From 6600043822d69d12020d339496fe3eeb378ff5bb Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 16 Apr 2026 13:26:35 +0200
Subject: [PATCH 1/5] refactor: batch-9 server-side plotting functions

---
 R/boxPlotGGDS.R                         |  8 +++++---
 R/densityGridDS.R                       | 13 ++++++++-----
 R/heatmapPlotDS.R                       |  9 ++++++---
 R/histogramDS1.R                        |  6 ++++--
 R/histogramDS2.R                        |  6 ++++--
 R/scatterPlotDS.R                       | 11 +++++++----
 tests/testthat/test-smk-densityGridDS.R | 11 ++++++++++-
 7 files changed, 44 insertions(+), 20 deletions(-)

diff --git a/R/boxPlotGGDS.R b/R/boxPlotGGDS.R
index 11b6fd90..1cad869f 100644
--- a/R/boxPlotGGDS.R
+++ b/R/boxPlotGGDS.R
@@ -5,7 +5,7 @@
 #' parameters are passed. There are three different cases depending if there are grouping variables. 
 #' The outliers are also removed from the graphical parameters.
 #'
-#' @param data_table \code{data frame} Table that holds the information to be plotted, arranged as: \cr
+#' @param data_table.name \code{character} Name of a server-side data frame that holds the information to be plotted, arranged as: \cr
 #' 
 #'  Column 'x': Names on the X axis of the boxplot, aka variables to plot \cr
 #'  Column 'value': Values for that variable (raw data of columns rbinded) \cr
@@ -21,8 +21,10 @@
 #' 
 #' @export
 
-boxPlotGGDS <- function(data_table, group = NULL, group2 = NULL){
-  
+boxPlotGGDS <- function(data_table.name, group = NULL, group2 = NULL){
+
+  data_table <- .loadServersideObject(data_table.name)
+
   ###################################################################
   # MODULE 1: CAPTURE THE subset filter SETTINGS                    #
   thr <- dsBase::listDisclosureSettingsDS()                         #
diff --git a/R/densityGridDS.R b/R/densityGridDS.R
index 1569d5c1..2622c90d 100644
--- a/R/densityGridDS.R
+++ b/R/densityGridDS.R
@@ -3,8 +3,8 @@
 #' @description Generates a density grid that can then be used for heatmap or contour plots.
 #' @details Invalid cells (cells with count < to the set filter value for the minimum allowed
 #' counts in table cells) are turn to 0.
-#' @param xvect a numerical vector
-#' @param yvect a numerical vector
+#' @param x a character string providing the name of a server-side numerical vector
+#' @param y a character string providing the name of a server-side numerical vector
 #' @param limits a logical expression for whether or not limits of the density grid are defined by
 #' a user. If \code{limits} is set to "FALSE", min and max of xvect and yvect are used as a range.
 #' If \code{limits} is set to "TRUE", limits defined by x.min, x.max, y.min and y.max are used.
@@ -17,10 +17,13 @@
 #' @author Julia Isaeva, Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
 #' @export
 #' 
-densityGridDS  <- function(xvect, yvect, limits=FALSE, x.min=NULL, x.max=NULL, y.min=NULL, y.max=NULL, numints=20){
-  
+densityGridDS  <- function(x, y, limits=FALSE, x.min=NULL, x.max=NULL, y.min=NULL, y.max=NULL, numints=20){
+
+  xvect <- .loadServersideObject(x)
+  yvect <- .loadServersideObject(y)
+
   #############################################################
-  # MODULE 1: CAPTURE THE nfilter SETTINGS                    
+  # MODULE 1: CAPTURE THE nfilter SETTINGS
   thr <- dsBase::listDisclosureSettingsDS()				
   nfilter.tab <- as.numeric(thr$nfilter.tab)					
   #nfilter.glm <- as.numeric(thr$nfilter.glm)					
diff --git a/R/heatmapPlotDS.R b/R/heatmapPlotDS.R
index 349f57b9..629bb6db 100644
--- a/R/heatmapPlotDS.R
+++ b/R/heatmapPlotDS.R
@@ -9,8 +9,8 @@
 #' neighbours and the y-coordinate of the centroid is the average of the y-coordinates of the n nearest
 #' neighbours. The coordinates of the centroids return to the client side function and can be used for the
 #' plot of non-disclosive graphs (e.g. scatter plots, heatmap plots, contour plots, etc).    
-#' @param x the name of a numeric vector, the x-variable.
-#' @param y the name of a numeric vector, the y-variable.
+#' @param x.name a character string providing the name of a server-side numeric vector, the x-variable.
+#' @param y.name a character string providing the name of a server-side numeric vector, the y-variable.
 #' @param k the number of the nearest neighbours for which their centroid is calculated if the 
 #' \code{method.indicator} is equal to 1 (i.e. deterministic method).
 #' @param noise the percentage of the initial variance that is used as the variance of the embedded
@@ -22,7 +22,10 @@
 #' @author Demetris Avraam for DataSHIELD Development Team
 #' @export
 #' 
-heatmapPlotDS <- function(x, y, k, noise, method.indicator){
+heatmapPlotDS <- function(x.name, y.name, k, noise, method.indicator){
+
+  x <- .loadServersideObject(x.name)
+  y <- .loadServersideObject(y.name)
 
   ###################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                          #
diff --git a/R/histogramDS1.R b/R/histogramDS1.R
index 71ffc439..f9b1a940 100644
--- a/R/histogramDS1.R
+++ b/R/histogramDS1.R
@@ -7,7 +7,7 @@
 #' function returns the minimum and maximum values of the vector with the scaled centroids. If the
 #' method.indicator is set to 3 (i.e. the 'probabilistic' method is used) the function returns the
 #' minimum and maximum values of the generated 'noisy' vector.
-#' @param xvect the numeric vector for which the histogram is desired.
+#' @param x a character string providing the name of the server-side numeric vector for which the histogram is desired.
 #' @param method.indicator a number equal to either 1, 2 or 3 indicating the method of disclosure
 #' control that is used for the generation of the histogram. If the value is equal to 1 then the
 #' 'smallCellsRule' is used. If the value is equal to 2 then the 'deterministic' method is used.
@@ -20,7 +20,9 @@
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
 #' @export
 #'
-histogramDS1 <- function(xvect, method.indicator, k, noise){
+histogramDS1 <- function(x, method.indicator, k, noise){
+
+  xvect <- .loadServersideObject(x)
 
   ##################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                         #
diff --git a/R/histogramDS2.R b/R/histogramDS2.R
index 001ab0dd..c753a17b 100644
--- a/R/histogramDS2.R
+++ b/R/histogramDS2.R
@@ -6,7 +6,7 @@
 #' size of a table. If a bin has less counts than this threshold then their counts 
 #' and its density are replaced by a 0 value.
 #' @details Please find more details in the documentation of the clientside ds.histogram function.
-#' @param xvect the numeric vector for which the histogram is desired.
+#' @param x a character string providing the name of the server-side numeric vector for which the histogram is desired.
 #' @param num.breaks the number of breaks that the range of the variable is divided.
 #' @param min a numeric, the lower limit of the distribution.
 #' @param max a numeric, the upper limit of the distribution.
@@ -22,7 +22,9 @@
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
 #' @export
 #' 
-histogramDS2 <- function (xvect, num.breaks, min, max, method.indicator, k, noise){
+histogramDS2 <- function (x, num.breaks, min, max, method.indicator, k, noise){
+
+  xvect <- .loadServersideObject(x)
 
