From 43398e8452b45322f8762cf2c3e19e826f68a492 Mon Sep 17 00:00:00 2001 From: ESCRI11 Date: Mon, 27 Oct 2025 18:57:32 +0100 Subject: [PATCH 01/30] =?UTF-8?q?feat=C3=91=20mdPatterns=20fct?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- NAMESPACE | 1 + R/mdPatternDS.R | 121 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 R/mdPatternDS.R diff --git a/NAMESPACE b/NAMESPACE index 897148d1..e52e5d10 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -82,6 +82,7 @@ export(matrixDimnamesDS) export(matrixInvertDS) export(matrixMultDS) export(matrixTransposeDS) +export(mdPatternDS) export(meanDS) export(meanSdGpDS) export(mergeDS) diff --git a/R/mdPatternDS.R b/R/mdPatternDS.R new file mode 100644 index 00000000..0f817034 --- /dev/null +++ b/R/mdPatternDS.R @@ -0,0 +1,121 @@ +#' +#' @title Missing data pattern with disclosure control +#' @description This function is a serverside aggregate function that computes the +#' missing data pattern using mice::md.pattern and applies disclosure control to +#' prevent revealing small cell counts. +#' @details This function calls the mice::md.pattern function to generate a matrix +#' showing the missing data patterns in the input data. To ensure disclosure control, +#' any pattern counts that are below the threshold (nfilter.tab, default=3) are +#' suppressed. +#' +#' \strong{Suppression Method:} +#' +#' When a pattern count is below threshold: +#' - Row name is changed to "suppressed()" where N is the threshold +#' - All pattern values in that row are set to NA +#' - Summary row is also set to NA (prevents back-calculation) +#' +#' \strong{Output Matrix Structure:} +#' +#' - Rows represent different missing data patterns (plus a summary row at the bottom) +#' - Row names contain pattern counts (or "suppressed()" for invalid patterns) +#' - Columns show 1 if variable is observed, 0 if missing +#' - Last column shows total number of missing values per pattern +#' - Last row shows total number of missing values per variable +#' +#' \strong{Note for Pooling:} +#' +#' When this function is called from ds.mdPattern with type='combine', suppressed +#' patterns are excluded from pooling to prevent disclosure through subtraction. +#' This means pooled counts may underestimate the true total when patterns are +#' suppressed in some studies. +#' +#' @param x a character string specifying the name of a data frame or matrix +#' containing the data to analyze for missing patterns. +#' @return A list containing: +#' \item{pattern}{The missing data pattern matrix with disclosure control applied} +#' \item{valid}{Logical indicating if all patterns meet disclosure requirements} +#' \item{message}{A message describing the validity status} +#' @author Xavier Escribà montagut for DataSHIELD Development Team +#' @import mice +#' @export +#' +mdPatternDS <- function(x){ + + ############################################################# + # MODULE 1: CAPTURE THE nfilter SETTINGS + thr <- dsBase::listDisclosureSettingsDS() + nfilter.tab <- as.numeric(thr$nfilter.tab) + ############################################################# + + # Parse the input data name with error handling + x.val <- tryCatch( + { + eval(parse(text=x), envir = parent.frame()) + }, + error = function(e) { + stop(paste0("Object '", x, "' does not exist on the server"), call. = FALSE) + } + ) + + # Check object class + typ <- class(x.val) + + # Check that input is a data frame or matrix + if(!("data.frame" %in% typ || "matrix" %in% typ)){ + stop(paste0("The input object must be of type 'data.frame' or 'matrix'. Current type: ", + paste(typ, collapse = ", ")), call. = FALSE) + } + + # Use x.val for further processing + x <- x.val + + # Call mice::md.pattern with plot=FALSE + pattern <- mice::md.pattern(x, plot = FALSE) + + # Apply disclosure control + # Pattern counts are stored in row names (except last row which is empty/summary) + # The last row contains variable-level missing counts + + validity <- "valid" + n_patterns <- nrow(pattern) - 1 # exclude the summary row + + if(n_patterns > 0){ + # Check pattern counts (stored in row names, excluding last row) + pattern_counts <- as.numeric(rownames(pattern)[1:n_patterns]) + + # Find patterns with counts below threshold + invalid_idx <- which(pattern_counts > 0 & pattern_counts < nfilter.tab) + + if(length(invalid_idx) > 0){ + validity <- "invalid" + + # For invalid patterns, suppress by: + # - Setting row name to "suppressed" + # - Setting all pattern values to NA + rnames <- rownames(pattern) + for(idx in invalid_idx){ + rnames[idx] <- paste0("suppressed(<", nfilter.tab, ")") + pattern[idx, ] <- NA + } + rownames(pattern) <- rnames + + # Also need to recalculate the last row (summary) if patterns were suppressed + # Set to NA to avoid disclosures + pattern[nrow(pattern), seq_len(ncol(pattern))] <- NA + } + } + + # Return the pattern with validity information + return(list( + pattern = pattern, + valid = (validity == "valid"), + message = ifelse(validity == "valid", + "Valid: all pattern counts meet disclosure requirements", + paste0("Invalid: some pattern counts below threshold (", + nfilter.tab, ") have been suppressed")) + )) +} + +#AGGREGATE FUNCTION +# mdPatternDS From 987fbcc2f1129a491ce8e9793268a263451a2d8b Mon Sep 17 00:00:00 2001 From: ESCRI11 Date: Mon, 27 Oct 2025 19:00:24 +0100 Subject: [PATCH 02/30] add mdPatterns to DATASHIELD --- inst/DATASHIELD | 1 + 1 file changed, 1 insertion(+) diff --git a/inst/DATASHIELD b/inst/DATASHIELD index c9dd9390..0c59f0c2 100644 --- a/inst/DATASHIELD +++ b/inst/DATASHIELD @@ -37,6 +37,7 @@ AggregateMethods: lmerSLMADS2, lsDS, matrixDetDS1, + mdPatternDS, meanDS, meanSdGpDS, messageDS, From eda4bdc3e075170e2cf6c39f5b6f378585bdd85f Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 3 Nov 2025 00:14:29 +0000 Subject: [PATCH 03/30] Initial 'mdPatternDS' tests --- man/mdPatternDS.Rd | 54 +++++++++++++++++++++++++++ tests/testthat/test-arg-mdPatternDS.R | 41 ++++++++++++++++++++ tests/testthat/test-smk-mdPatternDS.R | 37 ++++++++++++++++++ 3 files changed, 132 insertions(+) create mode 100644 man/mdPatternDS.Rd create mode 100644 tests/testthat/test-arg-mdPatternDS.R create mode 100644 tests/testthat/test-smk-mdPatternDS.R diff --git a/man/mdPatternDS.Rd b/man/mdPatternDS.Rd new file mode 100644 index 00000000..1084565e --- /dev/null +++ b/man/mdPatternDS.Rd @@ -0,0 +1,54 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mdPatternDS.R +\name{mdPatternDS} +\alias{mdPatternDS} +\title{Missing data pattern with disclosure control} +\usage{ +mdPatternDS(x) +} +\arguments{ +\item{x}{a character string specifying the name of a data frame or matrix +containing the data to analyze for missing patterns.} +} +\value{ +A list containing: +\item{pattern}{The missing data pattern matrix with disclosure control applied} +\item{valid}{Logical indicating if all patterns meet disclosure requirements} +\item{message}{A message describing the validity status} +} +\description{ +This function is a serverside aggregate function that computes the +missing data pattern using mice::md.pattern and applies disclosure control to +prevent revealing small cell counts. +} +\details{ +This function calls the mice::md.pattern function to generate a matrix +showing the missing data patterns in the input data. To ensure disclosure control, +any pattern counts that are below the threshold (nfilter.tab, default=3) are +suppressed. + +\strong{Suppression Method:} + +When a pattern count is below threshold: +- Row name is changed to "suppressed()" where N is the threshold +- All pattern values in that row are set to NA +- Summary row is also set to NA (prevents back-calculation) + +\strong{Output Matrix Structure:} + +- Rows represent different missing data patterns (plus a summary row at the bottom) +- Row names contain pattern counts (or "suppressed()" for invalid patterns) +- Columns show 1 if variable is observed, 0 if missing +- Last column shows total number of missing values per pattern +- Last row shows total number of missing values per variable + +\strong{Note for Pooling:} + +When this function is called from ds.mdPattern with type='combine', suppressed +patterns are excluded from pooling to prevent disclosure through subtraction. +This means pooled counts may underestimate the true total when patterns are +suppressed in some studies. +} +\author{ +Xavier Escribà montagut for DataSHIELD Development Team +} diff --git a/tests/testthat/test-arg-mdPatternDS.R b/tests/testthat/test-arg-mdPatternDS.R new file mode 100644 index 00000000..f6b4f941 --- /dev/null +++ b/tests/testthat/test-arg-mdPatternDS.R @@ -0,0 +1,41 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2025 ProPASS Consortium. 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 . +#------------------------------------------------------------------------------- + +# +# Set up +# + +context("mdPatternDS::arg::setup") + +# +# Tests +# + +context("mdPatternDS::arg::x NULL") +test_that("mdPatternDS x NULL", { + x <- NULL + + expect_error(mdPatternDS(x), "The input object must be of type 'data.frame' or 'matrix'. Current type: NULL") +}) + +context("mdPatternDS::arg::x not valid variable") +test_that("mdPatternDS x not variable", { + x <- "not a variable" + + expect_error(mdPatternDS(x), "Object 'not a variable' does not exist on the server") +}) + +# +# Done +# + +context("mdPatternDS::arg::shutdown") + +context("mdPatternDS::arg::done") diff --git a/tests/testthat/test-smk-mdPatternDS.R b/tests/testthat/test-smk-mdPatternDS.R new file mode 100644 index 00000000..33e65055 --- /dev/null +++ b/tests/testthat/test-smk-mdPatternDS.R @@ -0,0 +1,37 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2025 ProPASS Consortium. 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 . +#------------------------------------------------------------------------------- + +# +# Set up +# + +context("mdPatternDS::smk::setup") + +# +# Tests +# + +context("mdPatternDS::smk::sample data.frame") +test_that("mdPatternDS: sample data.frame", { + x_val <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) + x <- "x_val" + + res <- mdPatternDS(x) + + expect_length(res, 3) +}) + +# +# Done +# + +context("mdPatternDS::smk::shutdown") + +context("mdPatternDS::smk::done") From e499d8d5873c671c31e7564cb868e1f140fdc42f Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 3 Nov 2025 13:24:58 +0000 Subject: [PATCH 04/30] Additional mdPattern tests --- tests/testthat/test-smk-mdPatternDS.R | 70 ++++++++++++++++++++++++++- 1 file changed, 68 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-smk-mdPatternDS.R b/tests/testthat/test-smk-mdPatternDS.R index 33e65055..f00feb84 100644 --- a/tests/testthat/test-smk-mdPatternDS.R +++ b/tests/testthat/test-smk-mdPatternDS.R @@ -18,14 +18,80 @@ context("mdPatternDS::smk::setup") # Tests # -context("mdPatternDS::smk::sample data.frame") -test_that("mdPatternDS: sample data.frame", { +context("mdPatternDS::smk::sample complete data.frame") +test_that("mdPatternDS: sample complete data.frame", { x_val <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) x <- "x_val" res <- mdPatternDS(x) expect_length(res, 3) + expect_length(class(res), 1) + expect_true(all(class(res) %in% c("list"))) + expect_length(class(res$pattern), 2) + expect_true(all(class(res$pattern) %in% c("matrix", "array"))) + + expect_length(colnames(res$pattern), 3) + expect_equal(colnames(res$pattern)[1], "v1") + expect_equal(colnames(res$pattern)[2], "v2") + expect_equal(colnames(res$pattern)[3], "") + expect_length(rownames(res$pattern), 2) + expect_equal(rownames(res$pattern)[1], "5") + expect_equal(rownames(res$pattern)[2], "") + + expect_equal(res$pattern[1, 1], 1) + expect_equal(res$pattern[1, 2], 1) + expect_equal(res$pattern[1, 3], 0) + expect_equal(res$pattern[2, 1], 0) + expect_equal(res$pattern[2, 2], 0) + expect_equal(res$pattern[2, 3], 0) + + expect_length(class(res$valid), 1) + expect_true(all(class(res$valid) %in% c("logical"))) + expect_true(res$valid) + expect_length(class(res$message), 1) + expect_true(all(class(res$message) %in% c("character"))) + expect_equal(res$message, "Valid: all pattern counts meet disclosure requirements") +}) + +context("mdPatternDS::smk::sample incomplete data.frame") +test_that("mdPatternDS: sample incomplete data.frame", { + x_val <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) + x <- "x_val" + + res <- mdPatternDS(x) + + expect_length(res, 3) + expect_length(class(res), 1) + expect_true(all(class(res) %in% c("list"))) + expect_length(class(res$pattern), 2) + expect_true(all(class(res$pattern) %in% c("matrix", "array"))) + + expect_length(colnames(res$pattern), 3) + expect_equal(colnames(res$pattern)[1], "v2") + expect_equal(colnames(res$pattern)[2], "v1") + expect_equal(colnames(res$pattern)[3], "") + expect_length(rownames(res$pattern), 3) + expect_equal(rownames(res$pattern)[1], "4") + expect_equal(rownames(res$pattern)[2], "1") + expect_equal(rownames(res$pattern)[3], "") + + expect_equal(res$pattern[1, 1], 1) + expect_equal(res$pattern[1, 2], 1) + expect_equal(res$pattern[1, 3], 0) + expect_equal(res$pattern[2, 1], 1) + expect_equal(res$pattern[2, 2], 0) + expect_equal(res$pattern[2, 3], 1) + expect_equal(res$pattern[3, 1], 0) + expect_equal(res$pattern[3, 2], 1) + expect_equal(res$pattern[3, 3], 1) + + expect_length(class(res$valid), 1) + expect_true(all(class(res$valid) %in% c("logical"))) + expect_true(res$valid) + expect_length(class(res$message), 1) + expect_true(all(class(res$message) %in% c("character"))) + expect_equal(res$message, "Valid: all pattern counts meet disclosure requirements") }) # From 2485816e6cf6a5f7872b935d00411002cd357593 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 3 Nov 2025 22:51:09 +0000 Subject: [PATCH 05/30] Increased data 'mdPatternDS' tests --- tests/testthat/test-smk-mdPatternDS.