple corTestDS, neg. full, without na, kendall", {
     res <- corTestDS("x", "y", "kendall", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -330,7 +330,7 @@ test_that("simple corTestDS, some, kendall, without na, kendall", {
     res <- corTestDS("x", "y", "kendall", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -377,7 +377,7 @@ test_that("simple corTestDS, some, with na, kendall", {
     res <- corTestDS("x", "y", "kendall", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 3)
@@ -424,7 +424,7 @@ test_that("simple corTestDS, full, without na, spearman", {
     res <- corTestDS("x", "y", "spearman", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -470,7 +470,7 @@ test_that("simple corTestDS, neg. full, without na, spearman", {
     res <- corTestDS("x", "y", "spearman", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -516,7 +516,7 @@ test_that("simple corTestDS, some, spearman, without na, spearman", {
     res <- corTestDS("x", "y", "spearman", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 8)
@@ -563,7 +563,7 @@ test_that("simple corTestDS, some, with na, spearman", {
     res <- corTestDS("x", "y", "spearman", NULL, 0.95)
     
     expect_equal(class(res), "list")
-    expect_length(res, 2)
+    expect_length(res, 3)
     
     expect_length(res$`Number of pairwise complete cases`, 1)
     expect_equal(res$`Number of pairwise complete cases`, 3)
diff --git a/tests/testthat/test-smk-covDS.R b/tests/testthat/test-smk-covDS.R
index 64710a72..24352ac7 100644
--- a/tests/testthat/test-smk-covDS.R
+++ b/tests/testthat/test-smk-covDS.R
@@ -27,7 +27,7 @@ test_that("numeric covDS, casewise.complete", {
 
     res <- covDS("input$v1", "input$v2", "casewise.complete")
 
-    expect_length(res, 5)
+    expect_length(res, 6)
     expect_equal(class(res), "list")
 
     res.sums.of.products.class <- class(res$sums.of.products)
@@ -130,7 +130,7 @@ test_that("numeric covDS, pairwise.complete", {
 
     res <- covDS("input$v1", "input$v2", "pairwise.complete")
 
-    expect_length(res, 5)
+    expect_length(res, 6)
     expect_equal(class(res), "list")
 
     res.sums.of.products.class <- class(res$sums.of.products)
diff --git a/tests/testthat/test-smk-kurtosisDS1.R b/tests/testthat/test-smk-kurtosisDS1.R
index 53d9e277..3a13786d 100644
--- a/tests/testthat/test-smk-kurtosisDS1.R
+++ b/tests/testthat/test-smk-kurtosisDS1.R
@@ -33,8 +33,7 @@ test_that("simple kurtosisDS1, method 1", {
     expect_equal(res$Kurtosis, -0.458210, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid,9)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("kurtosisDS1::smk::method 2")
@@ -49,8 +48,7 @@ test_that("simple kurtosisDS1, method 2", {
     expect_equal(res$Kurtosis, 0.270076, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid,9)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("kurtosisDS1::smk::method 3")
@@ -65,8 +63,7 @@ test_that("simple kurtosisDS1, method 3", {
     expect_equal(res$Kurtosis, -0.991672, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid,9)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 test_that("kurtosisDS1 throws error when object does not exist", {
diff --git a/tests/testthat/test-smk-kurtosisDS2.R b/tests/testthat/test-smk-kurtosisDS2.R
index f481b08f..69a735a6 100644
--- a/tests/testthat/test-smk-kurtosisDS2.R
+++ b/tests/testthat/test-smk-kurtosisDS2.R
@@ -36,8 +36,7 @@ test_that("simple kurtosisDS2", {
     expect_equal(res$Sum.squares, 3.25, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 test_that("kurtosisDS2 throws error when object does not exist", {
diff --git a/tests/testthat/test-smk-listDS.R b/tests/testthat/test-smk-listDS.R
index dfd0a171..51e75550 100644
--- a/tests/testthat/test-smk-listDS.R
+++ b/tests/testthat/test-smk-listDS.R
@@ -21,10 +21,11 @@
 
 # context("listDS::smk::simple")
 test_that("simple listDS", {
-    input    <- list(v1 = c(1, 2, 3), v2 = c(4, 5, 6))
+    v1 <- c(1, 2, 3)
+    v2 <- c(4, 5, 6)
     eltnames <- c('n1', 'n2')
 