   ##################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                         #
diff --git a/R/scatterPlotDS.R b/R/scatterPlotDS.R
index ab48be10..dcab7fea 100644
--- a/R/scatterPlotDS.R
+++ b/R/scatterPlotDS.R
@@ -14,8 +14,8 @@
 #' and variance equal to 10% of the true variance of $x$ and $y$ respectively. To avoid inferential
 #' disclosure we fix the random number generator in a value that is specified by the input
 #' variables. Thus the function returns always the same noisy data for a given pair of variables.
-#' @param x the name of a numeric vector, the x-variable.
-#' @param y the name of a numeric vector, the y-variable.
+#' @param x.name a character string providing the name of a server-side numeric vector, the x-variable.
+#' @param y.name a character string providing the name of a server-side numeric vector, the y-variable.
 #' @param method.indicator an integer either 1 or 2. If the user selects the deterministic
 #' method in the client side function the method.indicator is set to 1 while if the user selects
 #' the probabilistic method this argument is set to 2.
@@ -27,8 +27,11 @@
 #' @author Demetris Avraam for DataSHIELD Development Team
 #' @export
 #'
-scatterPlotDS <- function(x, y, method.indicator, k, noise){
-  
+scatterPlotDS <- function(x.name, y.name, method.indicator, k, noise){
+
+  x <- .loadServersideObject(x.name)
+  y <- .loadServersideObject(y.name)
+
   ###################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                          #
   thr <- dsBase::listDisclosureSettingsDS()                         #
diff --git a/tests/testthat/test-smk-densityGridDS.R b/tests/testthat/test-smk-densityGridDS.R
index 2c075a4b..b0b4f00c 100644
--- a/tests/testthat/test-smk-densityGridDS.R
+++ b/tests/testthat/test-smk-densityGridDS.R
@@ -36,7 +36,7 @@ test_that("densityGridDS", {
   y.max <- NULL
   numints <- 3
   
-  res <- densityGridDS(xvect=xvect, yvect=yvect, limits=FALSE, x.min=NULL, 
+  res <- densityGridDS(x="xvect", y="yvect", limits=FALSE, x.min=NULL,
                         x.max=NULL, y.min=NULL, y.max=NULL, numints=numints)
   
     expect_equal(class(res), c("matrix","array"))
@@ -50,6 +50,15 @@ test_that("densityGridDS", {
 })
 
 
+test_that("densityGridDS fails when x references nonexistent object", {
+    expect_error(densityGridDS(x="nonexistent_obj", y="yvect", numints=3), "does not exist")
+})
+
+test_that("densityGridDS fails when y references nonexistent object", {
+    yvect <- c(1:20)
+    expect_error(densityGridDS(x="yvect", y="nonexistent_obj", numints=3), "does not exist")
+})
+
 #
 # Done
 #

From ce633041082d1ed2c87bfc74333c90bf6050212b Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 16 Apr 2026 16:44:35 +0200
Subject: [PATCH 2/5] docs: updated authorship

---
 R/densityGridDS.R | 1 +
 R/heatmapPlotDS.R | 1 +
 R/histogramDS1.R  | 1 +
 R/histogramDS2.R  | 1 +
 R/scatterPlotDS.R | 1 +
 5 files changed, 5 insertions(+)

diff --git a/R/densityGridDS.R b/R/densityGridDS.R
index 2622c90d..a41245ac 100644
--- a/R/densityGridDS.R
+++ b/R/densityGridDS.R
@@ -15,6 +15,7 @@
 #' @param numints a number of intervals for the grid density object, by default is 20
 #' @return a grid density matrix
 #' @author Julia Isaeva, Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 densityGridDS  <- function(x, y, limits=FALSE, x.min=NULL, x.max=NULL, y.min=NULL, y.max=NULL, numints=20){
diff --git a/R/heatmapPlotDS.R b/R/heatmapPlotDS.R
index 629bb6db..951c6755 100644
--- a/R/heatmapPlotDS.R
+++ b/R/heatmapPlotDS.R
@@ -20,6 +20,7 @@
 #' @return a list with the x and y coordinates of the centroids if the deterministic method is used
 #' or the x and y coordinated of the noisy data if the probabilistic method is used.
 #' @author Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 heatmapPlotDS <- function(x.name, y.name, k, noise, method.indicator){
diff --git a/R/histogramDS1.R b/R/histogramDS1.R
index f9b1a940..f99d2449 100644
--- a/R/histogramDS1.R
+++ b/R/histogramDS1.R
@@ -18,6 +18,7 @@
 #' noise if the \code{method.indicator} is equal to 3 (i.e. probabilistic method).
 #' @return a numeric vector which contains the minimum and the maximum values of the vector
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 histogramDS1 <- function(x, method.indicator, k, noise){
diff --git a/R/histogramDS2.R b/R/histogramDS2.R
index c753a17b..f872d01a 100644
--- a/R/histogramDS2.R
+++ b/R/histogramDS2.R
@@ -20,6 +20,7 @@
 #' noise if the \code{method.indicator} is equal to 3 (i.e. probabilistic method).
 #' @return a list with an object of class \code{histogram} and the number of invalid cells
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 histogramDS2 <- function (x, num.breaks, min, max, method.indicator, k, noise){
diff --git a/R/scatterPlotDS.R b/R/scatterPlotDS.R
index dcab7fea..60832ecc 100644
--- a/R/scatterPlotDS.R
+++ b/R/scatterPlotDS.R
@@ -25,6 +25,7 @@
 #' noise if the probabilistic method is selected.
 #' @return a list with the x and y coordinates of the data to be plot
 #' @author Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 scatterPlotDS <- function(x.name, y.name, method.indicator, k, noise){

From 5906be8163f324dba7cf9b8e1286d1b5eac99661 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 16 Apr 2026 16:47:05 +0200
Subject: [PATCH 3/5] docs: redocumented

---
 man/boxPlotGGDS.Rd   |  4 ++--
 man/densityGridDS.Rd | 10 ++++++----
 man/heatmapPlotDS.Rd |  8 +++++---
 man/histogramDS1.Rd  |  6 ++++--
 man/histogramDS2.Rd  |  6 ++++--
 man/scatterPlotDS.Rd |  8 +++++---
 6 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/man/boxPlotGGDS.Rd b/man/boxPlotGGDS.Rd
index 3633b943..03f297a7 100644
--- a/man/boxPlotGGDS.Rd
+++ b/man/boxPlotGGDS.Rd
@@ -4,10 +4,10 @@
 \alias{boxPlotGGDS}
 \title{Create the identity stats and necessary data to draw a plot on the client}
 \usage{
-boxPlotGGDS(data_table, group = NULL, group2 = NULL)
+boxPlotGGDS(data_table.name, group = NULL, group2 = NULL)
 }
 \arguments{
-\item{data_table}{\code{data frame} Table that holds the information to be plotted, arranged as: \cr
+\item{data_table.name}{\code{character} Name of a server-side data frame that holds the information to be plotted, arranged as: \cr
 
  Column 'x': Names on the X axis of the boxplot, aka variables to plot \cr
  Column 'value': Values for that variable (raw data of columns rbinded) \cr
diff --git a/man/densityGridDS.Rd b/man/densityGridDS.Rd
index 2b254acf..55ff7b3e 100644
--- a/man/densityGridDS.Rd
+++ b/man/densityGridDS.Rd
@@ -5,8 +5,8 @@
 \title{Generates a density grid with or without a priori defined limits}
 \usage{
 densityGridDS(
-  xvect,
-  yvect,
+  x,
+  y,
   limits = FALSE,
   x.min = NULL,
   x.max = NULL,
@@ -16,9 +16,9 @@ densityGridDS(
 )
 }
 \arguments{
-\item{xvect}{a numerical vector}
+\item{x}{a character string providing the name of a server-side numerical vector}
 
-\item{yvect}{a numerical vector}
+\item{y}{a character string providing the name of a server-side numerical vector}
 
 \item{limits}{a logical expression for whether or not limits of the density grid are defined by
 a user. If \code{limits} is set to "FALSE", min and max of xvect and yvect are used as a range.
@@ -46,4 +46,6 @@ counts in table cells) are turn to 0.
 }
 \author{
 Julia Isaeva, Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/heatmapPlotDS.Rd b/man/heatmapPlotDS.Rd
index 950dbace..a8e21840 100644
--- a/man/heatmapPlotDS.Rd
+++ b/man/heatmapPlotDS.Rd
@@ -4,12 +4,12 @@
 \alias{heatmapPlotDS}
 \title{Calculates the coordinates of the centroid of each n nearest neighbours}
 \usage{
-heatmapPlotDS(x, y, k, noise, method.indicator)
+heatmapPlotDS(x.name, y.name, k, noise, method.indicator)
 }
 \arguments{
-\item{x}{the name of a numeric vector, the x-variable.}
+\item{x.name}{a character string providing the name of a server-side numeric vector, the x-variable.}
 