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-smk-mdPatternDS.R b/tests/testthat/test-smk-mdPatternDS.R index f00feb84..989fd06b 100644 --- a/tests/testthat/test-smk-mdPatternDS.R +++ b/tests/testthat/test-smk-mdPatternDS.R @@ -56,7 +56,7 @@ test_that("mdPatternDS: sample complete data.frame", { context("mdPatternDS::smk::sample incomplete data.frame") test_that("mdPatternDS: sample incomplete data.frame", { - x_val <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) + x_val <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, 4.0, 5.0, 6.0), v2 = c(6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0)) x <- "x_val" res <- mdPatternDS(x) @@ -72,7 +72,7 @@ test_that("mdPatternDS: sample incomplete data.frame", { expect_equal(colnames(res$pattern)[2], "v1") expect_equal(colnames(res$pattern)[3], "") expect_length(rownames(res$pattern), 3) - expect_equal(rownames(res$pattern)[1], "4") + expect_equal(rownames(res$pattern)[1], "6") expect_equal(rownames(res$pattern)[2], "1") expect_equal(rownames(res$pattern)[3], "") From cf61c2ba33f2087dbf3b135a708ca72494d74251 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 4 Nov 2025 12:57:27 +0000 Subject: [PATCH 06/30] Added 'set.standard.disclosure.settings()' --- tests/testthat/test-arg-mdPatternDS.R | 2 ++ tests/testthat/test-smk-mdPatternDS.R | 2 ++ 2 files changed, 4 insertions(+) diff --git a/tests/testthat/test-arg-mdPatternDS.R b/tests/testthat/test-arg-mdPatternDS.R index f6b4f941..bea53d22 100644 --- a/tests/testthat/test-arg-mdPatternDS.R +++ b/tests/testthat/test-arg-mdPatternDS.R @@ -14,6 +14,8 @@ context("mdPatternDS::arg::setup") +set.standard.disclosure.settings() + # # Tests # diff --git a/tests/testthat/test-smk-mdPatternDS.R b/tests/testthat/test-smk-mdPatternDS.R index f00feb84..4c2e4f92 100644 --- a/tests/testthat/test-smk-mdPatternDS.R +++ b/tests/testthat/test-smk-mdPatternDS.R @@ -14,6 +14,8 @@ context("mdPatternDS::smk::setup") +set.standard.disclosure.settings() + # # Tests # From da36ab8bc17caf6c7922c443ac2d75c5d4daf5bc Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 4 Nov 2025 16:23:31 +0000 Subject: [PATCH 07/30] Updated 'mdPatternDS' tests --- tests/testthat/test-disc-mdPatternDS.R | 69 ++++++++++++++++++++++++++ tests/testthat/test-smk-mdPatternDS.R | 30 ++++++----- 2 files changed, 83 insertions(+), 16 deletions(-) create mode 100644 tests/testthat/test-disc-mdPatternDS.R diff --git a/tests/testthat/test-disc-mdPatternDS.R b/tests/testthat/test-disc-mdPatternDS.R new file mode 100644 index 00000000..055974cc --- /dev/null +++ b/tests/testthat/test-disc-mdPatternDS.R @@ -0,0 +1,69 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2025 ProPASS Consortium. 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 . +#------------------------------------------------------------------------------- + +# +# Set up +# + +context("mdPatternDS::disc::setup") + +set.standard.disclosure.settings() + +# +# Tests +# + +context("mdPatternDS::disc::sample incomplete data.frame") +test_that("mdPatternDS: sample incomplete data.frame", { + x_val <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, 4.0, 5.0, 6.0), v2 = c(6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0)) + x <- "x_val" + + res <- mdPatternDS(x) + + expect_length(res, 3) + expect_length(class(res), 1) + expect_true(all(class(res) %in% c("list"))) + expect_length(class(res$pattern), 2) + expect_true(all(class(res$pattern) %in% c("matrix", "array"))) + + expect_length(colnames(res$pattern), 3) + expect_equal(colnames(res$pattern)[1], "v2") + expect_equal(colnames(res$pattern)[2], "v1") + expect_equal(colnames(res$pattern)[3], "") + expect_length(rownames(res$pattern), 3) + expect_equal(rownames(res$pattern)[1], "6") + expect_equal(rownames(res$pattern)[2], "suppressed(<3)") + expect_equal(rownames(res$pattern)[3], "") + + expect_equal(res$pattern[1, 1], 1) + expect_equal(res$pattern[1, 2], 1) + expect_equal(res$pattern[1, 3], 0) + expect_true(is.na(res$pattern[2, 1])) + expect_true(is.na(res$pattern[2, 2])) + expect_true(is.na(res$pattern[2, 3])) + expect_true(is.na(res$pattern[3, 1])) + expect_true(is.na(res$pattern[3, 2])) + expect_true(is.na(res$pattern[3, 3])) + + expect_length(class(res$valid), 1) + expect_true(all(class(res$valid) %in% c("logical"))) + expect_false(res$valid) + expect_length(class(res$message), 1) + expect_true(all(class(res$message) %in% c("character"))) + expect_equal(res$message, "Invalid: some pattern counts below threshold (3) have been suppressed") +}) + +# +# Done +# + +context("mdPatternDS::disc::shutdown") + +context("mdPatternDS::disc::done") diff --git a/tests/testthat/test-smk-mdPatternDS.R b/tests/testthat/test-smk-mdPatternDS.R index 96c43772..6cbe0062 100644 --- a/tests/testthat/test-smk-mdPatternDS.R +++ b/tests/testthat/test-smk-mdPatternDS.R @@ -20,8 +20,8 @@ set.standard.disclosure.settings() # Tests # -context("mdPatternDS::smk::sample complete data.frame") -test_that("mdPatternDS: sample complete data.frame", { +context("mdPatternDS::smk::sample 1 complete data.frame") +test_that("mdPatternDS: sample 1 complete data.frame", { x_val <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) x <- "x_val" @@ -56,9 +56,10 @@ test_that("mdPatternDS: sample complete data.frame", { expect_equal(res$message, "Valid: all pattern counts meet disclosure requirements") }) -context("mdPatternDS::smk::sample incomplete data.frame") -test_that("mdPatternDS: sample incomplete data.frame", { - x_val <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, 4.0, 5.0, 6.0), v2 = c(6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0)) + +context("mdPatternDS::smk::sample 2 complete data.frame") +test_that("mdPatternDS: sample 2 complete data.frame", { + x_val <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0), v2 = c(9.0, 8.0, 7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0)) x <- "x_val" res <- mdPatternDS(x) @@ -70,23 +71,20 @@ test_that("mdPatternDS: sample incomplete data.frame", { expect_true(all(class(res$pattern) %in% c("matrix", "array"))) expect_length(colnames(res$pattern), 3) - expect_equal(colnames(res$pattern)[1], "v2") - expect_equal(colnames(res$pattern)[2], "v1") + expect_equal(colnames(res$pattern)[1], "v1") + expect_equal(colnames(res$pattern)[2], "v2") expect_equal(colnames(res$pattern)[3], "") - expect_length(rownames(res$pattern), 3) - expect_equal(rownames(res$pattern)[1], "6") - expect_equal(rownames(res$pattern)[2], "1") - expect_equal(rownames(res$pattern)[3], "") + expect_length(rownames(res$pattern), 2) + expect_equal(rownames(res$pattern)[1], "10") + expect_equal(rownames(res$pattern)[2], "") + expect_true(is.na(rownames(res$pattern)[3])) expect_equal(res$pattern[1, 1], 1) expect_equal(res$pattern[1, 2], 1) expect_equal(res$pattern[1, 3], 0) - expect_equal(res$pattern[2, 1], 1) + expect_equal(res$pattern[2, 1], 0) expect_equal(res$pattern[2, 2], 0) - expect_equal(res$pattern[2, 3], 1) - expect_equal(res$pattern[3, 1], 0) - expect_equal(res$pattern[3, 2], 1) - expect_equal(res$pattern[3, 3], 1) + expect_equal(res$pattern[2, 3], 0) expect_length(class(res$valid), 1) expect_true(all(class(res$valid) %in% c("logical"))) From 9b0fec193d58d1d45519289037fe57647fffa1dd Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 21 Nov 2025 13:08:41 +0000 Subject: [PATCH 08/30] Fix version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d00d8a10..bc5e3973 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'. -Version: 6.3.4 +Version: 6.3.5.9000 Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), From 2a3b3feee138a0b975066118dbc5223a6b6223fa Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 21 Nov 2025 13:13:33 +0000 Subject: [PATCH 09/30] Update to docs --- docs/404.html | 4 +- docs/LICENSE.html | 4 +- docs/authors.html | 8 +- docs/index.html | 4 +- docs/pkgdown.yml | 4 +- docs/reference/BooleDS.html | 4 +- docs/reference/absDS.html | 4 +- docs/reference/asCharacterDS.html | 4 +- docs/reference/asDataMatrixDS.html | 4 +- docs/reference/asFactorDS1.html | 4 +- docs/reference/asFactorDS2.html | 4 +- docs/reference/asFactorSimpleDS.html | 4 +- docs/reference/asIntegerDS.html | 4 +- docs/reference/asListDS.html | 4 +- docs/reference/asLogicalDS.html | 4 +- docs/reference/asMatrixDS.html | 4 +- docs/reference/asNumericDS.html | 4 +- docs/reference/aucDS.html | 4 +- docs/reference/blackBoxDS.html | 4 +- docs/reference/blackBoxRanksDS.html | 4 +- docs/reference/boxPlotGGDS.html | 4 +- .../reference/boxPlotGG_data_TreatmentDS.html | 4 +- .../boxPlotGG_data_Treatment_numericDS.html | 4 +- docs/reference/bp_standardsDS.html | 4 +- docs/reference/cDS.html | 4 +- docs/reference/cbindDS.html | 4 +- docs/reference/changeRefGroupDS.html | 4 +- docs/reference/checkNegValueDS.html | 4 +- .../checkPermissivePrivacyControlLevel.html | 4 +- docs/reference/classDS.html | 4 +- docs/reference/colnamesDS.html | 4 +- docs/reference/completeCasesDS.html | 4 +- docs/reference/corDS.html | 4 +- docs/reference/corTestDS.html | 4 +- docs/reference/covDS.html | 4 +- docs/reference/dataFrameDS.html | 4 +- docs/reference/dataFrameFillDS.html | 4 +- docs/reference/dataFrameSortDS.html | 4 +- docs/reference/dataFrameSubsetDS1.html | 4 +- docs/reference/dataFrameSubsetDS2.html | 4 +- docs/reference/densityGridDS.html | 4 +- docs/reference/dimDS.html | 4 +- docs/reference/dmtC2SDS.html | 4 +- docs/reference/dsBase-package.html | 4 +- docs/reference/elsplineDS.html | 4 +- docs/reference/extractQuantilesDS1.html | 4 +- docs/reference/extractQuantilesDS2.html | 4 +- docs/reference/gamlssDS.html | 4 +- docs/reference/getWGSRDS.html | 4 +- docs/reference/glmDS1.html | 4 +- docs/reference/glmDS2.html | 4 +- docs/reference/glmPredictDS.ag.html | 4 +- docs/reference/glmPredictDS.as.html | 4 +- docs/reference/glmSLMADS.assign.html | 4 +- docs/reference/glmSLMADS1.html | 4 +- docs/reference/glmSLMADS2.html | 4 +- docs/reference/glmSummaryDS.ag.html | 4 +- docs/reference/glmSummaryDS.as.html | 4 +- docs/reference/glmerSLMADS.assign.html | 4 +- docs/reference/glmerSLMADS2.html | 4 +- docs/reference/heatmapPlotDS.html | 4 +- docs/reference/hetcorDS.html | 4 +- docs/reference/histogramDS1.html | 4 +- docs/reference/histogramDS2.html | 4 +- docs/reference/igb_standardsDS.html | 4 +- docs/reference/index.html | 8 +- docs/reference/isNaDS.html | 4 +- docs/reference/isValidDS.html | 4 +- docs/reference/kurtosisDS1.html | 4 +- docs/reference/kurtosisDS2.html | 4 +- docs/reference/lengthDS.html | 4 +- docs/reference/levelsDS.html | 4 +- docs/reference/lexisDS1.html | 4 +- docs/reference/lexisDS2.html | 4 +- docs/reference/lexisDS3.html | 4 +- docs/reference/listDS.html | 4 +- docs/reference/listDisclosureSettingsDS.html | 4 +- docs/reference/lmerSLMADS.assign.html | 4 +- docs/reference/lmerSLMADS2.html | 4 +- docs/reference/lsDS.html | 4 +- docs/reference/lsplineDS.html | 4 +- docs/reference/matrixDS.html | 4 +- docs/reference/matrixDetDS1.html | 4 +- docs/reference/matrixDetDS2.html | 4 +- docs/reference/matrixDiagDS.html | 4 +- docs/reference/matrixDimnamesDS.html | 4 +- docs/reference/matrixInvertDS.html | 4 +- docs/reference/matrixMultDS.html | 4 +- docs/reference/matrixTransposeDS.html | 4 +- docs/reference/mdPatternDS.html | 127 ++++++++++++++++++ docs/reference/meanDS.html | 4 +- docs/reference/meanSdGpDS.html | 4 +- docs/reference/mergeDS.html | 4 +- docs/reference/messageDS.html | 4 +- docs/reference/metadataDS.html | 4 +- docs/reference/miceDS.html | 4 +- docs/reference/minMaxRandDS.html | 4 +- docs/reference/namesDS.html | 4 +- docs/reference/nsDS.html | 4 +- docs/reference/numNaDS.html | 4 +- docs/reference/qlsplineDS.html | 4 +- docs/reference/quantileMeanDS.html | 4 +- docs/reference/rBinomDS.html | 4 +- docs/reference/rNormDS.html | 4 +- docs/reference/rPoisDS.html | 4 +- docs/reference/rUnifDS.html | 4 +- docs/reference/rangeDS.html | 4 +- docs/reference/ranksSecureDS1.html | 4 +- docs/reference/ranksSecureDS2.html | 4 +- docs/reference/ranksSecureDS3.html | 4 +- docs/reference/ranksSecureDS4.html | 4 +- docs/reference/ranksSecureDS5.html | 4 +- docs/reference/rbindDS.html | 4 +- docs/reference/reShapeDS.html | 4 +- docs/reference/recodeLevelsDS.html | 4 +- docs/reference/recodeValuesDS.html | 4 +- docs/reference/repDS.html | 4 +- docs/reference/replaceNaDS.html | 4 +- docs/reference/rmDS.html | 4 +- docs/reference/rowColCalcDS.html | 4 +- docs/reference/sampleDS.html | 4 +- docs/reference/scatterPlotDS.html | 4 +- docs/reference/seqDS.html | 4 +- docs/reference/setSeedDS.html | 4 +- docs/reference/skewnessDS1.html | 4 +- docs/reference/skewnessDS2.html | 4 +- docs/reference/sqrtDS.html | 4 +- docs/reference/subsetByClassDS.html | 4 +- docs/reference/subsetDS.html | 4 +- docs/reference/table1DDS.html | 4 +- docs/reference/table2DDS.html | 4 +- docs/reference/tableDS.assign.html | 4 +- docs/reference/tableDS.html | 4 +- docs/reference/tableDS2.html | 4 +- docs/reference/tapplyDS.assign.html | 4 +- docs/reference/tapplyDS.html | 4 +- docs/reference/testObjExistsDS.html | 4 +- docs/reference/unListDS.html | 4 +- docs/reference/uniqueDS.html | 4 +- docs/reference/varDS.html | 4 +- docs/reference/vectorDS.html | 4 +- docs/sitemap.xml | 1 + 142 files changed, 414 insertions(+), 282 deletions(-) create mode 100644 docs/reference/mdPatternDS.html diff --git a/docs/404.html b/docs/404.html index bd9ca2cd..828175ea 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -78,7 +78,7 @@