-    res <- listDS(input, eltnames)
+    res <- listDS(c("v1", "v2"), eltnames)
 
     expect_equal(class(res), "list")
     expect_length(res, 2)
diff --git a/tests/testthat/test-smk-meanDS.R b/tests/testthat/test-smk-meanDS.R
index 4a11f514..8bb47c69 100644
--- a/tests/testthat/test-smk-meanDS.R
+++ b/tests/testthat/test-smk-meanDS.R
@@ -37,8 +37,7 @@ test_that("numeric meanDS", {
     expect_equal(res$Nvalid, 5)
     expect_equal(class(res$Ntotal), "integer")
     expect_equal(res$Ntotal, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("meanDS::smk::numeric with NA")
@@ -57,8 +56,7 @@ test_that("numeric meanDS, with NA", {
     expect_equal(res$Nvalid, 3)
     expect_equal(class(res$Ntotal), "integer")
     expect_equal(res$Ntotal, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("meanDS::smk::numeric with all NA")
@@ -77,8 +75,7 @@ test_that("numeric meanDS, with all NA", {
     expect_equal(res$Nvalid, 0)
     expect_equal(class(res$Ntotal), "integer")
     expect_equal(res$Ntotal, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 test_that("meanDS throws error when object does not exist", {
diff --git a/tests/testthat/test-smk-quantileMeanDS.R b/tests/testthat/test-smk-quantileMeanDS.R
index f585cea3..d305c8de 100644
--- a/tests/testthat/test-smk-quantileMeanDS.R
+++ b/tests/testthat/test-smk-quantileMeanDS.R
@@ -25,18 +25,23 @@ test_that("numeric quantileMeanDS", {
 
     res <- quantileMeanDS("input")
 
-    expect_length(res, 8)
-    expect_equal(class(res), "numeric")
-    expect_equal(res[[1]], 0.2)
-    expect_equal(res[[2]], 0.4)
-    expect_equal(res[[3]], 1.0)
-    expect_equal(res[[4]], 2.0)
-    expect_equal(res[[5]], 3.0)
-    expect_equal(res[[6]], 3.6)
-    expect_equal(res[[7]], 3.8)
-    expect_equal(res[[8]], 2.0)
-
-    res.names <- names(res)
+    expect_equal(class(res), "list")
+    expect_equal(res$class, "numeric")
+
+    qq <- res$quantiles
+
+    expect_length(qq, 8)
+    expect_equal(class(qq), "numeric")
+    expect_equal(qq[[1]], 0.2)
+    expect_equal(qq[[2]], 0.4)
+    expect_equal(qq[[3]], 1.0)
+    expect_equal(qq[[4]], 2.0)
+    expect_equal(qq[[5]], 3.0)
+    expect_equal(qq[[6]], 3.6)
+    expect_equal(qq[[7]], 3.8)
+    expect_equal(qq[[8]], 2.0)
+
+    res.names <- names(qq)
 
     expect_length(res.names, 8)
     expect_equal(class(res.names), "character")
@@ -56,18 +61,23 @@ test_that("numeric quantileMeanDS, with NA", {
 
     res <- quantileMeanDS("input")
 
-    expect_length(res, 8)
-    expect_equal(class(res), "numeric")
-    expect_equal(res[[1]], 0.2)
-    expect_equal(res[[2]], 0.4)
-    expect_equal(res[[3]], 1.0)
-    expect_equal(res[[4]], 2.0)
-    expect_equal(res[[5]], 3.0)
-    expect_equal(res[[6]], 3.6)
-    expect_equal(res[[7]], 3.8)
-    expect_equal(res[[8]], 2.0)
-
-    res.names <- names(res)
+    expect_equal(class(res), "list")
+    expect_equal(res$class, "numeric")
+
+    qq <- res$quantiles
+
+    expect_length(qq, 8)
+    expect_equal(class(qq), "numeric")
+    expect_equal(qq[[1]], 0.2)
+    expect_equal(qq[[2]], 0.4)
+    expect_equal(qq[[3]], 1.0)
+    expect_equal(qq[[4]], 2.0)
+    expect_equal(qq[[5]], 3.0)
+    expect_equal(qq[[6]], 3.6)
+    expect_equal(qq[[7]], 3.8)
+    expect_equal(qq[[8]], 2.0)
+
+    res.names <- names(qq)
 