-\item{y}{the name of a numeric vector, the y-variable.}
+\item{y.name}{a character string providing the name of a server-side numeric vector, the y-variable.}
 
 \item{k}{the number of the nearest neighbours for which their centroid is calculated if the 
 \code{method.indicator} is equal to 1 (i.e. deterministic method).}
@@ -39,4 +39,6 @@ plot of non-disclosive graphs (e.g. scatter plots, heatmap plots, contour plots,
 }
 \author{
 Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/histogramDS1.Rd b/man/histogramDS1.Rd
index a8e8a551..ef91faef 100644
--- a/man/histogramDS1.Rd
+++ b/man/histogramDS1.Rd
@@ -4,10 +4,10 @@
 \alias{histogramDS1}
 \title{returns the minimum and the maximum of the input numeric vector}
 \usage{
-histogramDS1(xvect, method.indicator, k, noise)
+histogramDS1(x, method.indicator, k, noise)
 }
 \arguments{
-\item{xvect}{the numeric vector for which the histogram is desired.}
+\item{x}{a character string providing the name of the server-side numeric vector for which the histogram is desired.}
 
 \item{method.indicator}{a number equal to either 1, 2 or 3 indicating the method of disclosure
 control that is used for the generation of the histogram. If the value is equal to 1 then the
@@ -34,4 +34,6 @@ minimum and maximum values of the generated 'noisy' vector.
 }
 \author{
 Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/histogramDS2.Rd b/man/histogramDS2.Rd
index 76bf8ea3..17ea4261 100644
--- a/man/histogramDS2.Rd
+++ b/man/histogramDS2.Rd
@@ -4,10 +4,10 @@
 \alias{histogramDS2}
 \title{Computes a histogram of the input variable without plotting.}
 \usage{
-histogramDS2(xvect, num.breaks, min, max, method.indicator, k, noise)
+histogramDS2(x, num.breaks, min, max, method.indicator, k, noise)
 }
 \arguments{
-\item{xvect}{the numeric vector for which the histogram is desired.}
+\item{x}{a character string providing the name of the server-side numeric vector for which the histogram is desired.}
 
 \item{num.breaks}{the number of breaks that the range of the variable is divided.}
 
@@ -41,4 +41,6 @@ Please find more details in the documentation of the clientside ds.histogram fun
 }
 \author{
 Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/scatterPlotDS.Rd b/man/scatterPlotDS.Rd
index 7b2709fd..4f715d2c 100644
--- a/man/scatterPlotDS.Rd
+++ b/man/scatterPlotDS.Rd
@@ -4,12 +4,12 @@
 \alias{scatterPlotDS}
 \title{Calculates the coordinates of the data to be plot}
 \usage{
-scatterPlotDS(x, y, method.indicator, k, noise)
+scatterPlotDS(x.name, y.name, method.indicator, k, noise)
 }
 \arguments{
-\item{x}{the name of a numeric vector, the x-variable.}
+\item{x.name}{a character string providing the name of a server-side numeric vector, the x-variable.}
 
-\item{y}{the name of a numeric vector, the y-variable.}
+\item{y.name}{a character string providing the name of a server-side numeric vector, the y-variable.}
 
 \item{method.indicator}{an integer either 1 or 2. If the user selects the deterministic
 method in the client side function the method.indicator is set to 1 while if the user selects
@@ -44,4 +44,6 @@ variables. Thus the function returns always the same noisy data for a given pair
 }
 \author{
 Demetris Avraam for DataSHIELD Development Team
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }

From a94e23d03d3e7c1096ec997d1221ea3c72e85a39 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 14 Sep 2026 16:32:29 +0200
Subject: [PATCH 4/5] added back missing class checks

---
 R/boxPlotGGDS.R                               |   3 +-
 R/boxPlotGG_data_TreatmentDS.R                |  32 +--
 R/boxPlotGG_data_Treatment_numericDS.R        |  22 +-
 R/densityGridDS.R                             |  15 +-
 R/heatmapPlotDS.R                             |  11 +-
 R/histogramDS1.R                              | 197 +++++++++---------
 R/histogramDS2.R                              |   1 +
 R/scatterPlotDS.R                             |   9 +-
 man/boxPlotGGDS.Rd                            |   3 +
 man/boxPlotGG_data_TreatmentDS.Rd             |   7 +-
 man/boxPlotGG_data_Treatment_numericDS.Rd     |   9 +-
 man/densityGridDS.Rd                          |   5 +-
 man/heatmapPlotDS.Rd                          |   3 +-
 man/histogramDS1.Rd                           |   3 +-
 man/scatterPlotDS.Rd                          |   3 +-
 tests/testthat/test-smk-boxPlotGGDS.R         |  53 +++++
 .../test-smk-boxPlotGG_data_TreatmentDS.R     |  61 ++++++
 ...t-smk-boxPlotGG_data_Treatment_numericDS.R |  49 +++++
 tests/testthat/test-smk-densityGridDS.R       |  28 ++-
 tests/testthat/test-smk-heatmapPlotDS.R       |  66 ++++++
 tests/testthat/test-smk-histogramDS1.R        |  51 +++++
 tests/testthat/test-smk-histogramDS2.R        |  50 +++++
 tests/testthat/test-smk-scatterPlotDS.R       |  66 ++++++
 23 files changed, 592 insertions(+), 155 deletions(-)
 create mode 100644 tests/testthat/test-smk-boxPlotGGDS.R
 create mode 100644 tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R
 create mode 100644 tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R
 create mode 100644 tests/testthat/test-smk-heatmapPlotDS.R
 create mode 100644 tests/testthat/test-smk-histogramDS1.R
 create mode 100644 tests/testthat/test-smk-histogramDS2.R
 create mode 100644 tests/testthat/test-smk-scatterPlotDS.R

diff --git a/R/boxPlotGGDS.R b/R/boxPlotGGDS.R
index 1cad869f..6ee33824 100644
--- a/R/boxPlotGGDS.R
+++ b/R/boxPlotGGDS.R
@@ -18,7 +18,8 @@
 #' @return \code{list} with: \cr
 #' -\code{data frame} Geometrical parameters (identity stats of ggplot) \cr
 #' -\code{character} Type of plot (single_group, double_group or no_group) \cr
-#' 
+#'
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 
 boxPlotGGDS <- function(data_table.name, group = NULL, group2 = NULL){
diff --git a/R/boxPlotGG_data_TreatmentDS.R b/R/boxPlotGG_data_TreatmentDS.R
index 7d6613d1..c3a18e67 100644
--- a/R/boxPlotGG_data_TreatmentDS.R
+++ b/R/boxPlotGG_data_TreatmentDS.R
@@ -1,42 +1,46 @@
 #' @title Arrange data frame to pass it to the boxplot function
 #'
-#' @param table \code{data frame} Table that holds the information to be plotted later
+#' @param table.name \code{character} Name of a server-side data frame that holds the information to be plotted later
 #' @param variables \code{character vector} Name of the column(s) of the data frame to include on the boxplot
-#' @param group \code{character} (default \code{NULL}) Name of the first grouping variable. 
-#' @param group2 \code{character} (default \code{NULL}) Name of the second grouping variable. 
+#' @param group \code{character} (default \code{NULL}) Name of the first grouping variable.
+#' @param group2 \code{character} (default \code{NULL}) Name of the second grouping variable.
 #'
 #' @return \code{data frame} with the following structure: \cr
-#' 
+#'
 #'  Column 'x': Names on the X axis of the boxplot, aka variables to plot \cr
 #'  Column 'value': Values for that variable (raw data of columns rbinded) \cr
 #'  Column 'group': (Optional) Values of the grouping variable \cr
 #'  Column 'group2': (Optional) Values of the second grouping variable \cr
-#'  
+#'
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 
-boxPlotGG_data_TreatmentDS <- function(table, variables, group = NULL, group2 = NULL){
+boxPlotGG_data_TreatmentDS <- function(table.name, variables, group = NULL, group2 = NULL){
+
+  table <- .loadServersideObject(table.name)
+
+  for(variable in variables){
+    .checkClass(obj = table[[variable]], obj_name = variable, permitted_classes = c("numeric", "integer"))
+  }
 