Page not found (404)

-

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+

Site built with pkgdown 2.2.0.

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NA

-

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+

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diff --git a/docs/authors.html b/docs/authors.html index 0b165dc3..a1aec549 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -102,12 +102,12 @@

Citation

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. -R package version 6.3.4. +R package version 6.3.5.9000. 

@Manual{,
   title = {dsBase: 'DataSHIELD' Server Side Base Functions},
   author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
-  note = {R package version 6.3.4},
+  note = {R package version 6.3.5.9000},
 }

Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” @@ -168,7 +168,7 @@

Citation

-

Site built with pkgdown 2.1.3.

+

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diff --git a/docs/index.html b/docs/index.html index 0afa2dfa..1f70741d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -180,7 +180,7 @@

Developers

-

Site built with pkgdown 2.1.3.

+

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diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 45989012..ad3a64a8 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 3.1.3 -pkgdown: 2.1.3 +pkgdown: 2.2.0 pkgdown_sha: ~ articles: {} -last_built: 2025-09-17T15:04Z +last_built: 2025-11-21T13:10Z diff --git a/docs/reference/BooleDS.html b/docs/reference/BooleDS.html index e99c093a..7cecbed2 100644 --- a/docs/reference/BooleDS.html +++ b/docs/reference/BooleDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -115,7 +115,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

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Author

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+

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diff --git a/docs/reference/asCharacterDS.html b/docs/reference/asCharacterDS.html index ad7fee82..8f461038 100644 --- a/docs/reference/asCharacterDS.html +++ b/docs/reference/asCharacterDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -85,7 +85,7 @@

Author

-

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+

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diff --git a/docs/reference/asDataMatrixDS.html b/docs/reference/asDataMatrixDS.html index 043d39ca..2b8fb1d3 100644 --- a/docs/reference/asDataMatrixDS.html +++ b/docs/reference/asDataMatrixDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asFactorDS1.html b/docs/reference/asFactorDS1.html index 5fc2e8c2..a5463d70 100644 --- a/docs/reference/asFactorDS1.html +++ b/docs/reference/asFactorDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -80,7 +80,7 @@

Details

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asFactorDS2.html b/docs/reference/asFactorDS2.html index 8fc3ef70..7e1711d3 100644 --- a/docs/reference/asFactorDS2.html +++ b/docs/reference/asFactorDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -102,7 +102,7 @@

Details

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asFactorSimpleDS.html b/docs/reference/asFactorSimpleDS.html index 999c986c..971a9169 100644 --- a/docs/reference/asFactorSimpleDS.html +++ b/docs/reference/asFactorSimpleDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -85,7 +85,7 @@

Details

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asIntegerDS.html b/docs/reference/asIntegerDS.html index 77292901..0de6c670 100644 --- a/docs/reference/asIntegerDS.html +++ b/docs/reference/asIntegerDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -86,7 +86,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asListDS.html b/docs/reference/asListDS.html index 65cdc968..ab9910cc 100644 --- a/docs/reference/asListDS.html +++ b/docs/reference/asListDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -99,7 +99,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asLogicalDS.html b/docs/reference/asLogicalDS.html index 1f6ab041..689e2461 100644 --- a/docs/reference/asLogicalDS.html +++ b/docs/reference/asLogicalDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -85,7 +85,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asMatrixDS.html b/docs/reference/asMatrixDS.html index 24e13348..a85c0c7c 100644 --- a/docs/reference/asMatrixDS.html +++ b/docs/reference/asMatrixDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -85,7 +85,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/asNumericDS.html b/docs/reference/asNumericDS.html index 9f8e3871..da79a362 100644 --- a/docs/reference/asNumericDS.html +++ b/docs/reference/asNumericDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -86,7 +86,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/aucDS.html b/docs/reference/aucDS.html index d031f39e..4800d9d1 100644 --- a/docs/reference/aucDS.html +++ b/docs/reference/aucDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -87,7 +87,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/blackBoxDS.html b/docs/reference/blackBoxDS.html index 29be83ec..5d02e3a9 100644 --- a/docs/reference/blackBoxDS.html +++ b/docs/reference/blackBoxDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -134,7 +134,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/blackBoxRanksDS.html b/docs/reference/blackBoxRanksDS.html index a552e899..458737b0 100644 --- a/docs/reference/blackBoxRanksDS.html +++ b/docs/reference/blackBoxRanksDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -126,7 +126,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/boxPlotGGDS.html b/docs/reference/boxPlotGGDS.html index be71d316..a0177c41 100644 --- a/docs/reference/boxPlotGGDS.html +++ b/docs/reference/boxPlotGGDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -92,7 +92,7 @@

Value

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/boxPlotGG_data_TreatmentDS.html b/docs/reference/boxPlotGG_data_TreatmentDS.html index b7afc848..7acead1e 100644 --- a/docs/reference/boxPlotGG_data_TreatmentDS.html +++ b/docs/reference/boxPlotGG_data_TreatmentDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -88,7 +88,7 @@

Value

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/boxPlotGG_data_Treatment_numericDS.html b/docs/reference/boxPlotGG_data_Treatment_numericDS.html index 7d6902ab..1aa7bd26 100644 --- a/docs/reference/boxPlotGG_data_Treatment_numericDS.html +++ b/docs/reference/boxPlotGG_data_Treatment_numericDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -74,7 +74,7 @@

Value

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/bp_standardsDS.html b/docs/reference/bp_standardsDS.html index 18406769..b7e661c4 100644 --- a/docs/reference/bp_standardsDS.html +++ b/docs/reference/bp_standardsDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -116,7 +116,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/cDS.html b/docs/reference/cDS.html index 410b22da..3cc043db 100644 --- a/docs/reference/cDS.html +++ b/docs/reference/cDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -81,7 +81,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/cbindDS.html b/docs/reference/cbindDS.html index c4be7c18..3bed8b0a 100644 --- a/docs/reference/cbindDS.html +++ b/docs/reference/cbindDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -100,7 +100,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/changeRefGroupDS.html b/docs/reference/changeRefGroupDS.html index 06ebb201..fbf6ba5f 100644 --- a/docs/reference/changeRefGroupDS.html +++ b/docs/reference/changeRefGroupDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -94,7 +94,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/checkNegValueDS.html b/docs/reference/checkNegValueDS.html index f96f4e41..e9d00fca 100644 --- a/docs/reference/checkNegValueDS.html +++ b/docs/reference/checkNegValueDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -82,7 +82,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/completeCasesDS.html b/docs/reference/completeCasesDS.html index 56845bf1..d84a6ede 100644 --- a/docs/reference/completeCasesDS.html +++ b/docs/reference/completeCasesDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -108,7 +108,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/dataFrameSortDS.html b/docs/reference/dataFrameSortDS.html index 47246150..d8e8cd13 100644 --- a/docs/reference/dataFrameSortDS.html +++ b/docs/reference/dataFrameSortDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -120,7 +120,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/densityGridDS.html b/docs/reference/densityGridDS.html index 14c4e7b2..b84830f0 100644 --- a/docs/reference/densityGridDS.html +++ b/docs/reference/densityGridDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -120,7 +120,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/dimDS.html b/docs/reference/dimDS.html index ccda6820..36ae7dbf 100644 --- a/docs/reference/dimDS.html +++ b/docs/reference/dimDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -80,7 +80,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/dmtC2SDS.html b/docs/reference/dmtC2SDS.html index df76184d..e5bce26b 100644 --- a/docs/reference/dmtC2SDS.html +++ b/docs/reference/dmtC2SDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -149,7 +149,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/dsBase-package.html b/docs/reference/dsBase-package.html index e6269505..36aa5804 100644 --- a/docs/reference/dsBase-package.html +++ b/docs/reference/dsBase-package.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -73,7 +73,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/elsplineDS.html b/docs/reference/elsplineDS.html index 190483ae..699ad119 100644 --- a/docs/reference/elsplineDS.html +++ b/docs/reference/elsplineDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -105,7 +105,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/extractQuantilesDS1.html b/docs/reference/extractQuantilesDS1.html index dd55cbf1..8db3348b 100644 --- a/docs/reference/extractQuantilesDS1.html +++ b/docs/reference/extractQuantilesDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -119,7 +119,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/extractQuantilesDS2.html b/docs/reference/extractQuantilesDS2.html index 94fc91d4..ab0bab81 100644 --- a/docs/reference/extractQuantilesDS2.html +++ b/docs/reference/extractQuantilesDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -117,7 +117,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/gamlssDS.html b/docs/reference/gamlssDS.html index 94fbce79..fc7898fe 100644 --- a/docs/reference/gamlssDS.html +++ b/docs/reference/gamlssDS.html @@ -23,7 +23,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -212,7 +212,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/getWGSRDS.html b/docs/reference/getWGSRDS.html index fb40e162..7ed44dbb 100644 --- a/docs/reference/getWGSRDS.html +++ b/docs/reference/getWGSRDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -140,7 +140,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmDS1.html b/docs/reference/glmDS1.html index 058ae910..ecd2010f 100644 --- a/docs/reference/glmDS1.html +++ b/docs/reference/glmDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -104,7 +104,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmDS2.html b/docs/reference/glmDS2.html index 71ccd910..03731c72 100644 --- a/docs/reference/glmDS2.html +++ b/docs/reference/glmDS2.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -110,7 +110,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmPredictDS.ag.html b/docs/reference/glmPredictDS.ag.html index f99f1f21..8d31da48 100644 --- a/docs/reference/glmPredictDS.ag.html +++ b/docs/reference/glmPredictDS.ag.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -137,7 +137,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmPredictDS.as.html b/docs/reference/glmPredictDS.as.html index 763f05f2..62461b0b 100644 --- a/docs/reference/glmPredictDS.as.html +++ b/docs/reference/glmPredictDS.as.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -136,7 +136,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmSLMADS.assign.html b/docs/reference/glmSLMADS.assign.html index 13ea50d0..7a63760d 100644 --- a/docs/reference/glmSLMADS.assign.html +++ b/docs/reference/glmSLMADS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -104,7 +104,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmSLMADS1.html b/docs/reference/glmSLMADS1.html index 95fd50ed..a4d8badd 100644 --- a/docs/reference/glmSLMADS1.html +++ b/docs/reference/glmSLMADS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -106,7 +106,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmSLMADS2.html b/docs/reference/glmSLMADS2.html index 22858f93..b50e51c9 100644 --- a/docs/reference/glmSLMADS2.html +++ b/docs/reference/glmSLMADS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -114,7 +114,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmSummaryDS.ag.html b/docs/reference/glmSummaryDS.ag.html index b8b68d6d..e0f2239e 100644 --- a/docs/reference/glmSummaryDS.ag.html +++ b/docs/reference/glmSummaryDS.ag.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -94,7 +94,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmSummaryDS.as.html b/docs/reference/glmSummaryDS.as.html index a133e4f2..ca99af8e 100644 --- a/docs/reference/glmSummaryDS.as.html +++ b/docs/reference/glmSummaryDS.as.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -93,7 +93,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmerSLMADS.assign.html b/docs/reference/glmerSLMADS.assign.html index 932f8c63..983b845e 100644 --- a/docs/reference/glmerSLMADS.assign.html +++ b/docs/reference/glmerSLMADS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -148,7 +148,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/glmerSLMADS2.html b/docs/reference/glmerSLMADS2.html index a7672b28..d1c2c9c2 100644 --- a/docs/reference/glmerSLMADS2.html +++ b/docs/reference/glmerSLMADS2.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -156,7 +156,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/heatmapPlotDS.html b/docs/reference/heatmapPlotDS.html index 459a5a98..7c0acfa9 100644 --- a/docs/reference/heatmapPlotDS.html +++ b/docs/reference/heatmapPlotDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -107,7 +107,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/hetcorDS.html b/docs/reference/hetcorDS.html index ac02df16..f080e55c 100644 --- a/docs/reference/hetcorDS.html +++ b/docs/reference/hetcorDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -114,7 +114,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/histogramDS1.html b/docs/reference/histogramDS1.html index dfae6675..3d90be9e 100644 --- a/docs/reference/histogramDS1.html +++ b/docs/reference/histogramDS1.html @@ -23,7 +23,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -105,7 +105,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/histogramDS2.html b/docs/reference/histogramDS2.html index e897cb2a..21f77287 100644 --- a/docs/reference/histogramDS2.html +++ b/docs/reference/histogramDS2.html @@ -21,7 +21,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -117,7 +117,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/igb_standardsDS.html b/docs/reference/igb_standardsDS.html index 357d8b12..56a62b4a 100644 --- a/docs/reference/igb_standardsDS.html +++ b/docs/reference/igb_standardsDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -118,7 +118,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 59255ef6..ce6e0a97 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -369,6 +369,10 @@

All functions matrixTransposeDS()

matrixTransposeDS serverside assign function called by ds.matrixTranspose

+ +

mdPatternDS()

+ +

Missing data pattern with disclosure control

meanDS()

@@ -586,7 +590,7 @@

All functions
-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/isNaDS.html b/docs/reference/isNaDS.html index 06080e50..60110a6c 100644 --- a/docs/reference/isNaDS.html +++ b/docs/reference/isNaDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -78,7 +78,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/isValidDS.html b/docs/reference/isValidDS.html index 57359377..453aa84d 100644 --- a/docs/reference/isValidDS.html +++ b/docs/reference/isValidDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -80,7 +80,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/kurtosisDS1.html b/docs/reference/kurtosisDS1.html index d65a39fb..6c942ba4 100644 --- a/docs/reference/kurtosisDS1.html +++ b/docs/reference/kurtosisDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -87,7 +87,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/kurtosisDS2.html b/docs/reference/kurtosisDS2.html index 7758f44c..a3be6590 100644 --- a/docs/reference/kurtosisDS2.html +++ b/docs/reference/kurtosisDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lengthDS.html b/docs/reference/lengthDS.html index 7c14412d..550e337b 100644 --- a/docs/reference/lengthDS.html +++ b/docs/reference/lengthDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -80,7 +80,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/levelsDS.html b/docs/reference/levelsDS.html index 5d7163fb..93bec9bb 100644 --- a/docs/reference/levelsDS.html +++ b/docs/reference/levelsDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -80,7 +80,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lexisDS1.html b/docs/reference/lexisDS1.html index acf40341..d59e1378 100644 --- a/docs/reference/lexisDS1.html +++ b/docs/reference/lexisDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -81,7 +81,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lexisDS2.html b/docs/reference/lexisDS2.html index 203d290c..9e1e61a3 100644 --- a/docs/reference/lexisDS2.html +++ b/docs/reference/lexisDS2.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -136,7 +136,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lexisDS3.html b/docs/reference/lexisDS3.html index c16502f5..97182f3d 100644 --- a/docs/reference/lexisDS3.html +++ b/docs/reference/lexisDS3.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -71,7 +71,7 @@

Details

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/listDS.html b/docs/reference/listDS.html index 517bff8d..8e1f3729 100644 --- a/docs/reference/listDS.html +++ b/docs/reference/listDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -85,7 +85,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/listDisclosureSettingsDS.html b/docs/reference/listDisclosureSettingsDS.html index 2f6252fa..37e561ee 100644 --- a/docs/reference/listDisclosureSettingsDS.html +++ b/docs/reference/listDisclosureSettingsDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -74,7 +74,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lmerSLMADS.assign.html b/docs/reference/lmerSLMADS.assign.html index 48630bbd..160ae781 100644 --- a/docs/reference/lmerSLMADS.assign.html +++ b/docs/reference/lmerSLMADS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -129,7 +129,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lmerSLMADS2.html b/docs/reference/lmerSLMADS2.html index 963b4627..e34c8da9 100644 --- a/docs/reference/lmerSLMADS2.html +++ b/docs/reference/lmerSLMADS2.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -139,7 +139,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lsDS.html b/docs/reference/lsDS.html index 104bc735..886204b6 100644 --- a/docs/reference/lsDS.html +++ b/docs/reference/lsDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -102,7 +102,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/lsplineDS.html b/docs/reference/lsplineDS.html index 777dd690..bced6894 100644 --- a/docs/reference/lsplineDS.html +++ b/docs/reference/lsplineDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -102,7 +102,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixDS.html b/docs/reference/matrixDS.html index 6a64f8b4..c095cf58 100644 --- a/docs/reference/matrixDS.html +++ b/docs/reference/matrixDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -113,7 +113,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixDetDS1.html b/docs/reference/matrixDetDS1.html index 63f81b79..1f6f482a 100644 --- a/docs/reference/matrixDetDS1.html +++ b/docs/reference/matrixDetDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -91,7 +91,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixDetDS2.html b/docs/reference/matrixDetDS2.html index 9792ce23..85e2457e 100644 --- a/docs/reference/matrixDetDS2.html +++ b/docs/reference/matrixDetDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -91,7 +91,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixDiagDS.html b/docs/reference/matrixDiagDS.html index 8b140d6b..8939f343 100644 --- a/docs/reference/matrixDiagDS.html +++ b/docs/reference/matrixDiagDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -101,7 +101,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixDimnamesDS.html b/docs/reference/matrixDimnamesDS.html index 3b09658c..bb2d6cfb 100644 --- a/docs/reference/matrixDimnamesDS.html +++ b/docs/reference/matrixDimnamesDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -98,7 +98,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixInvertDS.html b/docs/reference/matrixInvertDS.html index 8c4157ef..31bf8aee 100644 --- a/docs/reference/matrixInvertDS.html +++ b/docs/reference/matrixInvertDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -83,7 +83,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixMultDS.html b/docs/reference/matrixMultDS.html index 8bae8648..4a473555 100644 --- a/docs/reference/matrixMultDS.html +++ b/docs/reference/matrixMultDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -91,7 +91,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/matrixTransposeDS.html b/docs/reference/matrixTransposeDS.html index fc9337f2..2dc8d9a7 100644 --- a/docs/reference/matrixTransposeDS.html +++ b/docs/reference/matrixTransposeDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -84,7 +84,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/mdPatternDS.html b/docs/reference/mdPatternDS.html new file mode 100644 index 00000000..6ed7c777 --- /dev/null +++ b/docs/reference/mdPatternDS.html @@ -0,0 +1,127 @@ + +Missing data pattern with disclosure control — mdPatternDS • dsBase + + +
+
+ + + +
+
+
+

Missing data pattern with disclosure control

+ + +
+ +
+

This function is a serverside aggregate function that computes the +missing data pattern using mice::md.pattern and applies disclosure control to +prevent revealing small cell counts.