     expect_length(res.names, 8)
     expect_equal(class(res.names), "character")
diff --git a/tests/testthat/test-smk-skewnessDS1.R b/tests/testthat/test-smk-skewnessDS1.R
index 48093a37..f5d3357b 100644
--- a/tests/testthat/test-smk-skewnessDS1.R
+++ b/tests/testthat/test-smk-skewnessDS1.R
@@ -33,8 +33,7 @@ test_that("simple skewnessDS1, method 1", {
     expect_equal(res$Skewness, 0.443147, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid,9)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("skewnessDS1::smk::method 2")
@@ -49,8 +48,7 @@ test_that("simple skewnessDS1, method 2", {
     expect_equal(res$Skewness, 0.537175, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid,9)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("skewnessDS1::smk::method 3")
@@ -65,8 +63,7 @@ test_that("simple skewnessDS1, method 3", {
     expect_equal(res$Skewness, 0.3713805, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid,9)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 test_that("skewnessDS1 throws error when object does not exist", {
diff --git a/tests/testthat/test-smk-skewnessDS2.R b/tests/testthat/test-smk-skewnessDS2.R
index 3c32f2e8..9e2ccea4 100644
--- a/tests/testthat/test-smk-skewnessDS2.R
+++ b/tests/testthat/test-smk-skewnessDS2.R
@@ -36,8 +36,7 @@ test_that("simple skewnessDS2", {
     expect_equal(res$Sum.squares, 3.25, tolerance = 1e-6)
     expect_equal(class(res$Nvalid), "integer")
     expect_equal(res$Nvalid, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 test_that("skewnessDS2 throws error when object does not exist", {
diff --git a/tests/testthat/test-smk-varDS.R b/tests/testthat/test-smk-varDS.R
index bfe5ce2e..51eac8e2 100644
--- a/tests/testthat/test-smk-varDS.R
+++ b/tests/testthat/test-smk-varDS.R
@@ -39,8 +39,7 @@ test_that("numeric varDS", {
     expect_equal(res$Nvalid, 5)
     expect_equal(class(res$Ntotal), "integer")
     expect_equal(res$Ntotal, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("varDS::smk::numeric with NA")
@@ -61,8 +60,7 @@ test_that("numeric varDS, with NA", {
     expect_equal(res$Nvalid, 3)
     expect_equal(class(res$Ntotal), "integer")
     expect_equal(res$Ntotal, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 # context("varDS::smk::numeric with all NA")
@@ -83,8 +81,7 @@ test_that("numeric varDS, with all NA", {
     expect_equal(res$Nvalid, 0)
     expect_equal(class(res$Ntotal), "integer")
     expect_equal(res$Ntotal, 5)
-    expect_equal(class(res$ValidityMessage), "character")
-    expect_equal(res$ValidityMessage, "VALID ANALYSIS")
+    expect_equal(res$class, "numeric")
 })
 
 test_that("varDS throws error when object does not exist", {

From b8ba4805513de5d1aa590422687479e56bcdf87e Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 14:19:15 +0200
Subject: [PATCH 10/12] docs: updated docs with authorship and parameters

---
 R/cDS.R       | 22 ++++++++++++----------
 R/lengthDS.R  |  1 +
 R/listDS.R    | 18 +++++++++++-------
 man/cDS.Rd    |  6 ++++--
 man/listDS.Rd |  8 +++++---
 5 files changed, 33 insertions(+), 22 deletions(-)

diff --git a/R/cDS.R b/R/cDS.R
index 0b5b96ba..dbc224b6 100644
--- a/R/cDS.R
+++ b/R/cDS.R
@@ -3,27 +3,29 @@
 #' @description This function is similar to the R base function 'c'.
 #' @details Unlike the R base function 'c' on vector or list of certain 
 #' length are allowed as output
-#' @param objs a list which contains the the objects to concatenate.
+#' @param x.names a character vector of object names to concatenate.
 #' @return a vector or list
 #' @author Gaye, A.
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#' 
-cDS <- function (objs) {
-  
+#'
+cDS <- function (x.names) {
+
   # Check Permissive Privacy Control Level.
   dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'avocado'))
-  
-  # this filter sets the minimum number of observations that are allowed 
+
+  # this filter sets the minimum number of observations that are allowed
 