   if(is.null(group) & !is.null(group2)){
     group <- group2
     group2 <- NULL
   }
-  
+
   if(is.null(group2)){
     if(is.null(group)){
       data <- table[, c(variables)]
     }
     else{
-      if(! any(c("factor") %in% class(table[[group]]))) {
-        stop("Grouping variable must be of class factor")
-      }
+      .checkClass(obj = table[[group]], obj_name = group, permitted_classes = c("factor"))
       data <- table[, c(variables, group)]
     }
-    
+
   }
   else{
-    if((! any(c("factor") %in% class(table[[group]]))) | (! any(c("factor") %in% class(table[[group2]])))){
-      stop("Grouping variable must be of class factor")
-    }
+    .checkClass(obj = table[[group]], obj_name = group, permitted_classes = c("factor"))
+    .checkClass(obj = table[[group2]], obj_name = group2, permitted_classes = c("factor"))
     data <- table[, c(variables, group, group2)]
     # Handle case group == group2 
     if(group == group2){
diff --git a/R/boxPlotGG_data_Treatment_numericDS.R b/R/boxPlotGG_data_Treatment_numericDS.R
index 7374ca7d..feff4f0e 100644
--- a/R/boxPlotGG_data_Treatment_numericDS.R
+++ b/R/boxPlotGG_data_Treatment_numericDS.R
@@ -1,18 +1,22 @@
 #' @title Arrange vector to pass it to the boxplot function
 #'
-#' @param vector \code{numeric vector} Vector to arrange to be plotted later
+#' @param vector.name \code{character} Name of a server-side numeric vector to arrange to be plotted later
 #'
 #' @return \code{data frame} with the following structure: \cr
-#' 
-#'  Column 'x': Names on the X axis of the boxplot, aka name of the vector (vector argument) \cr
+#'
+#'  Column 'x': Names on the X axis of the boxplot, aka name of the vector (vector.name argument) \cr
 #'  Column 'value': Values for that variable \cr
-#'  
+#'
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 
-boxPlotGG_data_Treatment_numericDS <- function(vector){
-  
-  data <- data.frame(x = deparse(substitute(vector)), value = vector)
-  
+boxPlotGG_data_Treatment_numericDS <- function(vector.name){
+
+  vector <- .loadServersideObject(vector.name)
+  .checkClass(obj = vector, obj_name = vector.name, permitted_classes = c("numeric", "integer"))
+
+  data <- data.frame(x = vector.name, value = vector)
+
   return(data)
-  
+
 }
\ No newline at end of file
diff --git a/R/densityGridDS.R b/R/densityGridDS.R
index a41245ac..1e16fc8a 100644
--- a/R/densityGridDS.R
+++ b/R/densityGridDS.R
@@ -6,22 +6,25 @@
 #' @param x a character string providing the name of a server-side numerical vector
 #' @param y a character string providing the name of a server-side numerical vector
 #' @param limits a logical expression for whether or not limits of the density grid are defined by
-#' a user. If \code{limits} is set to "FALSE", min and max of xvect and yvect are used as a range.
+#' a user. If \code{limits} is set to "FALSE", min and max of x and y are used as a range.
 #' If \code{limits} is set to "TRUE", limits defined by x.min, x.max, y.min and y.max are used.
 #' @param x.min a minimum value for the x axis of the grid density object, if needed
 #' @param x.max a maximum value for the x axis of the grid density object, if needed
 #' @param y.min a minimum value for the y axis of the grid density object, if needed
 #' @param y.max a maximum value for the y axis of the grid density object, if needed
 #' @param numints a number of intervals for the grid density object, by default is 20
-#' @return a grid density matrix
+#' @return a list with the grid density matrix (\code{grid}) and the classes of the x and y inputs
+#' (\code{class.x} and \code{class.y})
 #' @author Julia Isaeva, Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#' 
+#'
 densityGridDS  <- function(x, y, limits=FALSE, x.min=NULL, x.max=NULL, y.min=NULL, y.max=NULL, numints=20){
 
   xvect <- .loadServersideObject(x)
   yvect <- .loadServersideObject(y)
+  .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer"))
+  .checkClass(obj = yvect, obj_name = y, permitted_classes = c("numeric", "integer"))
 
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
@@ -97,9 +100,9 @@ densityGridDS  <- function(x, y, limits=FALSE, x.min=NULL, x.max=NULL, y.min=NUL
   
   names(dimnames(grid.density.obj))[2] <- title.text
   names(dimnames(grid.density.obj))[1] <- ''
-  
-  return(grid.density.obj)
-  
+
+  return(list(grid=grid.density.obj, class.x=class(xvect), class.y=class(yvect)))
+
 }
 # AGGREGATE FUNCTION
 # densityGridDS
diff --git a/R/heatmapPlotDS.R b/R/heatmapPlotDS.R
index 951c6755..d8afc61e 100644
--- a/R/heatmapPlotDS.R
+++ b/R/heatmapPlotDS.R
@@ -18,15 +18,18 @@
 #' @param method.indicator a number equal to either 1 or 2. If the value is equal to 1 then the
 #' 'deterministic' method is used. If the value is set to 2 the 'probabilistic' method is used. 
 #' @return a list with the x and y coordinates of the centroids if the deterministic method is used
-#' or the x and y coordinated of the noisy data if the probabilistic method is used.
+#' or the x and y coordinated of the noisy data if the probabilistic method is used, along with the
+#' classes of the x and y inputs (\code{class.x} and \code{class.y})
 #' @author Demetris Avraam for DataSHIELD Development Team
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#' 
+#'
 heatmapPlotDS <- function(x.name, y.name, k, noise, method.indicator){
 
   x <- .loadServersideObject(x.name)
   y <- .loadServersideObject(y.name)
+  .checkClass(obj = x, obj_name = x.name, permitted_classes = c("numeric", "integer"))
+  .checkClass(obj = y, obj_name = y.name, permitted_classes = c("numeric", "integer"))
 
   ###################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                          #
@@ -129,8 +132,8 @@ heatmapPlotDS <- function(x.name, y.name, k, noise, method.indicator){
   }
   
   # Return a list with the x and y coordinates of the centroids
-  return(list(x.new, y.new))
-  
+  return(list(x.new, y.new, class.x=class(x), class.y=class(y)))
+
 }
 # AGGREGATE FUNCTION
 # heatmapPlotDS
diff --git a/R/histogramDS1.R b/R/histogramDS1.R
index f99d2449..97e09780 100644
--- a/R/histogramDS1.R
+++ b/R/histogramDS1.R
@@ -16,7 +16,8 @@
 #' \code{method.indicator} is equal to 2 (i.e. deterministic method).
 #' @param noise the percentage of the initial variance that is used as the variance of the embedded
 #' noise if the \code{method.indicator} is equal to 3 (i.e. probabilistic method).
-#' @return a numeric vector which contains the minimum and the maximum values of the vector
+#' @return a list with the numeric vector containing the minimum and the maximum values of the
+#' vector (\code{range}) and the class of the input vector (\code{class})
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
@@ -24,6 +25,7 @@
 histogramDS1 <- function(x, method.indicator, k, noise){
 
   xvect <- .loadServersideObject(x)
+  .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer"))
 
   ##################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                         #
@@ -46,110 +48,103 @@ histogramDS1 <- function(x, method.indicator, k, noise){
   } else
       on.exit(if (exists(x = ".Random.seed", envir = globalenv())) remove(".Random.seed", envir = globalenv()), add = TRUE)
   