+
+ +
+ 
mdPatternDS(x)
+
+ +
+

Arguments

+ + +
x
+

a character string specifying the name of a data frame or matrix +containing the data to analyze for missing patterns.

+ +
+
+

Value

+

A list containing:

+
pattern
+

The missing data pattern matrix with disclosure control applied

+ +
valid
+

Logical indicating if all patterns meet disclosure requirements

+ +
message
+

A message describing the validity status

+ +
+
+

Details

+

This function calls the mice::md.pattern function to generate a matrix +showing the missing data patterns in the input data. To ensure disclosure control, +any pattern counts that are below the threshold (nfilter.tab, default=3) are +suppressed.

+

Suppression Method:

+

When a pattern count is below threshold: +- Row name is changed to "suppressed(<N>)" where N is the threshold +- All pattern values in that row are set to NA +- Summary row is also set to NA (prevents back-calculation)

+

Output Matrix Structure:

+

- Rows represent different missing data patterns (plus a summary row at the bottom) +- Row names contain pattern counts (or "suppressed(<N>)" for invalid patterns) +- Columns show 1 if variable is observed, 0 if missing +- Last column shows total number of missing values per pattern +- Last row shows total number of missing values per variable

+

Note for Pooling:

+

When this function is called from ds.mdPattern with type='combine', suppressed +patterns are excluded from pooling to prevent disclosure through subtraction. +This means pooled counts may underestimate the true total when patterns are +suppressed in some studies.

+
+
+

Author

+

Xavier Escribà montagut for DataSHIELD Development Team

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.0.

+
+ +
+ + + + + + + + diff --git a/docs/reference/meanDS.html b/docs/reference/meanDS.html index e8946d90..7806e4e4 100644 --- a/docs/reference/meanDS.html +++ b/docs/reference/meanDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -81,7 +81,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/meanSdGpDS.html b/docs/reference/meanSdGpDS.html index 44cf811b..da49bc49 100644 --- a/docs/reference/meanSdGpDS.html +++ b/docs/reference/meanSdGpDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -87,7 +87,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/qlsplineDS.html b/docs/reference/qlsplineDS.html index 231fcb89..5db49162 100644 --- a/docs/reference/qlsplineDS.html +++ b/docs/reference/qlsplineDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -113,7 +113,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rBinomDS.html b/docs/reference/rBinomDS.html index 1e494c8c..fe27c36a 100644 --- a/docs/reference/rBinomDS.html +++ b/docs/reference/rBinomDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -106,7 +106,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

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Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rPoisDS.html b/docs/reference/rPoisDS.html index c560901e..5eae496f 100644 --- a/docs/reference/rPoisDS.html +++ b/docs/reference/rPoisDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -99,7 +99,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rUnifDS.html b/docs/reference/rUnifDS.html index 7af321e6..5fdd2c11 100644 --- a/docs/reference/rUnifDS.html +++ b/docs/reference/rUnifDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -114,7 +114,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rangeDS.html b/docs/reference/rangeDS.html index fb661e2f..e05a1a91 100644 --- a/docs/reference/rangeDS.html +++ b/docs/reference/rangeDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -78,7 +78,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/ranksSecureDS1.html b/docs/reference/ranksSecureDS1.html index dac835d7..6ed0128f 100644 --- a/docs/reference/ranksSecureDS1.html +++ b/docs/reference/ranksSecureDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -88,7 +88,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/ranksSecureDS2.html b/docs/reference/ranksSecureDS2.html index b50f0029..904eee81 100644 --- a/docs/reference/ranksSecureDS2.html +++ b/docs/reference/ranksSecureDS2.html @@ -24,7 +24,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -103,7 +103,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/ranksSecureDS3.html b/docs/reference/ranksSecureDS3.html index ddc7e933..3d5df277 100644 --- a/docs/reference/ranksSecureDS3.html +++ b/docs/reference/ranksSecureDS3.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -100,7 +100,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/ranksSecureDS4.html b/docs/reference/ranksSecureDS4.html index c5db0477..ae6ef70a 100644 --- a/docs/reference/ranksSecureDS4.html +++ b/docs/reference/ranksSecureDS4.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -115,7 +115,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/ranksSecureDS5.html b/docs/reference/ranksSecureDS5.html index bb98ac56..1b6788c3 100644 --- a/docs/reference/ranksSecureDS5.html +++ b/docs/reference/ranksSecureDS5.html @@ -20,7 +20,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -115,7 +115,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rbindDS.html b/docs/reference/rbindDS.html index 646c1d25..43b5148a 100644 --- a/docs/reference/rbindDS.html +++ b/docs/reference/rbindDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -113,7 +113,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/reShapeDS.html b/docs/reference/reShapeDS.html index 0b5ebc94..3efbac3d 100644 --- a/docs/reference/reShapeDS.html +++ b/docs/reference/reShapeDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -146,7 +146,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/recodeLevelsDS.html b/docs/reference/recodeLevelsDS.html index a7279d5c..a2d5b275 100644 --- a/docs/reference/recodeLevelsDS.html +++ b/docs/reference/recodeLevelsDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -82,7 +82,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/recodeValuesDS.html b/docs/reference/recodeValuesDS.html index d58ae97e..da0679e3 100644 --- a/docs/reference/recodeValuesDS.html +++ b/docs/reference/recodeValuesDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -116,7 +116,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/repDS.html b/docs/reference/repDS.html index 1299f1e9..d7a1fb03 100644 --- a/docs/reference/repDS.html +++ b/docs/reference/repDS.html @@ -21,7 +21,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -196,7 +196,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/replaceNaDS.html b/docs/reference/replaceNaDS.html index 17b516b6..60d2bb00 100644 --- a/docs/reference/replaceNaDS.html +++ b/docs/reference/replaceNaDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rmDS.html b/docs/reference/rmDS.html index 190067c5..0e722d5b 100644 --- a/docs/reference/rmDS.html +++ b/docs/reference/rmDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -94,7 +94,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/rowColCalcDS.html b/docs/reference/rowColCalcDS.html index 2e657383..d5acc41a 100644 --- a/docs/reference/rowColCalcDS.html +++ b/docs/reference/rowColCalcDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -88,7 +88,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/sampleDS.html b/docs/reference/sampleDS.html index add11002..9e63a62b 100644 --- a/docs/reference/sampleDS.html +++ b/docs/reference/sampleDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -122,7 +122,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/scatterPlotDS.html b/docs/reference/scatterPlotDS.html index 337a3393..e7391a39 100644 --- a/docs/reference/scatterPlotDS.html +++ b/docs/reference/scatterPlotDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -113,7 +113,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/seqDS.html b/docs/reference/seqDS.html index 34a78997..5436c17f 100644 --- a/docs/reference/seqDS.html +++ b/docs/reference/seqDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -139,7 +139,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/setSeedDS.html b/docs/reference/setSeedDS.html index 4e49ec86..3f93d5d5 100644 --- a/docs/reference/setSeedDS.html +++ b/docs/reference/setSeedDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -114,7 +114,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/skewnessDS1.html b/docs/reference/skewnessDS1.html index e5e3fb6b..7fcff17c 100644 --- a/docs/reference/skewnessDS1.html +++ b/docs/reference/skewnessDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -87,7 +87,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/skewnessDS2.html b/docs/reference/skewnessDS2.html index f86c7490..96ca37f2 100644 --- a/docs/reference/skewnessDS2.html +++ b/docs/reference/skewnessDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/sqrtDS.html b/docs/reference/sqrtDS.html index e4685e8c..7b232fd0 100644 --- a/docs/reference/sqrtDS.html +++ b/docs/reference/sqrtDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -84,7 +84,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/subsetByClassDS.html b/docs/reference/subsetByClassDS.html index 92b0197c..fc546a46 100644 --- a/docs/reference/subsetByClassDS.html +++ b/docs/reference/subsetByClassDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -93,7 +93,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/subsetDS.html b/docs/reference/subsetDS.html index 9a8aa624..82f92ba4 100644 --- a/docs/reference/subsetDS.html +++ b/docs/reference/subsetDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -128,7 +128,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/table1DDS.html b/docs/reference/table1DDS.html index 3df80b76..574f90e4 100644 --- a/docs/reference/table1DDS.html +++ b/docs/reference/table1DDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -87,7 +87,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/table2DDS.html b/docs/reference/table2DDS.html index 46cc9336..b120d9ab 100644 --- a/docs/reference/table2DDS.html +++ b/docs/reference/table2DDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -91,7 +91,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/tableDS.assign.html b/docs/reference/tableDS.assign.html index 60498ea1..5c5ea7d7 100644 --- a/docs/reference/tableDS.assign.html +++ b/docs/reference/tableDS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -139,7 +139,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/tableDS.html b/docs/reference/tableDS.html index ad0ace8f..96b9b031 100644 --- a/docs/reference/tableDS.html +++ b/docs/reference/tableDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -143,7 +143,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/tableDS2.html b/docs/reference/tableDS2.html index 05b130b5..360bd692 100644 --- a/docs/reference/tableDS2.html +++ b/docs/reference/tableDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -113,7 +113,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/tapplyDS.assign.html b/docs/reference/tapplyDS.assign.html index 8ebff9e1..325a9d7c 100644 --- a/docs/reference/tapplyDS.assign.html +++ b/docs/reference/tapplyDS.assign.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -97,7 +97,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/tapplyDS.html b/docs/reference/tapplyDS.html index 36a9d184..ba1dec6d 100644 --- a/docs/reference/tapplyDS.html +++ b/docs/reference/tapplyDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -97,7 +97,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/testObjExistsDS.html b/docs/reference/testObjExistsDS.html index 489f9f7c..d8baf8bd 100644 --- a/docs/reference/testObjExistsDS.html +++ b/docs/reference/testObjExistsDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -84,7 +84,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/unListDS.html b/docs/reference/unListDS.html index d7b8aaf4..c59d955e 100644 --- a/docs/reference/unListDS.html +++ b/docs/reference/unListDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -108,7 +108,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/uniqueDS.html b/docs/reference/uniqueDS.html index a25aeaca..c65fdb87 100644 --- a/docs/reference/uniqueDS.html +++ b/docs/reference/uniqueDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -81,7 +81,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/varDS.html b/docs/reference/varDS.html index 37a4d212..f4a05a39 100644 --- a/docs/reference/varDS.html +++ b/docs/reference/varDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -84,7 +84,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/vectorDS.html b/docs/reference/vectorDS.html index c7cca023..36faaa54 100644 --- a/docs/reference/vectorDS.html +++ b/docs/reference/vectorDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.4 + 6.3.5.9000 @@ -81,7 +81,7 @@