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
   thr <- dsBase::listDisclosureSettingsDS()
   nfilter.tab <- as.numeric(thr$nfilter.tab)
-  #nfilter.glm <- as.numeric(thr$nfilter.glm)
-  #nfilter.subset <- as.numeric(thr$nfilter.subset)
-  #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
-  
+
+  objs <- list()
+  for (i in seq_along(x.names)) {
+    objs[[i]] <- .loadServersideObject(x.names[i])
+  }
   x <-  unlist(objs)
 
   # check if the output is valid and output accordingly
diff --git a/R/lengthDS.R b/R/lengthDS.R
index 1c793aa0..7975d7f8 100644
--- a/R/lengthDS.R
+++ b/R/lengthDS.R
@@ -1,3 +1,4 @@
+
 #'
 #' @title Returns the length of a vector or list
 #' @description This function is similar to R function \code{length}.
diff --git a/R/listDS.R b/R/listDS.R
index 162ae8b5..88706176 100644
--- a/R/listDS.R
+++ b/R/listDS.R
@@ -3,17 +3,21 @@
 #' @description this function is similar to R function 'list'
 #' @details Unlike the R function 'list' it takes also a vector of characters,
 #' the names of the elements in the output list.
-#' @param input a list of objects to coerce into a list
-#' @param eltnames a character list, the names of the elements in the list.
+#' @param x.names a character vector of object names to coerce into a list.
+#' @param eltnames a character vector, the names of the elements in the list.
 #' @return a list
 #' @author Gaye, A.
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#' 
-listDS <-function (input=NULL, eltnames=NULL){
-  
-  mylist <- input
+#'
+listDS <-function (x.names=NULL, eltnames=NULL){
+
+  mylist <- list()
+  for (i in seq_along(x.names)) {
+    mylist[[i]] <- .loadServersideObject(x.names[i])
+  }
   names(mylist) <- unlist(eltnames)
 
   return(mylist)
-  
+
 }
\ No newline at end of file
diff --git a/man/cDS.Rd b/man/cDS.Rd
index 7b4e448a..e3da7bf2 100644
--- a/man/cDS.Rd
+++ b/man/cDS.Rd
@@ -4,10 +4,10 @@
 \alias{cDS}
 \title{Concatenates objects into a vector or list}
 \usage{
-cDS(objs)
+cDS(x.names)
 }
 \arguments{
-\item{objs}{a list which contains the the objects to concatenate.}
+\item{x.names}{a character vector of object names to concatenate.}
 }
 \value{
 a vector or list
@@ -21,4 +21,6 @@ length are allowed as output
 }
 \author{
 Gaye, A.
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/listDS.Rd b/man/listDS.Rd
index 36b1c236..4f0401a1 100644
--- a/man/listDS.Rd
+++ b/man/listDS.Rd
@@ -4,12 +4,12 @@
 \alias{listDS}
 \title{Coerce objects into a list}
 \usage{
-listDS(input = NULL, eltnames = NULL)
+listDS(x.names = NULL, eltnames = NULL)
 }
 \arguments{
-\item{input}{a list of objects to coerce into a list}
+\item{x.names}{a character vector of object names to coerce into a list.}
 
-\item{eltnames}{a character list, the names of the elements in the list.}
+\item{eltnames}{a character vector, the names of the elements in the list.}
 }
 \value{
 a list
@@ -23,4 +23,6 @@ the names of the elements in the output list.
 }
 \author{
 Gaye, A.
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }

From 1ff323f41429ecb5fcb60f406c1a4bf0cfbac85a Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 14:54:12 +0200
Subject: [PATCH 11/12] revert: remove batch-4 cDS/listDS work leaked onto
 batch-3

---
 R/cDS.R                          | 22 ++++++++++------------
 R/listDS.R                       | 18 +++++++-----------
 man/cDS.Rd                       |  6 ++----
 man/listDS.Rd                    |  8 +++-----
 tests/testthat/test-smk-cDS.R    | 16 +++++++++-------
 tests/testthat/test-smk-listDS.R |  5 ++---
 6 files changed, 33 insertions(+), 42 deletions(-)

diff --git a/R/cDS.R b/R/cDS.R
index dbc224b6..0b5b96ba 100644
--- a/R/cDS.R
+++ b/R/cDS.R
@@ -3,29 +3,27 @@
 #' @description This function is similar to the R base function 'c'.
 #' @details Unlike the R base function 'c' on vector or list of certain 
 #' length are allowed as output
-#' @param x.names a character vector of object names to concatenate.
+#' @param objs a list which contains the the objects to concatenate.
 #' @return a vector or list
 #' @author Gaye, A.
-#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#'
-cDS <- function (x.names) {
-
+#' 
+cDS <- function (objs) {
+  
   # Check Permissive Privacy Control Level.
   dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'avocado'))
-
-  # this filter sets the minimum number of observations that are allowed
+  
+  # this filter sets the minimum number of observations that are allowed 
 