-  # print an error message if the input vector is not a numeric
-  if(!(is.numeric(xvect))){
-    output <- "The input vector is not a numeric!"
-  }else{
-    
-    if (method.indicator==1){
-      
-      # the study-specific seed for random number generation
-      seed <- getOption("datashield.seed")
-      if (is.null(seed))
-        stop("histogramDS1 requires 'datashield.seed' R option to operate", call.=FALSE)
-      set.seed(seed)
-      
-      rr <- c(min(xvect, na.rm=TRUE), max(xvect, na.rm=TRUE))
-      if(rr[1] < 0){ min <- rr[1] * stats::runif(1, 1.01, 1.05) }else{ min <- rr[1] * stats::runif(1, 0.95, 0.99) }
-      if(rr[2] < 0){ max <- rr[2] * stats::runif(1, 0.95, 0.99) }else{ max <- rr[2] * stats::runif(1, 1.01, 1.05) }
-    
-      output <- c(min, max)
-      
+  if (method.indicator==1){
+
+    # the study-specific seed for random number generation
+    seed <- getOption("datashield.seed")
+    if (is.null(seed))
+      stop("histogramDS1 requires 'datashield.seed' R option to operate", call.=FALSE)
+    set.seed(seed)
+
+    rr <- c(min(xvect, na.rm=TRUE), max(xvect, na.rm=TRUE))
+    if(rr[1] < 0){ min <- rr[1] * stats::runif(1, 1.01, 1.05) }else{ min <- rr[1] * stats::runif(1, 0.95, 0.99) }
+    if(rr[2] < 0){ max <- rr[2] * stats::runif(1, 0.95, 0.99) }else{ max <- rr[2] * stats::runif(1, 1.01, 1.05) }
+
+    output <- c(min, max)
+
+  }
+
+  if(method.indicator==2){
+
+    # Remove any missing values
+    x <- stats::na.omit(xvect)
+
+    # Standardise the variable
+    x.standardised <- (x-mean(x))/stats::sd(x)
+
+    # Calculate the length of the variable after ommitting any NAs
+    N.data <- length(x)
+
+    # Check if k is integer and has a value greater than or equal to the pre-specified threshold
+    # and less than or equal to the length of rows of data.complete minus the pre-specified threshold
+    if(k < nfilter.kNN | k > (N.data - nfilter.kNN)){
+      stop(paste0("k must be greater than or equal to ", nfilter.kNN, " and less than or equal to ", (N.data-nfilter.kNN), "."), call.=FALSE)
+    }else{
+      neighbours = k
     }
-    
-    if(method.indicator==2){
-      
-      # Remove any missing values
-      x <- stats::na.omit(xvect)
-      
-      # Standardise the variable
-      x.standardised <- (x-mean(x))/stats::sd(x)
-      
-      # Calculate the length of the variable after ommitting any NAs
-      N.data <- length(x)
-      
-      # Check if k is integer and has a value greater than or equal to the pre-specified threshold
-      # and less than or equal to the length of rows of data.complete minus the pre-specified threshold
-      if(k < nfilter.kNN | k > (N.data - nfilter.kNN)){
-        stop(paste0("k must be greater than or equal to ", nfilter.kNN, " and less than or equal to ", (N.data-nfilter.kNN), "."), call.=FALSE)
-      }else{
-        neighbours = k
-      }
-      
-      # Find the k-1 nearest neighbours of each data point
-      nearest <- RANN::nn2(x.standardised, k = neighbours)
-      
-      # Calculate the centroid of each n nearest data points
-      x.centroid <- matrix()
-      for (i in 1:N.data){
-        x.centroid[i] <- mean(x.standardised[nearest$nn.idx[i,1:neighbours]])
-      }
-      
-      # Calculate the scaling factor
-      x.scalingFactor <- stats::sd(x.standardised)/stats::sd(x.centroid)
-      
-      # Apply the scaling factor to the centroids
-      x.masked <- x.centroid * x.scalingFactor
-      
-      # Shift the centroids back to the actual position and scale of the original data
-      x.new <- (x.masked * stats::sd(x)) + mean(x)
-      
-      # find the minimum and the maximum of the distribution
-      min <- min(x.new)
-      max <- max(x.new)
-      
-      output <- c(min, max)
-    
+
+    # Find the k-1 nearest neighbours of each data point
+    nearest <- RANN::nn2(x.standardised, k = neighbours)
+
+    # Calculate the centroid of each n nearest data points
+    x.centroid <- matrix()
+    for (i in 1:N.data){
+      x.centroid[i] <- mean(x.standardised[nearest$nn.idx[i,1:neighbours]])
     }
-    
-    if(method.indicator==3){
-      
-      # Remove any missing values
-      x <- stats::na.omit(xvect)
-      
-      # Calculate the length of the variable after ommitting any NAs
-      N.data <- length(x)
-      
-      # Check if the percentage of the variance that is specified in the argument 'noise'
-      # and is used as the variance of the embedded noise is a greater
-      # than the minimum threshold specified in the filter 'nfilter.noise'
-      if(noise < nfilter.noise){
-        stop(paste0("'noise' must be greater than or equal to ", nfilter.noise), call.=FALSE)
-      }else{
-        percentage <- noise
-      }
-      
-      # the study-specific seed for random number generation
-      seed <- getOption("datashield.seed")
-      if (is.null(seed))
-        stop("histogramDS requires 'datashield.seed' R option to operate", call.=FALSE)
-      set.seed(seed)
-      
-      # generate the noise-augmented vector
-      x.new <- x + stats::rnorm(N.data, mean=0, sd=sqrt(percentage*stats::var(x)))
-      
-      # find the minimum and the maximum of the distribution
-      min <- min(x.new)
-      max <- max(x.new)
-      
-      output <- c(min, max)
-      
+
+    # Calculate the scaling factor
+    x.scalingFactor <- stats::sd(x.standardised)/stats::sd(x.centroid)
+
+    # Apply the scaling factor to the centroids
+    x.masked <- x.centroid * x.scalingFactor
+
+    # Shift the centroids back to the actual position and scale of the original data
+    x.new <- (x.masked * stats::sd(x)) + mean(x)
+
+    # find the minimum and the maximum of the distribution
+    min <- min(x.new)
+    max <- max(x.new)
+
+    output <- c(min, max)
+
+  }
+
+  if(method.indicator==3){
+
+    # Remove any missing values
+    x <- stats::na.omit(xvect)
+
+    # Calculate the length of the variable after ommitting any NAs
+    N.data <- length(x)
+
+    # Check if the percentage of the variance that is specified in the argument 'noise'
+    # and is used as the variance of the embedded noise is a greater
+    # than the minimum threshold specified in the filter 'nfilter.noise'
+    if(noise < nfilter.noise){
+      stop(paste0("'noise' must be greater than or equal to ", nfilter.noise), call.=FALSE)
+    }else{
+      percentage <- noise
     }
-      
+
+    # the study-specific seed for random number generation
+    seed <- getOption("datashield.seed")
+    if (is.null(seed))
+      stop("histogramDS requires 'datashield.seed' R option to operate", call.=FALSE)
+    set.seed(seed)
+
+    # generate the noise-augmented vector
+    x.new <- x + stats::rnorm(N.data, mean=0, sd=sqrt(percentage*stats::var(x)))
+
+    # find the minimum and the maximum of the distribution
+    min <- min(x.new)
+    max <- max(x.new)
+
+    output <- c(min, max)
+
   }
-  
-  return (output)
-  
+
+  return(list(range=output, class=class(xvect)))
+
 }
 # AGGREGATE FUNCTION
 # histogramDS1
diff --git a/R/histogramDS2.R b/R/histogramDS2.R
index f872d01a..4e85b83f 100644
--- a/R/histogramDS2.R
+++ b/R/histogramDS2.R
@@ -26,6 +26,7 @@
 histogramDS2 <- function (x, num.breaks, min, max, method.indicator, k, noise){
 
   xvect <- .loadServersideObject(x)
+  .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer"))
 
   ##################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                         #
diff --git a/R/scatterPlotDS.R b/R/scatterPlotDS.R
index 60832ecc..3599c8f0 100644
--- a/R/scatterPlotDS.R
+++ b/R/scatterPlotDS.R
@@ -23,7 +23,8 @@
 #' deterministic method is selected.
 #' @param noise the percentage of the initial variance that is used as the variance of the embedded
 #' noise if the probabilistic method is selected.
-#' @return a list with the x and y coordinates of the data to be plot
+#' @return a list with the x and y coordinates of the data to be plot, along with the classes of
+#' the x and y inputs (\code{class.x} and \code{class.y})
 #' @author Demetris Avraam for DataSHIELD Development Team
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
@@ -32,6 +33,8 @@ scatterPlotDS <- function(x.name, y.name, method.indicator, k, noise){
 
   x <- .loadServersideObject(x.name)
   y <- .loadServersideObject(y.name)
+  .checkClass(obj = x, obj_name = x.name, permitted_classes = c("numeric", "integer"))
+  .checkClass(obj = y, obj_name = y.name, permitted_classes = c("numeric", "integer"))
 