Author

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 04ef332c..0d5e1008 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -89,6 +89,7 @@ /reference/matrixInvertDS.html /reference/matrixMultDS.html /reference/matrixTransposeDS.html +/reference/mdPatternDS.html /reference/meanDS.html /reference/meanSdGpDS.html /reference/mergeDS.html From 81f5f64c69a99ef88f7e5bf25a3ca92f9e5a536d Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 26 Nov 2025 18:40:32 +0000 Subject: [PATCH 10/30] Remove nightly scheduled run and update call to parse_test_report.R --- .github/workflows/dsBase_test_suite.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 8f03b10f..2cbe5ff3 100755 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -15,7 +15,6 @@ on: push: schedule: - cron: '0 0 * * 0' # Weekly - - cron: '0 1 * * *' # Nightly jobs: dsBase_test_suite: @@ -157,8 +156,11 @@ jobs: - name: Parse results from testthat and covr run: | - Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/ + Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '[^-:.]+' '(?<=::)[^:]+(?=::)' working-directory: dsBase + env: + PROJECT_NAME: ${{ env.PROJECT_NAME }} + BRANCH_NAME: ${{ env.BRANCH_NAME }} - name: Render report run: | From e0d234fe71bb61894984e6abf142ebe7e41a3151 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 26 Nov 2025 19:05:10 +0000 Subject: [PATCH 11/30] Add session_info_*.txt as one of the log outputs and avoid storing duplicated HTML reports --- .github/workflows/dsBase_test_suite.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 2cbe5ff3..bea80e31 100755 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -152,6 +152,7 @@ jobs: echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt + Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ env.WORKFLOW_ID }}.txt working-directory: dsBase/logs - name: Parse results from testthat and covr @@ -167,7 +168,6 @@ jobs: cd testStatus mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ - mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/ # Copy logs to new logs directory location @@ -175,8 +175,7 @@ jobs: cp -rv ../${{ env.PROJECT_NAME }}/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))' - mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html - cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest + mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/index.html env: PROJECT_NAME: ${{ env.PROJECT_NAME }} From 42efdb6f852356525667798af41d3ab90ae61b87 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Sun, 30 Nov 2025 14:53:56 +0000 Subject: [PATCH 12/30] Update 'perf' support --- tests/testthat/perf_tests/perf_rate.R | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 1884cda8..64b638db 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 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. @@ -8,7 +8,8 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -.perf.reference.filename <- 'perf_files/default_perf_profile.csv' +.perf.reference.filename <- 'perf_files/default_perf_profile.csv' +.perf.reference.save.filename <- NULL .perf.reference <- NULL @@ -22,7 +23,13 @@ perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance. .perf.reference[nrow(.perf.reference)+1,] <- c(perf.ref.name, rate, tolerance.lower, tolerance.upper) - write.csv(.perf.reference, .perf.reference.filename, row.names = FALSE) + if (is.null(.perf.reference.save.filename)) + { + .perf.reference.save.filename <<- base::tempfile(pattern = "perf_file_", fileext = ".csv") + message(paste0("Additional perf record added to '", .perf.reference.save.filename, "'")) + } + + write.csv(.perf.reference, .perf.reference.save.filename, row.names = FALSE) .perf.reference <<- .perf.reference } @@ -47,4 +54,3 @@ perf.reference.tolerance.upper <- function(perf.ref.name) { return(as.numeric(.perf.reference[which(.perf.reference$refer_name == perf.ref.name),]$upper_tolerance)) } - From 998482cac34d0d4af778c4d320d5244ca9cc58a8 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Sun, 30 Nov 2025 17:15:04 +0000 Subject: [PATCH 13/30] Minor docs update --- docs/pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ad3a64a8..c3eb19af 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.1.3 pkgdown: 2.2.0 pkgdown_sha: ~ articles: {} -last_built: 2025-11-21T13:10Z +last_built: 2025-11-30T16:44Z From bcfb6ae6892151ee42aaa8d8446ec6185715691e Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 6 Jan 2026 13:17:49 +0000 Subject: [PATCH 14/30] Reworking of performance profiles --- azure-pipelines.yml | 1 + ...ne.csv => azure-pipeline_perf-profile.csv} | 0 ...circleci.csv => circleci_perf-profile.csv} | 0 ..._check.cvs => cran-check_perf-profile.cvs} | 0 ...f_profile.csv => default_perf-profile.csv} | 0 ...ay.csv => hp-laptop-quay_perf-profile.csv} | 0 tests/testthat/perf_tests/perf_rate.R | 19 +++++++++++++++---- 7 files changed, 16 insertions(+), 4 deletions(-) rename tests/testthat/perf_files/{azure-pipeline.csv => azure-pipeline_perf-profile.csv} (100%) rename tests/testthat/perf_files/{circleci.csv => circleci_perf-profile.csv} (100%) rename tests/testthat/perf_files/{cran_check.cvs => cran-check_perf-profile.cvs} (100%) rename tests/testthat/perf_files/{default_perf_profile.csv => default_perf-profile.csv} (100%) rename tests/testthat/perf_files/{hp-laptop_quay.csv => hp-laptop-quay_perf-profile.csv} (100%) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index abbcc444..2d3bc950 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -188,6 +188,7 @@ jobs: # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter # R output and messages are redirected by sink() to test_console_output.txt # junit reporter output is to test_results.xml + export PERF_PROFILE="azure-pipeline" sudo R -q -e ' library(covr); write.csv( diff --git a/tests/testthat/perf_files/azure-pipeline.csv b/tests/testthat/perf_files/azure-pipeline_perf-profile.csv similarity index 100% rename from tests/testthat/perf_files/azure-pipeline.csv rename to tests/testthat/perf_files/azure-pipeline_perf-profile.csv diff --git a/tests/testthat/perf_files/circleci.csv b/tests/testthat/perf_files/circleci_perf-profile.csv similarity index 100% rename from tests/testthat/perf_files/circleci.csv rename to tests/testthat/perf_files/circleci_perf-profile.csv diff --git a/tests/testthat/perf_files/cran_check.cvs b/tests/testthat/perf_files/cran-check_perf-profile.cvs similarity index 100% rename from tests/testthat/perf_files/cran_check.cvs rename to tests/testthat/perf_files/cran-check_perf-profile.cvs diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf-profile.csv similarity index 100% rename from tests/testthat/perf_files/default_perf_profile.csv rename to tests/testthat/perf_files/default_perf-profile.csv diff --git a/tests/testthat/perf_files/hp-laptop_quay.csv b/tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv similarity index 100% rename from tests/testthat/perf_files/hp-laptop_quay.csv rename to tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 64b638db..8de658c3 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 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. @@ -8,13 +8,24 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -.perf.reference.filename <- 'perf_files/default_perf_profile.csv' -.perf.reference.save.filename <- NULL +.perf.reference.filename.base.prefix <- 'perf_files/' +.perf.reference.filename.base.postfix <- '_perf-profile.csv' +.perf.reference.save.filename <- NULL .perf.reference <- NULL .load.pref <- function() { - .perf.reference <<- read.csv(.perf.reference.filename, header = TRUE, sep = ",") + perf.profile = base::Sys.getenv("PERF_PROFILE") + if (nchar(perf.profile) > 0) + perf.reference.filename.platform.infix <- base::tolower(perf.profile) + else + { + perf.reference.filename.platform.infix <- "default" + warning("Unknown performance profile platform, using 'default'") + } + + perf.reference.filename <- paste(.perf.reference.filename.base.prefix, perf.reference.filename.platform.infix, .perf.reference.filename.base.postfix, sep = "") + .perf.reference <<- read.csv(perf.reference.filename, header = TRUE, sep = ",") } perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance.upper) { From 2b201d6930e56433b0149712297cfd6ceec0e74f Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 6 Jan 2026 14:14:46 +0000 Subject: [PATCH 15/30] Rework setting of variable --- azure-pipelines.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 2d3bc950..79a26fbe 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -27,6 +27,7 @@ variables: branchName: $(Build.SourceBranchName) test_filter: '*' _r_check_system_clock_: 0 + PERF_PROFILE: 'azure-pipeline' @@ -188,7 +189,7 @@ jobs: # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter # R output and messages are redirected by sink() to test_console_output.txt # junit reporter output is to test_results.xml - export PERF_PROFILE="azure-pipeline" + sudo R -q -e ' library(covr); write.csv( From 9e3892d9ad22484bcc3f275bd88314c935df675a Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 7 Jan 2026 09:46:47 +0000 Subject: [PATCH 16/30] Fixed Type --- tests/testthat/perf_tests/perf_rate.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 8de658c3..90905e12 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -15,7 +15,7 @@ .perf.reference <- NULL .load.pref <- function() { - perf.profile = base::Sys.getenv("PERF_PROFILE") + perf.profile <- base::Sys.getenv("PERF_PROFILE") if (nchar(perf.profile) > 0) perf.reference.filename.platform.infix <- base::tolower(perf.profile) else From 56ee2f15aaee7a230ba23d6aeb146b166b183dc3 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 5 Feb 2026 16:56:31 +0000 Subject: [PATCH 17/30] Update test schedual --- azure-pipelines.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 79a26fbe..4a207074 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -47,17 +47,18 @@ resources: # When and under what condition to run the pipeline. schedules: - cron: "0 0 * * 0" - displayName: Weekly build - master + displayName: Weekly build - latest release branches: include: - - master - - 6.3.0 + - 6.3.4 always: true - cron: "0 1 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - development branchs branches: include: - - v6.3.1-dev + - v6.3.5-dev + - v6.4.0-dev + - v7.0.0-dev always: true jobs: From 8c8378295d231452a974acd75ee3a9eaa648837d Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 20 Feb 2026 11:00:52 +0000 Subject: [PATCH 18/30] Update version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bc5e3973..fabf52d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'. -Version: 6.3.5.9000 +Version: 6.3.5 Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), From 69d4bb426b9e2e84fff7d2f761aa7aba92a6290a Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 20 Feb 2026 11:01:28 +0000 Subject: [PATCH 19/30] Update to glmSLMADS.assign --- R/glmSLMADS.assign.R | 41 +++++++++++++---------------------------- 1 file changed, 13 insertions(+), 28 deletions(-) diff --git a/R/glmSLMADS.assign.R b/R/glmSLMADS.assign.R index 275e1f47..68fe6929 100644 --- a/R/glmSLMADS.assign.R +++ b/R/glmSLMADS.assign.R @@ -18,40 +18,25 @@ #' @export glmSLMADS.assign <- function(formula, family, offsetName, weightsName, dataName){ -############################################################# -#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$nfilter.string) # -############################################################# + # Convert transmitable text for special link variance combinations back to full representation + if(family=="quasigamma.link_log") + {family<-"quasi(link=log,variance=mu^2)"} -######################################## -############ -#Convert transmitable text for special link variance combinations back to full representation -if(family=="quasigamma.link_log") -{family<-"quasi(link=log,variance=mu^2)"} + if(family=="Gamma.link_log") + {family<-"Gamma(link=log)"} -if(family=="Gamma.link_log") -{family<-"Gamma(link=log)"} -############# + # Correctly name offset, weights and data objects in function call + # (to allow glmPredict to work correctly later) + calltext <- paste0("mg<-glm(formula,family=",family,",offset=", + offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)") -#Activate family object (this may not be necessary as character string may already be OK -#but just checking -final.family.object<-eval(parse(text=family)) + eval(parse(text=calltext)) + # update the call object to include the actual formula + mg$call$formula <- formula -#Correctly name offset, weights and data objects in function call -#(to allow glmPredict to work correctly later) -calltext<-paste0("mg<-glm(formula,family=",family,",offset=", - offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)") - -eval(parse(text=calltext)) - -return(mg) + return(mg) } - # ASSIGN FUNCTION # glmSLMADS.assign From 2a4a3496f810b7ad4cfeaf5390afda6f45439631 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 20 Feb 2026 11:02:18 +0000 Subject: [PATCH 20/30] Update to documents --- docs/404.html | 2 +- docs/LICENSE.html | 2 +- docs/authors.html | 6 +++--- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/BooleDS.html | 2 +- docs/reference/absDS.html | 2 +- docs/reference/asCharacterDS.html | 2 +- docs/reference/asDataMatrixDS.html | 2 +- docs/reference/asFactorDS1.html | 2 +- docs/reference/asFactorDS2.html | 2 +- docs/reference/asFactorSimpleDS.html | 2 +- docs/reference/asIntegerDS.html | 2 +- docs/reference/asListDS.html | 2 +- docs/reference/asLogicalDS.html | 2 +- docs/reference/asMatrixDS.html | 2 +- docs/reference/asNumericDS.html | 2 +- docs/reference/aucDS.html | 2 +- docs/reference/blackBoxDS.html | 2 +- docs/reference/blackBoxRanksDS.html | 2 +- docs/reference/boxPlotGGDS.html | 2 +- docs/reference/boxPlotGG_data_TreatmentDS.html | 2 +- docs/reference/boxPlotGG_data_Treatment_numericDS.html | 2 +- docs/reference/bp_standardsDS.html | 2 +- docs/reference/cDS.html | 2 +- docs/reference/cbindDS.html | 2 +- docs/reference/changeRefGroupDS.html | 2 +- docs/reference/checkNegValueDS.html | 2 +- docs/reference/checkPermissivePrivacyControlLevel.html | 2 +- docs/reference/classDS.html | 2 +- docs/reference/colnamesDS.html | 2 +- docs/reference/completeCasesDS.html | 2 +- docs/reference/corDS.html | 2 +- docs/reference/corTestDS.html | 2 +- docs/reference/covDS.html | 2 +- docs/reference/dataFrameDS.html | 2 +- docs/reference/dataFrameFillDS.html | 2 +- docs/reference/dataFrameSortDS.html | 2 +- docs/reference/dataFrameSubsetDS1.html | 2 +- docs/reference/dataFrameSubsetDS2.html | 2 +- docs/reference/densityGridDS.html | 2 +- docs/reference/dimDS.html | 2 +- docs/reference/dmtC2SDS.html | 2 +- docs/reference/dsBase-package.html | 2 +- docs/reference/elsplineDS.html | 2 +- docs/reference/extractQuantilesDS1.html | 2 +- docs/reference/extractQuantilesDS2.html | 2 +- docs/reference/gamlssDS.html | 2 +- docs/reference/getWGSRDS.html | 2 +- docs/reference/glmDS1.html | 2 +- docs/reference/glmDS2.html | 2 +- docs/reference/glmPredictDS.ag.html | 2 +- docs/reference/glmPredictDS.as.html | 2 +- docs/reference/glmSLMADS.assign.html | 2 +- docs/reference/glmSLMADS1.html | 2 +- docs/reference/glmSLMADS2.html | 2 +- docs/reference/glmSummaryDS.ag.html | 2 +- docs/reference/glmSummaryDS.as.html | 2 +- docs/reference/glmerSLMADS.assign.html | 2 +- docs/reference/glmerSLMADS2.html | 2 +- docs/reference/heatmapPlotDS.html | 2 +- docs/reference/hetcorDS.html | 2 +- docs/reference/histogramDS1.html | 2 +- docs/reference/histogramDS2.html | 2 +- docs/reference/igb_standardsDS.html | 2 +- docs/reference/index.html | 2 +- docs/reference/isNaDS.html | 2 +- docs/reference/isValidDS.html | 2 +- docs/reference/kurtosisDS1.html | 2 +- docs/reference/kurtosisDS2.html | 2 +- docs/reference/lengthDS.html | 2 +- docs/reference/levelsDS.html | 2 +- docs/reference/lexisDS1.html | 2 +- docs/reference/lexisDS2.html | 2 +- docs/reference/lexisDS3.html | 2 +- docs/reference/listDS.html | 2 +- docs/reference/listDisclosureSettingsDS.html | 2 +- docs/reference/lmerSLMADS.assign.html | 2 +- docs/reference/lmerSLMADS2.html | 2 +- docs/reference/lsDS.html | 2 +- docs/reference/lsplineDS.html | 2 +- docs/reference/matrixDS.html | 2 +- docs/reference/matrixDetDS1.html | 2 +- docs/reference/matrixDetDS2.html | 2 +- docs/reference/matrixDiagDS.html | 2 +- docs/reference/matrixDimnamesDS.html | 2 +- docs/reference/matrixInvertDS.html | 2 +- docs/reference/matrixMultDS.html | 2 +- docs/reference/matrixTransposeDS.html | 2 +- docs/reference/mdPatternDS.html | 2 +- docs/reference/meanDS.html | 2 +- docs/reference/meanSdGpDS.html | 2 +- docs/reference/mergeDS.html | 2 +- docs/reference/messageDS.html | 2 +- docs/reference/metadataDS.html | 2 +- docs/reference/miceDS.html | 2 +- docs/reference/minMaxRandDS.html | 2 +- docs/reference/namesDS.html | 2 +- docs/reference/nsDS.html | 2 +- docs/reference/numNaDS.html | 2 +- docs/reference/qlsplineDS.html | 2 +- docs/reference/quantileMeanDS.html | 2 +- docs/reference/rBinomDS.html | 2 +- docs/reference/rNormDS.html | 2 +- docs/reference/rPoisDS.html | 2 +- docs/reference/rUnifDS.html | 2 +- docs/reference/rangeDS.html | 2 +- docs/reference/ranksSecureDS1.html | 2 +- docs/reference/ranksSecureDS2.html | 2 +- docs/reference/ranksSecureDS3.html | 2 +- docs/reference/ranksSecureDS4.html | 2 +- docs/reference/ranksSecureDS5.html | 2 +- docs/reference/rbindDS.html | 2 +- docs/reference/reShapeDS.html | 2 +- docs/reference/recodeLevelsDS.html | 2 +- docs/reference/recodeValuesDS.html | 2 +- docs/reference/repDS.html | 2 +- docs/reference/replaceNaDS.html | 2 +- docs/reference/rmDS.html | 2 +- docs/reference/rowColCalcDS.html | 2 +- docs/reference/sampleDS.html | 2 +- docs/reference/scatterPlotDS.html | 2 +- docs/reference/seqDS.html | 2 +- docs/reference/setSeedDS.html | 2 +- docs/reference/skewnessDS1.html | 2 +- docs/reference/skewnessDS2.html | 2 +- docs/reference/sqrtDS.html | 2 +- docs/reference/subsetByClassDS.html | 2 +- docs/reference/subsetDS.html | 2 +- docs/reference/table1DDS.html | 2 +- docs/reference/table2DDS.html | 2 +- docs/reference/tableDS.assign.html | 2 +- docs/reference/tableDS.html | 2 +- docs/reference/tableDS2.html | 2 +- docs/reference/tapplyDS.assign.html | 2 +- docs/reference/tapplyDS.html | 2 +- docs/reference/testObjExistsDS.html | 2 +- docs/reference/unListDS.html | 2 +- docs/reference/uniqueDS.html | 2 +- docs/reference/varDS.html | 2 +- docs/reference/vectorDS.html | 2 +- 141 files changed, 143 insertions(+), 143 deletions(-) diff --git a/docs/404.html b/docs/404.html index 828175ea..91a82d08 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 5faa2d0e..7fde2a96 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/authors.html b/docs/authors.html index a1aec549..47c4a8d1 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 @@ -102,12 +102,12 @@

Citation

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. -R package version 6.3.5.9000. +R package version 6.3.5. 