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
   thr <- dsBase::listDisclosureSettingsDS()
   nfilter.tab <- as.numeric(thr$nfilter.tab)
+  #nfilter.glm <- as.numeric(thr$nfilter.glm)
+  #nfilter.subset <- as.numeric(thr$nfilter.subset)
+  #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
-
-  objs <- list()
-  for (i in seq_along(x.names)) {
-    objs[[i]] <- .loadServersideObject(x.names[i])
-  }
+  
   x <-  unlist(objs)
 
   # check if the output is valid and output accordingly
diff --git a/R/listDS.R b/R/listDS.R
index 88706176..162ae8b5 100644
--- a/R/listDS.R
+++ b/R/listDS.R
@@ -3,21 +3,17 @@
 #' @description this function is similar to R function 'list'
 #' @details Unlike the R function 'list' it takes also a vector of characters,
 #' the names of the elements in the output list.
-#' @param x.names a character vector of object names to coerce into a list.
-#' @param eltnames a character vector, the names of the elements in the list.
+#' @param input a list of objects to coerce into a list
+#' @param eltnames a character list, the names of the elements in the list.
 #' @return a list
 #' @author Gaye, A.
-#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#'
-listDS <-function (x.names=NULL, eltnames=NULL){
-
-  mylist <- list()
-  for (i in seq_along(x.names)) {
-    mylist[[i]] <- .loadServersideObject(x.names[i])
-  }
+#' 
+listDS <-function (input=NULL, eltnames=NULL){
+  
+  mylist <- input
   names(mylist) <- unlist(eltnames)
 
   return(mylist)
-
+  
 }
\ No newline at end of file
diff --git a/man/cDS.Rd b/man/cDS.Rd
index e3da7bf2..7b4e448a 100644
--- a/man/cDS.Rd
+++ b/man/cDS.Rd
@@ -4,10 +4,10 @@
 \alias{cDS}
 \title{Concatenates objects into a vector or list}
 \usage{
-cDS(x.names)
+cDS(objs)
 }
 \arguments{
-\item{x.names}{a character vector of object names to concatenate.}
+\item{objs}{a list which contains the the objects to concatenate.}
 }
 \value{
 a vector or list
@@ -21,6 +21,4 @@ length are allowed as output
 }
 \author{
 Gaye, A.
-
-Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/listDS.Rd b/man/listDS.Rd
index 4f0401a1..36b1c236 100644
--- a/man/listDS.Rd
+++ b/man/listDS.Rd
@@ -4,12 +4,12 @@
 \alias{listDS}
 \title{Coerce objects into a list}
 \usage{
-listDS(x.names = NULL, eltnames = NULL)
+listDS(input = NULL, eltnames = NULL)
 }
 \arguments{
-\item{x.names}{a character vector of object names to coerce into a list.}
+\item{input}{a list of objects to coerce into a list}
 
-\item{eltnames}{a character vector, the names of the elements in the list.}
+\item{eltnames}{a character list, the names of the elements in the list.}
 }
 \value{
 a list
@@ -23,6 +23,4 @@ the names of the elements in the output list.
 }
 \author{
 Gaye, A.
-
-Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/tests/testthat/test-smk-cDS.R b/tests/testthat/test-smk-cDS.R
index 518d9ac5..0f9842fc 100644
--- a/tests/testthat/test-smk-cDS.R
+++ b/tests/testthat/test-smk-cDS.R
@@ -23,9 +23,9 @@ set.standard.disclosure.settings()
 
 # context("cDS::smk::numeric list")
 test_that("numeric list cDS", {
-    a <- 0.0; b <- 1.0; c <- 2.0; d <- 3.0
+    input <- list(a=0.0, b=1.0, c=2.0, d=3.0)
 
-    res <- cDS(c("a", "b", "c", "d"))
+    res <- cDS(input)
 
     expect_length(res, 4)
     expect_equal(class(res), "numeric")
@@ -37,9 +37,9 @@ test_that("numeric list cDS", {
 