   ###################################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS                          #
@@ -135,8 +138,8 @@ scatterPlotDS <- function(x.name, y.name, method.indicator, k, noise){
   }
   
   # Return a list with the x and y coordinates of the centroids
-  return(list(x.new, y.new))
-  
+  return(list(x.new, y.new, class.x=class(x), class.y=class(y)))
+
 }
 # AGGREGATE FUNCTION
 # scatterPlotDS
diff --git a/man/boxPlotGGDS.Rd b/man/boxPlotGGDS.Rd
index 03f297a7..b0d325ac 100644
--- a/man/boxPlotGGDS.Rd
+++ b/man/boxPlotGGDS.Rd
@@ -29,3 +29,6 @@ is purely geometrical aspects of the plot, as a ggplot object contains all the d
 parameters are passed. There are three different cases depending if there are grouping variables. 
 The outliers are also removed from the graphical parameters.
 }
+\author{
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
+}
diff --git a/man/boxPlotGG_data_TreatmentDS.Rd b/man/boxPlotGG_data_TreatmentDS.Rd
index a1ba9781..a38e838e 100644
--- a/man/boxPlotGG_data_TreatmentDS.Rd
+++ b/man/boxPlotGG_data_TreatmentDS.Rd
@@ -4,10 +4,10 @@
 \alias{boxPlotGG_data_TreatmentDS}
 \title{Arrange data frame to pass it to the boxplot function}
 \usage{
-boxPlotGG_data_TreatmentDS(table, variables, group = NULL, group2 = NULL)
+boxPlotGG_data_TreatmentDS(table.name, variables, group = NULL, group2 = NULL)
 }
 \arguments{
-\item{table}{\code{data frame} Table that holds the information to be plotted later}
+\item{table.name}{\code{character} Name of a server-side data frame that holds the information to be plotted later}
 
 \item{variables}{\code{character vector} Name of the column(s) of the data frame to include on the boxplot}
 
@@ -26,3 +26,6 @@ boxPlotGG_data_TreatmentDS(table, variables, group = NULL, group2 = NULL)
 \description{
 Arrange data frame to pass it to the boxplot function
 }
+\author{
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
+}
diff --git a/man/boxPlotGG_data_Treatment_numericDS.Rd b/man/boxPlotGG_data_Treatment_numericDS.Rd
index 914493b6..d43e961d 100644
--- a/man/boxPlotGG_data_Treatment_numericDS.Rd
+++ b/man/boxPlotGG_data_Treatment_numericDS.Rd
@@ -4,17 +4,20 @@
 \alias{boxPlotGG_data_Treatment_numericDS}
 \title{Arrange vector to pass it to the boxplot function}
 \usage{
-boxPlotGG_data_Treatment_numericDS(vector)
+boxPlotGG_data_Treatment_numericDS(vector.name)
 }
 \arguments{
-\item{vector}{\code{numeric vector} Vector to arrange to be plotted later}
+\item{vector.name}{\code{character} Name of a server-side numeric vector to arrange to be plotted later}
 }
 \value{
 \code{data frame} with the following structure: \cr
 
- Column 'x': Names on the X axis of the boxplot, aka name of the vector (vector argument) \cr
+ Column 'x': Names on the X axis of the boxplot, aka name of the vector (vector.name argument) \cr
  Column 'value': Values for that variable \cr
 }
 \description{
 Arrange vector to pass it to the boxplot function
 }
+\author{
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
+}
diff --git a/man/densityGridDS.Rd b/man/densityGridDS.Rd
index 55ff7b3e..8a8c1ee0 100644
--- a/man/densityGridDS.Rd
+++ b/man/densityGridDS.Rd
@@ -21,7 +21,7 @@ densityGridDS(
 \item{y}{a character string providing the name of a server-side numerical vector}
 
 \item{limits}{a logical expression for whether or not limits of the density grid are defined by
-a user. If \code{limits} is set to "FALSE", min and max of xvect and yvect are used as a range.
+a user. If \code{limits} is set to "FALSE", min and max of x and y are used as a range.
 If \code{limits} is set to "TRUE", limits defined by x.min, x.max, y.min and y.max are used.}
 