@Manual{,
   title = {dsBase: 'DataSHIELD' Server Side Base Functions},
   author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
-  note = {R package version 6.3.5.9000},
+  note = {R package version 6.3.5},
 }

Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” diff --git a/docs/index.html b/docs/index.html index 1f70741d..9ae6f613 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c3eb19af..9cfbee88 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.1.3 pkgdown: 2.2.0 pkgdown_sha: ~ articles: {} -last_built: 2025-11-30T16:44Z +last_built: 2026-02-20T10:54Z diff --git a/docs/reference/BooleDS.html b/docs/reference/BooleDS.html index 7cecbed2..b6c3e109 100644 --- a/docs/reference/BooleDS.html +++ b/docs/reference/BooleDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/absDS.html b/docs/reference/absDS.html index ca83bf9d..2c9094a2 100644 --- a/docs/reference/absDS.html +++ b/docs/reference/absDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asCharacterDS.html b/docs/reference/asCharacterDS.html index 8f461038..066e14ec 100644 --- a/docs/reference/asCharacterDS.html +++ b/docs/reference/asCharacterDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asDataMatrixDS.html b/docs/reference/asDataMatrixDS.html index 2b8fb1d3..17007438 100644 --- a/docs/reference/asDataMatrixDS.html +++ b/docs/reference/asDataMatrixDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asFactorDS1.html b/docs/reference/asFactorDS1.html index a5463d70..ab9f62c7 100644 --- a/docs/reference/asFactorDS1.html +++ b/docs/reference/asFactorDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asFactorDS2.html b/docs/reference/asFactorDS2.html index 7e1711d3..009d6ff3 100644 --- a/docs/reference/asFactorDS2.html +++ b/docs/reference/asFactorDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asFactorSimpleDS.html b/docs/reference/asFactorSimpleDS.html index 971a9169..ba2b1e93 100644 --- a/docs/reference/asFactorSimpleDS.html +++ b/docs/reference/asFactorSimpleDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asIntegerDS.html b/docs/reference/asIntegerDS.html index 0de6c670..dd246175 100644 --- a/docs/reference/asIntegerDS.html +++ b/docs/reference/asIntegerDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asListDS.html b/docs/reference/asListDS.html index ab9910cc..834ff96d 100644 --- a/docs/reference/asListDS.html +++ b/docs/reference/asListDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asLogicalDS.html b/docs/reference/asLogicalDS.html index 689e2461..e6255513 100644 --- a/docs/reference/asLogicalDS.html +++ b/docs/reference/asLogicalDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asMatrixDS.html b/docs/reference/asMatrixDS.html index a85c0c7c..06eb9e9f 100644 --- a/docs/reference/asMatrixDS.html +++ b/docs/reference/asMatrixDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/asNumericDS.html b/docs/reference/asNumericDS.html index da79a362..2c014e7c 100644 --- a/docs/reference/asNumericDS.html +++ b/docs/reference/asNumericDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/aucDS.html b/docs/reference/aucDS.html index 4800d9d1..a5cb55e8 100644 --- a/docs/reference/aucDS.html +++ b/docs/reference/aucDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/blackBoxDS.html b/docs/reference/blackBoxDS.html index 5d02e3a9..88d9dd8e 100644 --- a/docs/reference/blackBoxDS.html +++ b/docs/reference/blackBoxDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/blackBoxRanksDS.html b/docs/reference/blackBoxRanksDS.html index 458737b0..79d6e36e 100644 --- a/docs/reference/blackBoxRanksDS.html +++ b/docs/reference/blackBoxRanksDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/boxPlotGGDS.html b/docs/reference/boxPlotGGDS.html index a0177c41..d4d1e5b2 100644 --- a/docs/reference/boxPlotGGDS.html +++ b/docs/reference/boxPlotGGDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/boxPlotGG_data_TreatmentDS.html b/docs/reference/boxPlotGG_data_TreatmentDS.html index 7acead1e..7810441d 100644 --- a/docs/reference/boxPlotGG_data_TreatmentDS.html +++ b/docs/reference/boxPlotGG_data_TreatmentDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/boxPlotGG_data_Treatment_numericDS.html b/docs/reference/boxPlotGG_data_Treatment_numericDS.html index 1aa7bd26..4dd00885 100644 --- a/docs/reference/boxPlotGG_data_Treatment_numericDS.html +++ b/docs/reference/boxPlotGG_data_Treatment_numericDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/bp_standardsDS.html b/docs/reference/bp_standardsDS.html index b7e661c4..733a4804 100644 --- a/docs/reference/bp_standardsDS.html +++ b/docs/reference/bp_standardsDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/cDS.html b/docs/reference/cDS.html index 3cc043db..2ffc1148 100644 --- a/docs/reference/cDS.html +++ b/docs/reference/cDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/cbindDS.html b/docs/reference/cbindDS.html index 3bed8b0a..b8b31245 100644 --- a/docs/reference/cbindDS.html +++ b/docs/reference/cbindDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/changeRefGroupDS.html b/docs/reference/changeRefGroupDS.html index fbf6ba5f..c33cd976 100644 --- a/docs/reference/changeRefGroupDS.html +++ b/docs/reference/changeRefGroupDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/checkNegValueDS.html b/docs/reference/checkNegValueDS.html index e9d00fca..04101e3e 100644 --- a/docs/reference/checkNegValueDS.html +++ b/docs/reference/checkNegValueDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/checkPermissivePrivacyControlLevel.html b/docs/reference/checkPermissivePrivacyControlLevel.html index 6c19c2b0..962d61c6 100644 --- a/docs/reference/checkPermissivePrivacyControlLevel.html +++ b/docs/reference/checkPermissivePrivacyControlLevel.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/classDS.html b/docs/reference/classDS.html index 47976968..107f1659 100644 --- a/docs/reference/classDS.html +++ b/docs/reference/classDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/colnamesDS.html b/docs/reference/colnamesDS.html index 4282c514..10e7d0e9 100644 --- a/docs/reference/colnamesDS.html +++ b/docs/reference/colnamesDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/completeCasesDS.html b/docs/reference/completeCasesDS.html index d84a6ede..3c77cf08 100644 --- a/docs/reference/completeCasesDS.html +++ b/docs/reference/completeCasesDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/corDS.html b/docs/reference/corDS.html index a1972b2c..00770184 100644 --- a/docs/reference/corDS.html +++ b/docs/reference/corDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/corTestDS.html b/docs/reference/corTestDS.html index 40678688..fe0e9a3c 100644 --- a/docs/reference/corTestDS.html +++ b/docs/reference/corTestDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/covDS.html b/docs/reference/covDS.html index b92bbd44..45147a8e 100644 --- a/docs/reference/covDS.html +++ b/docs/reference/covDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dataFrameDS.html b/docs/reference/dataFrameDS.html index 8791fbbe..ba349247 100644 --- a/docs/reference/dataFrameDS.html +++ b/docs/reference/dataFrameDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dataFrameFillDS.html b/docs/reference/dataFrameFillDS.html index 6114470e..08a058c5 100644 --- a/docs/reference/dataFrameFillDS.html +++ b/docs/reference/dataFrameFillDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dataFrameSortDS.html b/docs/reference/dataFrameSortDS.html index d8e8cd13..ba4bc8cf 100644 --- a/docs/reference/dataFrameSortDS.html +++ b/docs/reference/dataFrameSortDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dataFrameSubsetDS1.html b/docs/reference/dataFrameSubsetDS1.html index 98c1bb41..392231b0 100644 --- a/docs/reference/dataFrameSubsetDS1.html +++ b/docs/reference/dataFrameSubsetDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dataFrameSubsetDS2.html b/docs/reference/dataFrameSubsetDS2.html index 91a1413e..4f976476 100644 --- a/docs/reference/dataFrameSubsetDS2.html +++ b/docs/reference/dataFrameSubsetDS2.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/densityGridDS.html b/docs/reference/densityGridDS.html index b84830f0..4326881e 100644 --- a/docs/reference/densityGridDS.html +++ b/docs/reference/densityGridDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dimDS.html b/docs/reference/dimDS.html index 36ae7dbf..978a17ae 100644 --- a/docs/reference/dimDS.html +++ b/docs/reference/dimDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dmtC2SDS.html b/docs/reference/dmtC2SDS.html index e5bce26b..2dfce50b 100644 --- a/docs/reference/dmtC2SDS.html +++ b/docs/reference/dmtC2SDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/dsBase-package.html b/docs/reference/dsBase-package.html index 36aa5804..7b685ecd 100644 --- a/docs/reference/dsBase-package.html +++ b/docs/reference/dsBase-package.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/elsplineDS.html b/docs/reference/elsplineDS.html index 699ad119..b49663ff 100644 --- a/docs/reference/elsplineDS.html +++ b/docs/reference/elsplineDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/extractQuantilesDS1.html b/docs/reference/extractQuantilesDS1.html index 8db3348b..737a022f 100644 --- a/docs/reference/extractQuantilesDS1.html +++ b/docs/reference/extractQuantilesDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/extractQuantilesDS2.html b/docs/reference/extractQuantilesDS2.html index ab0bab81..1bc21891 100644 --- a/docs/reference/extractQuantilesDS2.html +++ b/docs/reference/extractQuantilesDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/gamlssDS.html b/docs/reference/gamlssDS.html index fc7898fe..506f33aa 100644 --- a/docs/reference/gamlssDS.html +++ b/docs/reference/gamlssDS.html @@ -23,7 +23,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/getWGSRDS.html b/docs/reference/getWGSRDS.html index 7ed44dbb..fe30a859 100644 --- a/docs/reference/getWGSRDS.html +++ b/docs/reference/getWGSRDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmDS1.html b/docs/reference/glmDS1.html index ecd2010f..4a752e2d 100644 --- a/docs/reference/glmDS1.html +++ b/docs/reference/glmDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmDS2.html b/docs/reference/glmDS2.html index 03731c72..bf885f71 100644 --- a/docs/reference/glmDS2.html +++ b/docs/reference/glmDS2.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmPredictDS.ag.html b/docs/reference/glmPredictDS.ag.html index 8d31da48..62d1c17f 100644 --- a/docs/reference/glmPredictDS.ag.html +++ b/docs/reference/glmPredictDS.ag.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmPredictDS.as.html b/docs/reference/glmPredictDS.as.html index 62461b0b..c3522e90 100644 --- a/docs/reference/glmPredictDS.as.html +++ b/docs/reference/glmPredictDS.as.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmSLMADS.assign.html b/docs/reference/glmSLMADS.assign.html index 7a63760d..18208778 100644 --- a/docs/reference/glmSLMADS.assign.html +++ b/docs/reference/glmSLMADS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmSLMADS1.html b/docs/reference/glmSLMADS1.html index a4d8badd..326b4688 100644 --- a/docs/reference/glmSLMADS1.html +++ b/docs/reference/glmSLMADS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmSLMADS2.html b/docs/reference/glmSLMADS2.html index b50e51c9..4ce4fc57 100644 --- a/docs/reference/glmSLMADS2.html +++ b/docs/reference/glmSLMADS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmSummaryDS.ag.html b/docs/reference/glmSummaryDS.ag.html index e0f2239e..33a50104 100644 --- a/docs/reference/glmSummaryDS.ag.html +++ b/docs/reference/glmSummaryDS.ag.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmSummaryDS.as.html b/docs/reference/glmSummaryDS.as.html index ca99af8e..d062eda8 100644 --- a/docs/reference/glmSummaryDS.as.html +++ b/docs/reference/glmSummaryDS.as.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmerSLMADS.assign.html b/docs/reference/glmerSLMADS.assign.html index 983b845e..984e1ea4 100644 --- a/docs/reference/glmerSLMADS.assign.html +++ b/docs/reference/glmerSLMADS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/glmerSLMADS2.html b/docs/reference/glmerSLMADS2.html index d1c2c9c2..84c47acb 100644 --- a/docs/reference/glmerSLMADS2.html +++ b/docs/reference/glmerSLMADS2.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/heatmapPlotDS.html b/docs/reference/heatmapPlotDS.html index 7c0acfa9..64dad8a2 100644 --- a/docs/reference/heatmapPlotDS.html +++ b/docs/reference/heatmapPlotDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/hetcorDS.html b/docs/reference/hetcorDS.html index f080e55c..d1ed8860 100644 --- a/docs/reference/hetcorDS.html +++ b/docs/reference/hetcorDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/histogramDS1.html b/docs/reference/histogramDS1.html index 3d90be9e..8b8c65ad 100644 --- a/docs/reference/histogramDS1.html +++ b/docs/reference/histogramDS1.html @@ -23,7 +23,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/histogramDS2.html b/docs/reference/histogramDS2.html index 21f77287..c89e0843 100644 --- a/docs/reference/histogramDS2.html +++ b/docs/reference/histogramDS2.html @@ -21,7 +21,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/igb_standardsDS.html b/docs/reference/igb_standardsDS.html index 56a62b4a..653f7718 100644 --- a/docs/reference/igb_standardsDS.html +++ b/docs/reference/igb_standardsDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/index.html b/docs/reference/index.html index ce6e0a97..a81cedd3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/isNaDS.html b/docs/reference/isNaDS.html index 60110a6c..c6234365 100644 --- a/docs/reference/isNaDS.html +++ b/docs/reference/isNaDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/isValidDS.html b/docs/reference/isValidDS.html index 453aa84d..9368da66 100644 --- a/docs/reference/isValidDS.html +++ b/docs/reference/isValidDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/kurtosisDS1.html b/docs/reference/kurtosisDS1.html index 6c942ba4..654f0f45 100644 --- a/docs/reference/kurtosisDS1.html +++ b/docs/reference/kurtosisDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/kurtosisDS2.html b/docs/reference/kurtosisDS2.html index a3be6590..f03b7e81 100644 --- a/docs/reference/kurtosisDS2.html +++ b/docs/reference/kurtosisDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lengthDS.html b/docs/reference/lengthDS.html index 550e337b..445ec690 100644 --- a/docs/reference/lengthDS.html +++ b/docs/reference/lengthDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/levelsDS.html b/docs/reference/levelsDS.html index 93bec9bb..add624c2 100644 --- a/docs/reference/levelsDS.html +++ b/docs/reference/levelsDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lexisDS1.html b/docs/reference/lexisDS1.html index d59e1378..5142ba62 100644 --- a/docs/reference/lexisDS1.html +++ b/docs/reference/lexisDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lexisDS2.html b/docs/reference/lexisDS2.html index 9e1e61a3..3ed488c7 100644 --- a/docs/reference/lexisDS2.html +++ b/docs/reference/lexisDS2.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lexisDS3.html b/docs/reference/lexisDS3.html index 97182f3d..4b128681 100644 --- a/docs/reference/lexisDS3.html +++ b/docs/reference/lexisDS3.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/listDS.html b/docs/reference/listDS.html index 8e1f3729..8d4a7c1a 100644 --- a/docs/reference/listDS.html +++ b/docs/reference/listDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/listDisclosureSettingsDS.html b/docs/reference/listDisclosureSettingsDS.html index 37e561ee..8a357ea2 100644 --- a/docs/reference/listDisclosureSettingsDS.html +++ b/docs/reference/listDisclosureSettingsDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lmerSLMADS.assign.html b/docs/reference/lmerSLMADS.assign.html index 160ae781..926390d9 100644 --- a/docs/reference/lmerSLMADS.assign.html +++ b/docs/reference/lmerSLMADS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lmerSLMADS2.html b/docs/reference/lmerSLMADS2.html index e34c8da9..1b3b1e08 100644 --- a/docs/reference/lmerSLMADS2.html +++ b/docs/reference/lmerSLMADS2.