 # context("cDS::smk::character list")
 test_that("character list cDS", {
-    a <- "0.0"; b <- "1.0"; c <- "2.0"; d <- "3.0"
+    input <- list(a="0.0", b="1.0", c="2.0", d="3.0")
 
-    res <- cDS(c("a", "b", "c", "d"))
+    res <- cDS(input)
 
     expect_length(res, 4)
     expect_equal(class(res), "character")
@@ -51,9 +51,9 @@ test_that("character list cDS", {
 
 # context("cDS::smk::numeric list small")
 test_that("single numeric list small cDS", {
-    a <- 0; b <- 1
+    input <- list(a=0, b=1)
 
-    res <- cDS(c("a", "b"))
+    res <- cDS(input)
 
     expect_length(res, 2)
     expect_equal(class(res), "logical")
@@ -63,7 +63,9 @@ test_that("single numeric list small cDS", {
 
 # context("cDS::smk::empty list")
 test_that("empty list cDS", {
-    res <- cDS(character(0))
+    input <- list()
+
+    res <- cDS(input)
 
     expect_length(res, 0)
     expect_equal(class(res), "NULL")
diff --git a/tests/testthat/test-smk-listDS.R b/tests/testthat/test-smk-listDS.R
index 51e75550..dfd0a171 100644
--- a/tests/testthat/test-smk-listDS.R
+++ b/tests/testthat/test-smk-listDS.R
@@ -21,11 +21,10 @@
 
 # context("listDS::smk::simple")
 test_that("simple listDS", {
-    v1 <- c(1, 2, 3)
-    v2 <- c(4, 5, 6)
+    input    <- list(v1 = c(1, 2, 3), v2 = c(4, 5, 6))
     eltnames <- c('n1', 'n2')
 
-    res <- listDS(c("v1", "v2"), eltnames)
+    res <- listDS(input, eltnames)
 
     expect_equal(class(res), "list")
     expect_length(res, 2)

From 0b6ab1aedc402105fb03391d4cf3adae9726250f Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 18:36:55 +0200
Subject: [PATCH 12/12] fix: restore numeric-vector-requires-y guard in
 cor/covDS

Server-side check preserves pre-refactor contract that was dropped
when client-side validation moved to server. Redocument levelsDS.
---
 R/corDS.R       | 6 +++++-
 R/covDS.R       | 6 +++++-
 man/levelsDS.Rd | 5 ++---
 3 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/R/corDS.R b/R/corDS.R
index fde5ad3d..f4e9fa23 100644
--- a/R/corDS.R
+++ b/R/corDS.R
@@ -38,7 +38,11 @@ corDS <- function(x=NULL, y=NULL){
   else{
     y.val <- NULL
   }
-  
+
+  if (is.null(y.val) && any(class(x.val) %in% c("numeric", "integer"))) {
+    stop("If x is a numeric vector, y must also be a numeric vector.", call. = FALSE)
+  }
+
   # create a data frame for the variables
   if (is.null(y.val)){
     dataframe <- as.data.frame(x.val)
diff --git a/R/covDS.R b/R/covDS.R
index b15b4a5a..57a99ae2 100644
--- a/R/covDS.R
+++ b/R/covDS.R
@@ -47,7 +47,11 @@ covDS <- function(x=NULL, y=NULL, use=NULL){
   else{
     y.val <- NULL
   }
-  
+
+  if (is.null(y.val) && any(class(x.val) %in% c("numeric", "integer"))) {
+    stop("If x is a numeric vector, y must also be a numeric vector.", call. = FALSE)
+  }
+
   # create a data frame for the variables
   if (is.null(y.val)){
     dataframe <- as.data.frame(x.val)
diff --git a/man/levelsDS.Rd b/man/levelsDS.Rd
index c54b7d13..4002c73c 100644
--- a/man/levelsDS.Rd
+++ b/man/levelsDS.Rd
@@ -10,9 +10,8 @@ levelsDS(x)
 \item{x}{a factor vector}
 }
 \value{
-a list with two elements: \code{Levels} (the factor levels present
-  in the vector) and \code{class} (the class of the input object, for
-  client-side consistency checking)
+a list with one element: \code{Levels} (the factor levels present
+  in the vector)
 }
 \description{
 This function is similar to R function \code{levels}.