 \item{x.min}{a minimum value for the x axis of the grid density object, if needed}
@@ -35,7 +35,8 @@ If \code{limits} is set to "TRUE", limits defined by x.min, x.max, y.min and y.m
 \item{numints}{a number of intervals for the grid density object, by default is 20}
 }
 \value{
-a grid density matrix
+a list with the grid density matrix (\code{grid}) and the classes of the x and y inputs
+(\code{class.x} and \code{class.y})
 }
 \description{
 Generates a density grid that can then be used for heatmap or contour plots.
diff --git a/man/heatmapPlotDS.Rd b/man/heatmapPlotDS.Rd
index a8e21840..f10c3e21 100644
--- a/man/heatmapPlotDS.Rd
+++ b/man/heatmapPlotDS.Rd
@@ -22,7 +22,8 @@ noise if the \code{method.indicator} is equal to 2 (i.e. probabilistic method).}
 }
 \value{
 a list with the x and y coordinates of the centroids if the deterministic method is used
-or the x and y coordinated of the noisy data if the probabilistic method is used.
+or the x and y coordinated of the noisy data if the probabilistic method is used, along with the
+classes of the x and y inputs (\code{class.x} and \code{class.y})
 }
 \description{
 This function calculates the coordinates of the centroids for each n nearest neighbours.
diff --git a/man/histogramDS1.Rd b/man/histogramDS1.Rd
index ef91faef..129ed632 100644
--- a/man/histogramDS1.Rd
+++ b/man/histogramDS1.Rd
@@ -21,7 +21,8 @@ If the value is set to 3 then the 'probabilistic' method is used.}
 noise if the \code{method.indicator} is equal to 3 (i.e. probabilistic method).}
 }
 \value{
-a numeric vector which contains the minimum and the maximum values of the vector
+a list with the numeric vector containing the minimum and the maximum values of the
+vector (\code{range}) and the class of the input vector (\code{class})
 }
 \description{
 this function returns the minimum and maximum of the input numeric vector which
diff --git a/man/scatterPlotDS.Rd b/man/scatterPlotDS.Rd
index 4f715d2c..96a08442 100644
--- a/man/scatterPlotDS.Rd
+++ b/man/scatterPlotDS.Rd
@@ -22,7 +22,8 @@ deterministic method is selected.}
 noise if the probabilistic method is selected.}
 }
 \value{
-a list with the x and y coordinates of the data to be plot
+a list with the x and y coordinates of the data to be plot, along with the classes of
+the x and y inputs (\code{class.x} and \code{class.y})
 }
 \description{
 This function uses two disclosure control methods to generate non-disclosive
diff --git a/tests/testthat/test-smk-boxPlotGGDS.R b/tests/testthat/test-smk-boxPlotGGDS.R
new file mode 100644
index 00000000..ff1a4070
--- /dev/null
+++ b/tests/testthat/test-smk-boxPlotGGDS.R
@@ -0,0 +1,53 @@
+#-------------------------------------------------------------------------------
+# 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("boxPlotGGDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("boxPlotGGDS::smk")
+test_that("boxPlotGGDS, no grouping", {
+    boxPlotRawData <- data.frame(x = rep("v1", 20), value = c(1:20))
+
+    res <- boxPlotGGDS("boxPlotRawData")
+
+    expect_length(res, 2)
+    expect_equal(res[[2]], "no_group")
+})
+
+test_that("boxPlotGGDS, single grouping", {
+    boxPlotRawData <- data.frame(x = rep("v1", 20), value = c(1:20), group = factor(rep(c("a", "b"), 10)))
+
+    res <- boxPlotGGDS("boxPlotRawData", group = "group")
+
+    expect_length(res, 2)
+    expect_equal(res[[2]], "single_group")
+})
+
+test_that("boxPlotGGDS fails when data_table.name references nonexistent object", {
+    expect_error(boxPlotGGDS("nonexistent_obj"), "does not exist")
+})
+
+#
+# Done
+#
+
+# context("boxPlotGGDS::smk::shutdown")
+
+# context("boxPlotGGDS::smk::done")
diff --git a/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R b/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R
new file mode 100644
index 00000000..30510817
--- /dev/null
+++ b/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R
@@ -0,0 +1,61 @@
+#-------------------------------------------------------------------------------
+# 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("boxPlotGG_data_TreatmentDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("boxPlotGG_data_TreatmentDS::smk")
+test_that("boxPlotGG_data_TreatmentDS, no grouping", {
+    D <- data.frame(v1 = c(1:20), v2 = c(20:1))
+
+    res <- boxPlotGG_data_TreatmentDS("D", variables = c("v1", "v2"))
+
+    expect_true(all(c("x", "value") %in% names(res)))
+})
+
+test_that("boxPlotGG_data_TreatmentDS, single grouping", {
+    D <- data.frame(v1 = c(1:20), group = factor(rep(c("a", "b"), 10)))
+
+    res <- boxPlotGG_data_TreatmentDS("D", variables = c("v1"), group = "group")
+
+    expect_true(all(c("x", "value", "group") %in% names(res)))
+})
+
+test_that("boxPlotGG_data_TreatmentDS fails when table.name references nonexistent object", {
+    expect_error(boxPlotGG_data_TreatmentDS("nonexistent_obj", variables = c("v1")), "does not exist")
+})
+
+test_that("boxPlotGG_data_TreatmentDS fails when a variable is not numeric or integer", {
+    D <- data.frame(v1 = c("a", "b", "c"))
+    expect_error(boxPlotGG_data_TreatmentDS("D", variables = c("v1")), "must be of type numeric or integer")
+})
+
+test_that("boxPlotGG_data_TreatmentDS fails when group is not a factor", {
+    D <- data.frame(v1 = c(1:20), group = c(1:20))
+    expect_error(boxPlotGG_data_TreatmentDS("D", variables = c("v1"), group = "group"), "must be of type factor")
+})
+
+#
+# Done
+#
+
+# context("boxPlotGG_data_TreatmentDS::smk::shutdown")
+
+# context("boxPlotGG_data_TreatmentDS::smk::done")
diff --git a/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R b/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R
new file mode 100644
index 00000000..58c14448
--- /dev/null
+++ b/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R
@@ -0,0 +1,49 @@
+#-------------------------------------------------------------------------------
+# 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("boxPlotGG_data_Treatment_numericDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("boxPlotGG_data_Treatment_numericDS::smk")
+test_that("boxPlotGG_data_Treatment_numericDS", {
+    v1 <- c(1:20)
+
+    res <- boxPlotGG_data_Treatment_numericDS("v1")
+
+    expect_equal(unique(res$x), "v1")
+    expect_equal(res$value, v1)
+})
+
+test_that("boxPlotGG_data_Treatment_numericDS fails when vector.name references nonexistent object", {
+    expect_error(boxPlotGG_data_Treatment_numericDS("nonexistent_obj"), "does not exist")
+})
+
+test_that("boxPlotGG_data_Treatment_numericDS fails when vector is not numeric or integer", {
+    v1 <- c("a", "b", "c")
+    expect_error(boxPlotGG_data_Treatment_numericDS("v1"), "must be of type numeric or integer")
+})
+
+#
+# Done
+#
+
+# context("boxPlotGG_data_Treatment_numericDS::smk::shutdown")
+
+# context("boxPlotGG_data_Treatment_numericDS::smk::done")
diff --git a/tests/testthat/test-smk-densityGridDS.R b/tests/testthat/test-smk-densityGridDS.R
index b0b4f00c..05efb14f 100644
--- a/tests/testthat/test-smk-densityGridDS.R
+++ b/tests/testthat/test-smk-densityGridDS.R
@@ -39,13 +39,15 @@ test_that("densityGridDS", {
   res <- densityGridDS(x="xvect", y="yvect", limits=FALSE, x.min=NULL,
                         x.max=NULL, y.min=NULL, y.max=NULL, numints=numints)
   
-    expect_equal(class(res), c("matrix","array"))
-    expect_equal(colnames(res), c("", "", "", "x.mids", "y.mids"))
-    expect_equal(as.numeric(round(res[1,], digits=3)), c(3.000, 0.000, 0.000, 8.798, 13.870))
-    expect_equal(as.numeric(round(res[2,], digits=3)), c(4.000, 5.000, 0.000, 10.195, 16.870))
-    expect_equal(as.numeric(round(res[3,], digits=3)), c(3.000, 0.000, 0.000, 11.592, 19.870))
-    
-    expect_equal(names(dimnames(res))[2], "Number of invalid cells (cells with counts >0 and < nfilter.tab ) is 4")
+    expect_equal(class(res$grid), c("matrix","array"))
+    expect_equal(colnames(res$grid), c("", "", "", "x.mids", "y.mids"))
+    expect_equal(as.numeric(round(res$grid[1,], digits=3)), c(3.000, 0.000, 0.000, 8.798, 13.870))
+    expect_equal(as.numeric(round(res$grid[2,], digits=3)), c(4.000, 5.000, 0.000, 10.195, 16.870))
+    expect_equal(as.numeric(round(res$grid[3,], digits=3)), c(3.000, 0.000, 0.000, 11.592, 19.870))
+
+    expect_equal(names(dimnames(res$grid))[2], "Number of invalid cells (cells with counts >0 and < nfilter.tab ) is 4")
+    expect_equal(res$class.x, "numeric")
+    expect_equal(res$class.y, "numeric")
     
 })
 
@@ -59,6 +61,18 @@ test_that("densityGridDS fails when y references nonexistent object", {
     expect_error(densityGridDS(x="yvect", y="nonexistent_obj", numints=3), "does not exist")
 })
 