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lsDS.html b/docs/reference/lsDS.html index 886204b6..e1584a8a 100644 --- a/docs/reference/lsDS.html +++ b/docs/reference/lsDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/lsplineDS.html b/docs/reference/lsplineDS.html index bced6894..8ebc4fdb 100644 --- a/docs/reference/lsplineDS.html +++ b/docs/reference/lsplineDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixDS.html b/docs/reference/matrixDS.html index c095cf58..4fd12e4b 100644 --- a/docs/reference/matrixDS.html +++ b/docs/reference/matrixDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixDetDS1.html b/docs/reference/matrixDetDS1.html index 1f6f482a..58e680b9 100644 --- a/docs/reference/matrixDetDS1.html +++ b/docs/reference/matrixDetDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixDetDS2.html b/docs/reference/matrixDetDS2.html index 85e2457e..3d61f58a 100644 --- a/docs/reference/matrixDetDS2.html +++ b/docs/reference/matrixDetDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixDiagDS.html b/docs/reference/matrixDiagDS.html index 8939f343..eb393686 100644 --- a/docs/reference/matrixDiagDS.html +++ b/docs/reference/matrixDiagDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixDimnamesDS.html b/docs/reference/matrixDimnamesDS.html index bb2d6cfb..6c004859 100644 --- a/docs/reference/matrixDimnamesDS.html +++ b/docs/reference/matrixDimnamesDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixInvertDS.html b/docs/reference/matrixInvertDS.html index 31bf8aee..859560e2 100644 --- a/docs/reference/matrixInvertDS.html +++ b/docs/reference/matrixInvertDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixMultDS.html b/docs/reference/matrixMultDS.html index 4a473555..0e2089e0 100644 --- a/docs/reference/matrixMultDS.html +++ b/docs/reference/matrixMultDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/matrixTransposeDS.html b/docs/reference/matrixTransposeDS.html index 2dc8d9a7..eafafa7f 100644 --- a/docs/reference/matrixTransposeDS.html +++ b/docs/reference/matrixTransposeDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/mdPatternDS.html b/docs/reference/mdPatternDS.html index 6ed7c777..c4bba870 100644 --- a/docs/reference/mdPatternDS.html +++ b/docs/reference/mdPatternDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/meanDS.html b/docs/reference/meanDS.html index 7806e4e4..d0fa735d 100644 --- a/docs/reference/meanDS.html +++ b/docs/reference/meanDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/meanSdGpDS.html b/docs/reference/meanSdGpDS.html index da49bc49..10e6d4c6 100644 --- a/docs/reference/meanSdGpDS.html +++ b/docs/reference/meanSdGpDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/mergeDS.html b/docs/reference/mergeDS.html index 3687174e..9f7e8b90 100644 --- a/docs/reference/mergeDS.html +++ b/docs/reference/mergeDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/messageDS.html b/docs/reference/messageDS.html index ec5f3f82..d06fb722 100644 --- a/docs/reference/messageDS.html +++ b/docs/reference/messageDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/metadataDS.html b/docs/reference/metadataDS.html index 83b97211..9809dedf 100644 --- a/docs/reference/metadataDS.html +++ b/docs/reference/metadataDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/miceDS.html b/docs/reference/miceDS.html index e8d36df9..22359341 100644 --- a/docs/reference/miceDS.html +++ b/docs/reference/miceDS.html @@ -23,7 +23,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/minMaxRandDS.html b/docs/reference/minMaxRandDS.html index 573110da..8da03fb2 100644 --- a/docs/reference/minMaxRandDS.html +++ b/docs/reference/minMaxRandDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/namesDS.html b/docs/reference/namesDS.html index c7de77a6..1a3f8cd7 100644 --- a/docs/reference/namesDS.html +++ b/docs/reference/namesDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/nsDS.html b/docs/reference/nsDS.html index 7d74fa0b..5573aecc 100644 --- a/docs/reference/nsDS.html +++ b/docs/reference/nsDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/numNaDS.html b/docs/reference/numNaDS.html index 7599a247..ccb1a8bd 100644 --- a/docs/reference/numNaDS.html +++ b/docs/reference/numNaDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/qlsplineDS.html b/docs/reference/qlsplineDS.html index 5db49162..ae647ca2 100644 --- a/docs/reference/qlsplineDS.html +++ b/docs/reference/qlsplineDS.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/quantileMeanDS.html b/docs/reference/quantileMeanDS.html index 741edf5f..c05c2f77 100644 --- a/docs/reference/quantileMeanDS.html +++ b/docs/reference/quantileMeanDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rBinomDS.html b/docs/reference/rBinomDS.html index fe27c36a..79ede53b 100644 --- a/docs/reference/rBinomDS.html +++ b/docs/reference/rBinomDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rNormDS.html b/docs/reference/rNormDS.html index 8f07ac7f..c8b84df5 100644 --- a/docs/reference/rNormDS.html +++ b/docs/reference/rNormDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rPoisDS.html b/docs/reference/rPoisDS.html index 5eae496f..481f25d2 100644 --- a/docs/reference/rPoisDS.html +++ b/docs/reference/rPoisDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rUnifDS.html b/docs/reference/rUnifDS.html index 5fdd2c11..bfad7b29 100644 --- a/docs/reference/rUnifDS.html +++ b/docs/reference/rUnifDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rangeDS.html b/docs/reference/rangeDS.html index e05a1a91..a5b8f7b8 100644 --- a/docs/reference/rangeDS.html +++ b/docs/reference/rangeDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/ranksSecureDS1.html b/docs/reference/ranksSecureDS1.html index 6ed0128f..0c281d79 100644 --- a/docs/reference/ranksSecureDS1.html +++ b/docs/reference/ranksSecureDS1.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/ranksSecureDS2.html b/docs/reference/ranksSecureDS2.html index 904eee81..d194174c 100644 --- a/docs/reference/ranksSecureDS2.html +++ b/docs/reference/ranksSecureDS2.html @@ -24,7 +24,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/ranksSecureDS3.html b/docs/reference/ranksSecureDS3.html index 3d5df277..53137542 100644 --- a/docs/reference/ranksSecureDS3.html +++ b/docs/reference/ranksSecureDS3.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/ranksSecureDS4.html b/docs/reference/ranksSecureDS4.html index ae6ef70a..d82516bd 100644 --- a/docs/reference/ranksSecureDS4.html +++ b/docs/reference/ranksSecureDS4.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/ranksSecureDS5.html b/docs/reference/ranksSecureDS5.html index 1b6788c3..4903f733 100644 --- a/docs/reference/ranksSecureDS5.html +++ b/docs/reference/ranksSecureDS5.html @@ -20,7 +20,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rbindDS.html b/docs/reference/rbindDS.html index 43b5148a..73c7e777 100644 --- a/docs/reference/rbindDS.html +++ b/docs/reference/rbindDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/reShapeDS.html b/docs/reference/reShapeDS.html index 3efbac3d..a3783c37 100644 --- a/docs/reference/reShapeDS.html +++ b/docs/reference/reShapeDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/recodeLevelsDS.html b/docs/reference/recodeLevelsDS.html index a2d5b275..50c2e55c 100644 --- a/docs/reference/recodeLevelsDS.html +++ b/docs/reference/recodeLevelsDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/recodeValuesDS.html b/docs/reference/recodeValuesDS.html index da0679e3..5adf8999 100644 --- a/docs/reference/recodeValuesDS.html +++ b/docs/reference/recodeValuesDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/repDS.html b/docs/reference/repDS.html index d7a1fb03..5375fbd3 100644 --- a/docs/reference/repDS.html +++ b/docs/reference/repDS.html @@ -21,7 +21,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/replaceNaDS.html b/docs/reference/replaceNaDS.html index 60d2bb00..5e26e986 100644 --- a/docs/reference/replaceNaDS.html +++ b/docs/reference/replaceNaDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rmDS.html b/docs/reference/rmDS.html index 0e722d5b..240767b7 100644 --- a/docs/reference/rmDS.html +++ b/docs/reference/rmDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/rowColCalcDS.html b/docs/reference/rowColCalcDS.html index d5acc41a..8d4ab25e 100644 --- a/docs/reference/rowColCalcDS.html +++ b/docs/reference/rowColCalcDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/sampleDS.html b/docs/reference/sampleDS.html index 9e63a62b..36b144f5 100644 --- a/docs/reference/sampleDS.html +++ b/docs/reference/sampleDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/scatterPlotDS.html b/docs/reference/scatterPlotDS.html index e7391a39..200b2e38 100644 --- a/docs/reference/scatterPlotDS.html +++ b/docs/reference/scatterPlotDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/seqDS.html b/docs/reference/seqDS.html index 5436c17f..355ba5a9 100644 --- a/docs/reference/seqDS.html +++ b/docs/reference/seqDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/setSeedDS.html b/docs/reference/setSeedDS.html index 3f93d5d5..f5a48255 100644 --- a/docs/reference/setSeedDS.html +++ b/docs/reference/setSeedDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/skewnessDS1.html b/docs/reference/skewnessDS1.html index 7fcff17c..18856c27 100644 --- a/docs/reference/skewnessDS1.html +++ b/docs/reference/skewnessDS1.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/skewnessDS2.html b/docs/reference/skewnessDS2.html index 96ca37f2..044b0cfb 100644 --- a/docs/reference/skewnessDS2.html +++ b/docs/reference/skewnessDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/sqrtDS.html b/docs/reference/sqrtDS.html index 7b232fd0..4bb74aae 100644 --- a/docs/reference/sqrtDS.html +++ b/docs/reference/sqrtDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/subsetByClassDS.html b/docs/reference/subsetByClassDS.html index fc546a46..7d022642 100644 --- a/docs/reference/subsetByClassDS.html +++ b/docs/reference/subsetByClassDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/subsetDS.html b/docs/reference/subsetDS.html index 82f92ba4..7bea1371 100644 --- a/docs/reference/subsetDS.html +++ b/docs/reference/subsetDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/table1DDS.html b/docs/reference/table1DDS.html index 574f90e4..a66f87d4 100644 --- a/docs/reference/table1DDS.html +++ b/docs/reference/table1DDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/table2DDS.html b/docs/reference/table2DDS.html index b120d9ab..97ce4b0b 100644 --- a/docs/reference/table2DDS.html +++ b/docs/reference/table2DDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/tableDS.assign.html b/docs/reference/tableDS.assign.html index 5c5ea7d7..3ce7fadc 100644 --- a/docs/reference/tableDS.assign.html +++ b/docs/reference/tableDS.assign.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/tableDS.html b/docs/reference/tableDS.html index 96b9b031..eec81395 100644 --- a/docs/reference/tableDS.html +++ b/docs/reference/tableDS.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/tableDS2.html b/docs/reference/tableDS2.html index 360bd692..8cbd6534 100644 --- a/docs/reference/tableDS2.html +++ b/docs/reference/tableDS2.html @@ -18,7 +18,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/tapplyDS.assign.html b/docs/reference/tapplyDS.assign.html index 325a9d7c..abb654ab 100644 --- a/docs/reference/tapplyDS.assign.html +++ b/docs/reference/tapplyDS.assign.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/tapplyDS.html b/docs/reference/tapplyDS.html index ba1dec6d..e657b616 100644 --- a/docs/reference/tapplyDS.html +++ b/docs/reference/tapplyDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/testObjExistsDS.html b/docs/reference/testObjExistsDS.html index d8baf8bd..879ac5cb 100644 --- a/docs/reference/testObjExistsDS.html +++ b/docs/reference/testObjExistsDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/unListDS.html b/docs/reference/unListDS.html index c59d955e..71ee1d0f 100644 --- a/docs/reference/unListDS.html +++ b/docs/reference/unListDS.html @@ -19,7 +19,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/uniqueDS.html b/docs/reference/uniqueDS.html index c65fdb87..890f8f44 100644 --- a/docs/reference/uniqueDS.html +++ b/docs/reference/uniqueDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/varDS.html b/docs/reference/varDS.html index f4a05a39..b2951662 100644 --- a/docs/reference/varDS.html +++ b/docs/reference/varDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 diff --git a/docs/reference/vectorDS.html b/docs/reference/vectorDS.html index 36faaa54..5660f127 100644 --- a/docs/reference/vectorDS.html +++ b/docs/reference/vectorDS.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.3.5 From d79c7d2158265b60204325fb9bc96d59edaac4c3 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 20 Feb 2026 12:15:29 +0000 Subject: [PATCH 21/30] Removed checking of 'opal' --- azure-pipelines.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 4a207074..e91b05ad 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -253,7 +253,6 @@ jobs: echo 'branch:'$(branchName) >> $(datetime).txt echo 'os:'$(lsb_release -ds) >> $(datetime).txt echo 'R:'$(R --version | head -n 1) >> $(datetime).txt - echo 'opal:'$(opal system --opal localhost:8080 --user administrator --password "datashield_test&" --version) >> $(datetime).txt workingDirectory: $(Pipeline.Workspace)/logs displayName: 'Write versions to file' From fbdfa42b431b6148ae8ad7ed0e0158d7a6db7f57 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 10 Apr 2026 11:38:37 +0100 Subject: [PATCH 22/30] Permit perf test duration to be set, seconds, by environment variable 'PERF_DURATION_SEC' --- tests/testthat/test-perf-meanDS.R | 6 +++--- tests/testthat/test-perf-varDS.R | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/testthat/test-perf-meanDS.R b/tests/testthat/test-perf-meanDS.R index 794e61b2..947c46ef 100644 --- a/tests/testthat/test-perf-meanDS.R +++ b/tests/testthat/test-perf-meanDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2026 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. @@ -30,7 +30,7 @@ test_that("numeric meanDS - performance", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -65,7 +65,7 @@ test_that("numeric meanDS, with NA - performance", { input <- c(0.0, NA, 2.0, NA, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-varDS.R b/tests/testthat/test-perf-varDS.R index d468c5da..1e81e646 100644 --- a/tests/testthat/test-perf-varDS.R +++ b/tests/testthat/test-perf-varDS.R @@ -30,7 +30,7 @@ test_that("numeric varDS - performance", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -65,7 +65,7 @@ test_that("numeric varDS, with NA - performance", { input <- c(0.0, NA, 2.0, NA, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time From 1f12d53330c09ea6107fa8b1fecfe4b0ac530af2 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 10 Apr 2026 11:54:51 +0100 Subject: [PATCH 23/30] Permit perf test duration to be set, seconds, by environment variable 'PERF_DURATION_SEC' --- tests/testthat/test-perf-meanDS.R | 4 ++-- tests/testthat/test-perf-varDS.R | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test-perf-meanDS.R b/tests/testthat/test-perf-meanDS.R index 794e61b2..5004a995 100644 --- a/tests/testthat/test-perf-meanDS.R +++ b/tests/testthat/test-perf-meanDS.R @@ -30,7 +30,7 @@ test_that("numeric meanDS - performance", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -65,7 +65,7 @@ test_that("numeric meanDS, with NA - performance", { input <- c(0.0, NA, 2.0, NA, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-varDS.R b/tests/testthat/test-perf-varDS.R index d468c5da..1e81e646 100644 --- a/tests/testthat/test-perf-varDS.R +++ b/tests/testthat/test-perf-varDS.R @@ -30,7 +30,7 @@ test_that("numeric varDS - performance", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -65,7 +65,7 @@ test_that("numeric varDS, with NA - performance", { input <- c(0.0, NA, 2.0, NA, 4.0) - .durationSec <- 30 # seconds + .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds .count <- 0 .start.time <- Sys.time() .current.time <- .start.time From e75797beb347b98c37e966937c24e0c8f2a4bf1b Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 13 Apr 2026 12:35:23 +0100 Subject: [PATCH 24/30] Refactor perf test duration obtaining --- tests/testthat/perf_tests/perf_rate.R | 5 +++++ tests/testthat/test-perf-meanDS.R | 4 ++-- tests/testthat/test-perf-varDS.R | 4 ++-- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 90905e12..b8930889 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -45,6 +45,11 @@ perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance. .perf.reference <<- .perf.reference } +# Obtain performance test duration from PERF_DURATION_SEC environment variable, otherwise default.duration argument, otherwise "30". +perf.testduration <- function(default.duration = 30) { + base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = base::as.character(default.duration))) +} + perf.reference.rate <- function(perf.ref.name) { if (is.null(.perf.reference)) .load.pref() diff --git a/tests/testthat/test-perf-meanDS.R b/tests/testthat/test-perf-meanDS.R index 5004a995..e0915068 100644 --- a/tests/testthat/test-perf-meanDS.R +++ b/tests/testthat/test-perf-meanDS.R @@ -30,7 +30,7 @@ test_that("numeric meanDS - performance", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) - .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -65,7 +65,7 @@ test_that("numeric meanDS, with NA - performance", { input <- c(0.0, NA, 2.0, NA, 4.0) - .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time diff --git a/tests/testthat/test-perf-varDS.R b/tests/testthat/test-perf-varDS.R index 1e81e646..5d9cec4a 100644 --- a/tests/testthat/test-perf-varDS.R +++ b/tests/testthat/test-perf-varDS.R @@ -30,7 +30,7 @@ test_that("numeric varDS - performance", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) - .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time @@ -65,7 +65,7 @@ test_that("numeric varDS, with NA - performance", { input <- c(0.0, NA, 2.0, NA, 4.0) - .durationSec <- base::as.integer(base::Sys.getenv("PERF_DURATION_SEC", unset = "30")) # defaults to 30 seconds + .durationSec <- perf.testduration(30) .count <- 0 .start.time <- Sys.time() .current.time <- .start.time From c4ff5611093722230911a3da786b5a24e039c1d0 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Tue, 21 Apr 2026 12:25:53 +0200 Subject: [PATCH 25/30] feat: add server-side functions for ds.standardiseDf --- DESCRIPTION | 5 +- R/standardiseDfDS.R | 133 ++++++++++++++++++++++++++++++++++++++++++++ inst/DATASHIELD | 9 ++- 3 files changed, 144 insertions(+), 3 deletions(-) create mode 100644 R/standardiseDfDS.R diff --git a/DESCRIPTION b/DESCRIPTION index fabf52d8..5dcee62a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'. -Version: 6.3.5 +Version: 6.3.6 Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), @@ -65,6 +65,9 @@ Imports: stringr, lme4, dplyr, + tibble, + purrr, + tidyselect, reshape2, polycor (>= 0.8), splines, diff --git a/R/standardiseDfDS.R b/R/standardiseDfDS.R new file mode 100644 index 00000000..24e3eecf --- /dev/null +++ b/R/standardiseDfDS.R @@ -0,0 +1,133 @@ +#' Get the Class of All Columns in a Data Frame +#' @param df.name A string representing the name of the data frame. +#' @return A tibble with the class of each column in the data frame. +#' @importFrom dplyr %>% +#' @importFrom tibble as_tibble +#' @importFrom purrr map +#' @export +getClassAllColsDS <- function(df.name){ + dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) + + df.name <- eval(parse(text = df.name), envir = parent.frame()) + all_classes <- map(df.name, class) %>% as_tibble() + return(all_classes) +} + +#' Change Class of Target Variables in a Data Frame +#' @param df.name A string representing the name of the data frame. +#' @param target_vars A character vector specifying the columns to be modified. +#' @param target_class A character vector specifying the new classes for each column (1 = factor, +#' 2 = integer, 3 = numeric, 4 = character, 5 = logical). +#' @return A modified data frame with the specified columns converted to the target classes. +#' @importFrom dplyr mutate across +#' @importFrom tidyselect all_of +#' @export +fixClassDS <- function(df.name, target_vars, target_class) { + dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) + + df <- eval(parse(text = df.name), envir = parent.frame()) + df_transformed <- df %>% + mutate( + across(all_of(target_vars), + ~ .convertClass(.x, target_class[which(target_vars == cur_column())]))) + return(df_transformed) +} + +#' Convert a Vector to a Specified Class +#' @param x The vector to be converted. +#' @param class_name A string indicating the target class (1 = factor, 2 = integer, 3 = numeric, +#' 4 = character, 5 = logical). +#' @return The converted vector. +#' @noRd +.convertClass <- function(target_var, target_class_code) { + switch(target_class_code, + "1" = as.factor(target_var), + "2" = as.integer(target_var), + "3" = as.numeric(target_var), + "4" = as.character(target_var), + "5" = as.logical(target_var) + ) +} + +#' Add Missing Columns with NA Values +#' @param .data A string representing the name of the data frame. +#' @param cols A character vector specifying the columns to be added if missing. +#' @return A modified data frame with missing columns added and filled with NA. +#' @importFrom dplyr mutate select +#' @importFrom tidyselect peek_vars +#' @importFrom purrr set_names +#' @export +fixColsDS <- function(.data, cols) { + dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) + + .data <- eval(parse(text = .data), envir = parent.frame()) + missing <- setdiff(cols, colnames(.data)) + out <- .data %>% + mutate(!!!set_names(rep(list(NA), length(missing)), missing)) %>% + select(sort(peek_vars())) + return(out) +} + +#' Retrieve Factor Levels for Specific Columns +#' @param df.name A string representing the name of the data frame. +#' @param factor_vars A character vector specifying the factor columns. +#' @return A list of factor levels for the specified columns. +#' @importFrom tidyselect all_of +#' @importFrom purrr map imap +#' @export +getAllLevelsDS <- function(df.name, factor_vars) { + dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) + + df <- eval(parse(text = df.name), envir = parent.frame()) + factor_vars_split <- strsplit(factor_vars, ",\\s*")[[1]] + levels <- purrr::map(df[factor_vars_split], base::levels) + + disclosure_check <- imap(levels, function(lvls, var) { + .checkLevelsDisclosure(df = df, var = var, levels = lvls) + }) + + failed_vars <- names(disclosure_check)[unlist(disclosure_check)] + + if(length(failed_vars) > 0) { + stop("Based on the value of nfilter.levels.density, these factor variables", " {", failed_vars, "} ", "have too many levels compared to the length of the variable. Please reduce the numnber of levels or change the variable type and try again") + } else { + return(levels) + } +} + +#' Check variable levels against disclosure thresholds +#' +#' Internal helper function to verify whether the number of levels in a variable +#' exceeds the allowed density threshold defined by `dsBase::listDisclosureSettingsDS()`. +#' +#' @param df A data frame containing the variable. +#' @param var Character string. Name of the variable to check. +#' @param levels Character vector. Levels of the variable. +#' +#' @return Logical. `TRUE` if the check fails (i.e., disclosure threshold is violated), +#' otherwise `FALSE`. +#' +#' @keywords internal +#' @noRd +.checkLevelsDisclosure <- function(df, var, levels) { + thr <- dsBase::listDisclosureSettingsDS() + nfilter.levels.density <- as.numeric(thr$nfilter.levels.density) + n_levels <- length(levels) + length_var <- length(df[[var]]) + fail <- (length_var * nfilter.levels.density) < n_levels + return(fail) +} + +#' Set Factor Levels for Specific Columns in a Data Frame +#' @param df.name A string representing the name of the data frame to modify. +#' @param vars A character vector specifying the columns to be modified. +#' @param levels A named list where each element contains the levels for the corresponding factor variable. +#' @return A modified data frame with the specified columns converted to factors with the provided levels. +#' @export +fixLevelsDS <- function(df.name, vars, levels) { + dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) + + df.name <- eval(parse(text = df.name), envir = parent.frame()) + out <- df.name %>% + mutate(across(all_of(vars), ~factor(., levels = levels[[dplyr::cur_column()]]))) +} diff --git a/inst/DATASHIELD b/inst/DATASHIELD index 0c59f0c2..a7acb62a 100644 --- a/inst/DATASHIELD +++ b/inst/DATASHIELD @@ -70,7 +70,9 @@ AggregateMethods: is.null=base::is.null, is.numeric=base::is.numeric, NROW=base::NROW, - t.test=stats::t.test + t.test=stats::t.test, + getClassAllColsDS, + getAllLevelsDS AssignMethods: absDS, asCharacterDS, @@ -161,7 +163,10 @@ AssignMethods: acos=base::acos, atan=base::atan, sum=base::sum, - unlist=base::unlist + unlist=base::unlist, + fixClassDS, + fixColsDS, + fixLevelsDS Options: datashield.privacyLevel=5, default.datashield.privacyControlLevel="banana", From dd6133f4ad4583339d8756d93ee408383d0729ac Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 21 Apr 2026 22:08:05 +0100 Subject: [PATCH 26/30] Added libuv1-dev to deployment --- azure-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index e91b05ad..7eb3e47e 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -106,7 +106,7 @@ jobs: sudo apt-get install -qq pkg-config -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgit2-dev libharfbuzz-dev libfribidi-dev libfontconfig1-dev -y - sudo apt-get install -qq libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y + sudo apt-get install -qq libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libuv1-dev -y sudo apt-get install -qq r-base -y sudo R -e "install.packages('devtools', dependencies=TRUE)" sudo R -e "install.packages('RANN', dependencies=TRUE)" From 3b7b9d43489831b158c11db20d6d97d2dbb90a79 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Wed, 22 Apr 2026 11:02:03 +0200 Subject: [PATCH 27/30] export functions --- NAMESPACE | 15 +++++++++++++++ man/fixClassDS.Rd | 22 ++++++++++++++++++++++ man/fixColsDS.Rd | 19 +++++++++++++++++++ man/fixLevelsDS.Rd | 21 +++++++++++++++++++++ man/getAllLevelsDS.Rd | 19 +++++++++++++++++++ man/getClassAllColsDS.Rd | 17 +++++++++++++++++ 6 files changed, 113 insertions(+) create mode 100644 man/fixClassDS.Rd create mode 100644 man/fixColsDS.Rd create mode 100644 man/fixLevelsDS.Rd create mode 100644 man/getAllLevelsDS.Rd create mode 100644 man/getClassAllColsDS.Rd diff --git a/NAMESPACE b/NAMESPACE index e52e5d10..6793ba57 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -41,7 +41,12 @@ export(dmtC2SDS) export(elsplineDS) export(extractQuantilesDS1) export(extractQuantilesDS2) +export(fixClassDS) +export(fixColsDS) +export(fixLevelsDS) export(gamlssDS) +export(getAllLevelsDS) +export(getClassAllColsDS) export(getWGSRDS) export(glmDS1) export(glmDS2) @@ -139,5 +144,15 @@ import(dplyr) import(gamlss) import(gamlss.dist) import(mice) +importFrom(dplyr,"%>%") +importFrom(dplyr,across) +importFrom(dplyr,mutate) +importFrom(dplyr,select) importFrom(gamlss.dist,pST3) importFrom(gamlss.dist,qST3) +importFrom(purrr,imap) +importFrom(purrr,map) +importFrom(purrr,set_names) +importFrom(tibble,as_tibble) +importFrom(tidyselect,all_of) +importFrom(tidyselect,peek_vars) diff --git a/man/fixClassDS.Rd b/man/fixClassDS.Rd new file mode 100644 index 00000000..d7b6bf17 --- /dev/null +++ b/man/fixClassDS.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{fixClassDS} +\alias{fixClassDS} +\title{Change Class of Target Variables in a Data Frame} +\usage{ +fixClassDS(df.name, target_vars, target_class) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame.} + +\item{target_vars}{A character vector specifying the columns to be modified.} + +\item{target_class}{A character vector specifying the new classes for each column (1 = factor, +2 = integer, 3 = numeric, 4 = character, 5 = logical).} +} +\value{ +A modified data frame with the specified columns converted to the target classes. +} +\description{ +Change Class of Target Variables in a Data Frame +} diff --git a/man/fixColsDS.Rd b/man/fixColsDS.Rd new file mode 100644 index 00000000..709d9472 --- /dev/null +++ b/man/fixColsDS.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{fixColsDS} +\alias{fixColsDS} +\title{Add Missing Columns with NA Values} +\usage{ +fixColsDS(.data, cols) +} +\arguments{ +\item{.data}{A string representing the name of the data frame.} + +\item{cols}{A character vector specifying the columns to be added if missing.} +} +\value{ +A modified data frame with missing columns added and filled with NA. +} +\description{ +Add Missing Columns with NA Values +} diff --git a/man/fixLevelsDS.Rd b/man/fixLevelsDS.Rd new file mode 100644 index 00000000..096757a9 --- /dev/null +++ b/man/fixLevelsDS.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{fixLevelsDS} +\alias{fixLevelsDS} +\title{Set Factor Levels for Specific Columns in a Data Frame} +\usage{ +fixLevelsDS(df.name, vars, levels) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame to modify.} + +\item{vars}{A character vector specifying the columns to be modified.} + +\item{levels}{A named list where each element contains the levels for the corresponding factor variable.} +} +\value{ +A modified data frame with the specified columns converted to factors with the provided levels. +} +\description{ +Set Factor Levels for Specific Columns in a Data Frame +} diff --git a/man/getAllLevelsDS.Rd b/man/getAllLevelsDS.Rd new file mode 100644 index 00000000..e5030725 --- /dev/null +++ b/man/getAllLevelsDS.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{getAllLevelsDS} +\alias{getAllLevelsDS} +\title{Retrieve Factor Levels for Specific Columns} +\usage{ +getAllLevelsDS(df.name, factor_vars) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame.} + +\item{factor_vars}{A character vector specifying the factor columns.} +} +\value{ +A list of factor levels for the specified columns. +} +\description{ +Retrieve Factor Levels for Specific Columns +} diff --git a/man/getClassAllColsDS.Rd b/man/getClassAllColsDS.Rd new file mode 100644 index 00000000..cb2de0e7 --- /dev/null +++ b/man/getClassAllColsDS.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{getClassAllColsDS} +\alias{getClassAllColsDS} +\title{Get the Class of All Columns in a Data Frame} +\usage{ +getClassAllColsDS(df.name) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame.} +} +\value{ +A tibble with the class of each column in the data frame. +} +\description{ +Get the Class of All Columns in a Data Frame +} From d40d899d8076b750b2c6c680092811d25ac6a23f Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 22 Apr 2026 13:10:54 +0100 Subject: [PATCH 28/30] Add 'libuv1' --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a59ed99d..ec6d40e9 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -22,7 +22,7 @@ jobs: sudo apt-get install -y r-base-core cmake - run: command: | - sudo apt-get install -y libxml2-dev + sudo apt-get install -y libxml2-dev libuv1-dev - run: command: | echo "options(Ncpus=4)" >> ~/.Rprofile From b01c92370763400703729bf9ec15f172f10635e5 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 22 Apr 2026 14:44:08 +0100 Subject: [PATCH 29/30] Updated version to 'v6.3.6-dev' --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index fabf52d8..18c70ac7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'. -Version: 6.3.5 +Version: 6.3.6.9000 Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), From 3c649652289491c8cc6ce0941069a9d8296b84fe Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 13 May 2026 18:22:52 +0100 Subject: [PATCH 30/30] Switched to 'RoxygenNote: 8.0.0' --- DESCRIPTION | 2 +- man/dsBase-package.Rd | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 18c70ac7..62f41ece 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -75,6 +75,6 @@ Imports: Suggests: spelling, testthat -RoxygenNote: 7.3.3 +RoxygenNote: 8.0.0 Encoding: UTF-8 Language: en-GB diff --git a/man/dsBase-package.Rd b/man/dsBase-package.Rd index 725c4131..be7f5744 100644 --- a/man/dsBase-package.Rd +++ b/man/dsBase-package.Rd @@ -13,6 +13,7 @@ Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software pack Authors: \itemize{ + \item Stuart Wheater \email{stuart.wheater@arjuna.com} (\href{https://orcid.org/0009-0003-2419-1964}{ORCID}) \item Paul Burton (\href{https://orcid.org/0000-0001-5799-9634}{ORCID}) \item Rebecca Wilson (\href{https://orcid.org/0000-0003-2294-593X}{ORCID}) \item Olly Butters (\href{https://orcid.org/0000-0003-0354-8461}{ORCID})