+test_that("densityGridDS fails when x is not numeric or integer", {
+    xvect <- c("a", "b", "c")
+    yvect <- c(1, 2, 3)
+    expect_error(densityGridDS(x="xvect", y="yvect", numints=3), "must be of type numeric or integer")
+})
+
+test_that("densityGridDS fails when y is not numeric or integer", {
+    xvect <- c(1, 2, 3)
+    yvect <- c("a", "b", "c")
+    expect_error(densityGridDS(x="xvect", y="yvect", numints=3), "must be of type numeric or integer")
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-heatmapPlotDS.R b/tests/testthat/test-smk-heatmapPlotDS.R
new file mode 100644
index 00000000..b205a9e3
--- /dev/null
+++ b/tests/testthat/test-smk-heatmapPlotDS.R
@@ -0,0 +1,66 @@
+#-------------------------------------------------------------------------------
+# 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("heatmapPlotDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("heatmapPlotDS::smk")
+test_that("heatmapPlotDS, deterministic method", {
+    xvect <- c(1:20)
+    yvect <- c(20:1)
+
+    res <- heatmapPlotDS("xvect", "yvect", k=3, noise=0.25, method.indicator=1)
+
+    expect_length(res, 4)
+    expect_length(res[[1]], 20)
+    expect_length(res[[2]], 20)
+    expect_equal(res$class.x, "integer")
+    expect_equal(res$class.y, "integer")
+})
+
+test_that("heatmapPlotDS fails when x references nonexistent object", {
+    yvect <- c(20:1)
+    expect_error(heatmapPlotDS("nonexistent_obj", "yvect", k=3, noise=0.25, method.indicator=1), "does not exist")
+})
+
+test_that("heatmapPlotDS fails when y references nonexistent object", {
+    xvect <- c(1:20)
+    expect_error(heatmapPlotDS("xvect", "nonexistent_obj", k=3, noise=0.25, method.indicator=1), "does not exist")
+})
+
+test_that("heatmapPlotDS fails when x is not numeric or integer", {
+    xvect <- c("a", "b", "c")
+    yvect <- c(1, 2, 3)
+    expect_error(heatmapPlotDS("xvect", "yvect", k=3, noise=0.25, method.indicator=1), "must be of type numeric or integer")
+})
+
+test_that("heatmapPlotDS fails when y is not numeric or integer", {
+    xvect <- c(1, 2, 3)
+    yvect <- c("a", "b", "c")
+    expect_error(heatmapPlotDS("xvect", "yvect", k=3, noise=0.25, method.indicator=1), "must be of type numeric or integer")
+})
+
+#
+# Done
+#
+
+# context("heatmapPlotDS::smk::shutdown")
+
+# context("heatmapPlotDS::smk::done")
diff --git a/tests/testthat/test-smk-histogramDS1.R b/tests/testthat/test-smk-histogramDS1.R
new file mode 100644
index 00000000..670c4eda
--- /dev/null
+++ b/tests/testthat/test-smk-histogramDS1.R
@@ -0,0 +1,51 @@
+#-------------------------------------------------------------------------------
+# 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("histogramDS1::smk::setup")
+
+set.standard.disclosure.settings()
+set.random.seed.setting(1234)
+
+#
+# Tests
+#
+
+# context("histogramDS1::smk")
+test_that("histogramDS1, smallCellsRule method", {
+    xvect <- c(1:100)
+
+    res <- histogramDS1("xvect", method.indicator=1, k=3, noise=0.25)
+
+    expect_length(res, 2)
+    expect_equal(res$class, "integer")
+    expect_length(res$range, 2)
+})
+
+test_that("histogramDS1 fails when x references nonexistent object", {
+    expect_error(histogramDS1("nonexistent_obj", method.indicator=1, k=3, noise=0.25), "does not exist")
+})
+
+test_that("histogramDS1 fails when x is not numeric or integer", {
+    xvect <- c("a", "b", "c")
+    expect_error(histogramDS1("xvect", method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer")
+})
+
+#
+# Done
+#
+
+# context("histogramDS1::smk::shutdown")
+
+# context("histogramDS1::smk::done")
diff --git a/tests/testthat/test-smk-histogramDS2.R b/tests/testthat/test-smk-histogramDS2.R
new file mode 100644
index 00000000..a0dd7c99
--- /dev/null
+++ b/tests/testthat/test-smk-histogramDS2.R
@@ -0,0 +1,50 @@
+#-------------------------------------------------------------------------------
+# 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("histogramDS2::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("histogramDS2::smk")
+test_that("histogramDS2, smallCellsRule method", {
+    xvect <- c(1:100)
+
+    res <- histogramDS2("xvect", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25)
+
+    expect_length(res, 2)
+    expect_true(inherits(res$histobject, "histogram"))
+    expect_equal(res$invalidcells, 0)
+})
+
+test_that("histogramDS2 fails when x references nonexistent object", {
+    expect_error(histogramDS2("nonexistent_obj", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), "does not exist")
+})
+
+test_that("histogramDS2 fails when x is not numeric or integer", {
+    xvect <- c("a", "b", "c")
+    expect_error(histogramDS2("xvect", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer")
+})
+
+#
+# Done
+#
+
+# context("histogramDS2::smk::shutdown")
+
+# context("histogramDS2::smk::done")
diff --git a/tests/testthat/test-smk-scatterPlotDS.R b/tests/testthat/test-smk-scatterPlotDS.R
new file mode 100644
index 00000000..94efdb0a
--- /dev/null
+++ b/tests/testthat/test-smk-scatterPlotDS.R
@@ -0,0 +1,66 @@
+#-------------------------------------------------------------------------------
+# 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("scatterPlotDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+# context("scatterPlotDS::smk")
+test_that("scatterPlotDS, deterministic method", {
+    xvect <- c(1:20)
+    yvect <- c(20:1)
+
+    res <- scatterPlotDS("xvect", "yvect", method.indicator=1, k=3, noise=0.25)
+
+    expect_length(res, 4)
+    expect_length(res[[1]], 20)
+    expect_length(res[[2]], 20)
+    expect_equal(res$class.x, "integer")
+    expect_equal(res$class.y, "integer")
+})
+
+test_that("scatterPlotDS fails when x references nonexistent object", {
+    yvect <- c(20:1)
+    expect_error(scatterPlotDS("nonexistent_obj", "yvect", method.indicator=1, k=3, noise=0.25), "does not exist")
+})
+
+test_that("scatterPlotDS fails when y references nonexistent object", {
+    xvect <- c(1:20)
+    expect_error(scatterPlotDS("xvect", "nonexistent_obj", method.indicator=1, k=3, noise=0.25), "does not exist")
+})
+
+test_that("scatterPlotDS fails when x is not numeric or integer", {
+    xvect <- c("a", "b", "c")
+    yvect <- c(1, 2, 3)
+    expect_error(scatterPlotDS("xvect", "yvect", method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer")
+})
+
+test_that("scatterPlotDS fails when y is not numeric or integer", {
+    xvect <- c(1, 2, 3)
+    yvect <- c("a", "b", "c")
+    expect_error(scatterPlotDS("xvect", "yvect", method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer")
+})
+
+#
+# Done
+#
+
+# context("scatterPlotDS::smk::shutdown")
+
+# context("scatterPlotDS::smk::done")

From 24f9939154fcadafca21fcb04ec53ec3f4501d87 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 15 Sep 2026 09:41:11 +0200
Subject: [PATCH 5/5] removed mistakenly added copywright

---
 tests/testthat/test-smk-boxPlotGGDS.R                 | 11 -----------
 tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R  | 11 -----------
 .../test-smk-boxPlotGG_data_Treatment_numericDS.R     | 11 -----------
 tests/testthat/test-smk-heatmapPlotDS.R               | 11 -----------
 tests/testthat/test-smk-histogramDS1.R                | 11 -----------
 tests/testthat/test-smk-histogramDS2.R                | 11 -----------
 tests/testthat/test-smk-scatterPlotDS.R               | 11 -----------
 7 files changed, 77 deletions(-)

diff --git a/tests/testthat/test-smk-boxPlotGGDS.R b/tests/testthat/test-smk-boxPlotGGDS.R
index ff1a4070..fe7db46e 100644
--- a/tests/testthat/test-smk-boxPlotGGDS.R
+++ b/tests/testthat/test-smk-boxPlotGGDS.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #
diff --git a/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R b/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R
index 30510817..0deb5ff5 100644
--- a/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R
+++ b/tests/testthat/test-smk-boxPlotGG_data_TreatmentDS.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #
diff --git a/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R b/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R
index 58c14448..354de5cd 100644
--- a/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R
+++ b/tests/testthat/test-smk-boxPlotGG_data_Treatment_numericDS.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #
diff --git a/tests/testthat/test-smk-heatmapPlotDS.R b/tests/testthat/test-smk-heatmapPlotDS.R
index b205a9e3..1313d608 100644
--- a/tests/testthat/test-smk-heatmapPlotDS.R
+++ b/tests/testthat/test-smk-heatmapPlotDS.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #
diff --git a/tests/testthat/test-smk-histogramDS1.R b/tests/testthat/test-smk-histogramDS1.R
index 670c4eda..10559b97 100644
--- a/tests/testthat/test-smk-histogramDS1.R
+++ b/tests/testthat/test-smk-histogramDS1.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #
diff --git a/tests/testthat/test-smk-histogramDS2.R b/tests/testthat/test-smk-histogramDS2.R
index a0dd7c99..da26d99a 100644
--- a/tests/testthat/test-smk-histogramDS2.R
+++ b/tests/testthat/test-smk-histogramDS2.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #
diff --git a/tests/testthat/test-smk-scatterPlotDS.R b/tests/testthat/test-smk-scatterPlotDS.R
index 94efdb0a..7fee3d3e 100644
--- a/tests/testthat/test-smk-scatterPlotDS.R
+++ b/tests/testthat/test-smk-scatterPlotDS.R
@@ -1,14 +1,3 @@
-#-------------------------------------------------------------------------------
-# 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
 #