From 6589423c5ea364ec0d65a6b30b19deda0457de43 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 15 Dec 2025 11:05:21 +0000 Subject: [PATCH 1/3] Updated Armadillo Profile - Azure Pipeline --- .../perf_files/armadillo_azure-pipeline.csv | 26 +++++++++---------- .../perf_files/default_perf_profile.csv | 26 +++++++++---------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/tests/testthat/perf_files/armadillo_azure-pipeline.csv b/tests/testthat/perf_files/armadillo_azure-pipeline.csv index e913cff92..ca8a229ca 100644 --- a/tests/testthat/perf_files/armadillo_azure-pipeline.csv +++ b/tests/testthat/perf_files/armadillo_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.1225","0.5","2" -"ds.abs::perf::0","5.820","0.5","2" -"ds.asInteger::perf:0","5.328","0.5","2" -"ds.asList::perf:0","11.71","0.5","2" -"ds.asNumeric::perf:0","5.268","0.5","2" -"ds.assign::perf::0","9.229","0.5","2" -"ds.class::perf::combine:0","10.84","0.5","2" -"ds.colnames::perf:0","7.993","0.5","2" -"ds.exists::perf::combine:0","21.68","0.5","2" -"ds.length::perf::combine:0","21.84","0.5","2" -"ds.mean::perf::combine:0","22.01","0.5","2" -"ds.mean::perf::split:0","22.22","0.5","2" -"void::perf::void::0","48520.0","0.5","2" +"conndisconn::perf::simple0","0.1661","0.5","2" +"ds.abs::perf::0","6.247","0.5","2" +"ds.asInteger::perf:0","5.691","0.5","2" +"ds.asList::perf:0","12.50","0.5","2" +"ds.asNumeric::perf:0","5.723","0.5","2" +"ds.assign::perf::0","10.52","0.5","2" +"ds.class::perf::combine:0","13.73","0.5","2" +"ds.colnames::perf:0","25.64","0.5","2" +"ds.exists::perf::combine:0","25.73","0.5","2" +"ds.length::perf::combine:0","25.44","0.5","2" +"ds.mean::perf::combine:0","25.70","0.5","2" +"ds.mean::perf::split:0","25.72","0.5","2" +"void::perf::void::0","53016.0","0.5","2" diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index 58614204f..ca8a229ca 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.2725","0.5","2" -"ds.abs::perf::0","2.677","0.5","2" -"ds.asInteger::perf:0","2.294","0.5","2" -"ds.asList::perf:0","4.587","0.5","2" -"ds.asNumeric::perf:0","2.185","0.5","2" -"ds.assign::perf::0","5.490","0.5","2" -"ds.class::perf::combine:0","4.760","0.5","2" -"ds.colnames::perf:0","9.079","0.5","2" -"ds.exists::perf::combine:0","11.09","0.5","2" -"ds.length::perf::combine:0","9.479","0.5","2" -"ds.mean::perf::combine:0","9.650","0.5","2" -"ds.mean::perf::split:0","11.26","0.5","2" -"void::perf::void::0","46250.0","0.5","2" +"conndisconn::perf::simple0","0.1661","0.5","2" +"ds.abs::perf::0","6.247","0.5","2" +"ds.asInteger::perf:0","5.691","0.5","2" +"ds.asList::perf:0","12.50","0.5","2" +"ds.asNumeric::perf:0","5.723","0.5","2" +"ds.assign::perf::0","10.52","0.5","2" +"ds.class::perf::combine:0","13.73","0.5","2" +"ds.colnames::perf:0","25.64","0.5","2" +"ds.exists::perf::combine:0","25.73","0.5","2" +"ds.length::perf::combine:0","25.44","0.5","2" +"ds.mean::perf::combine:0","25.70","0.5","2" +"ds.mean::perf::split:0","25.72","0.5","2" +"void::perf::void::0","53016.0","0.5","2" From b33d01effa94928814d0c4535331a8eb06ee5488 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Sun, 21 Dec 2025 16:06:59 +0000 Subject: [PATCH 2/3] Updates for export of 'R/subsetHelper.R' --- NAMESPACE | 1 + R/ds.boxPlot.R | 18 +++++++++--------- R/subsetHelper.R | 1 + 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index a41b8f0af..289592525 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -118,6 +118,7 @@ export(ds.unList) export(ds.unique) export(ds.var) export(ds.vectorCalc) +export(subsetHelper) import(DSI) import(data.table) importFrom(stats,as.formula) diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index 84d7a2790..7d86a79b1 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -48,37 +48,37 @@ #' symbol = "D") #' #' ## Create a boxplot of one variable -#' ds.boxPlot("D", "LAB_HDL", datasources = connections) +#' ds.boxPlot("D", "LAB_HDL", datasources = connections) #' #' ## Create a boxplot that is split by study: -#' ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) +#' ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) #' #' ## Create a boxplot of two variables variable -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="pooled", -#' datasources = connections) +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), type="pooled", +#' datasources = connections) #' # only one plot is created (of the aggregated results of all servers) #' #' ## Create a boxplot of two variables, which are split by a factor -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", #' datasources = connections) #' #' ## Create a boxplot with x- and y-axis labels -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", #' xlabel = "Variable", ylabel = "Measurement", datasources = connections) #' #' ## Improve the presentation of ds.boxplot output using ggplot: #' ### User must save the output, which is in a ggplot format already: -#' a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", +#' a <- ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG"), group = "GENDER", #' xlabel = "Variable", ylabel = "Measurement", datasources = connections) #' #' ### Then customise output "a" using ggplot tools: #' a + ggplot2::scale_fill_discrete(name = "Gender", labels = c("Male", "Female")) #' #' ### Or use an alternative way, to maintain the aesthetics: -#' a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) +#' a + ggplot2::scale_fill_brewer(name = "Gender", labels = c("Male", "Female")) #' #' # Clear the Datashield R sessions and logout -#' datashield.logout(connections) +#' datashield.logout(connections) #' #' } #' diff --git a/R/subsetHelper.R b/R/subsetHelper.R index 025a06803..82eae7271 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -17,6 +17,7 @@ #' @keywords internal #' @return \code{subsetHelper} returns a message or the class of the object if the #' object has the same class in all studies. +#' @export #' @examples #' \dontrun{ #' From f3e8bf526c9922af6e6c88786d3535ca9a5e0e6a Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Sun, 21 Dec 2025 16:07:49 +0000 Subject: [PATCH 3/3] Update 'docs' and 'man' --- docs/404.html | 2 +- docs/LICENSE.html | 2 +- docs/authors.html | 6 +- docs/index.html | 4 +- docs/pkgdown.yml | 2 +- docs/reference/checkClass.html | 2 +- docs/reference/colPercent.html | 2 +- docs/reference/computeWeightedMeans.html | 6 +- docs/reference/dot-pool_md_patterns.html | 2 +- docs/reference/ds.Boole.html | 2 +- docs/reference/ds.abs.html | 2 +- docs/reference/ds.asCharacter.html | 2 +- docs/reference/ds.asDataMatrix.html | 2 +- docs/reference/ds.asFactor.html | 2 +- docs/reference/ds.asFactorSimple.html | 2 +- docs/reference/ds.asInteger.html | 2 +- docs/reference/ds.asList.html | 2 +- docs/reference/ds.asLogical.html | 2 +- docs/reference/ds.asMatrix.html | 2 +- docs/reference/ds.asNumeric.html | 2 +- docs/reference/ds.assign.html | 2 +- docs/reference/ds.auc.html | 2 +- docs/reference/ds.boxPlot.html | 69 ++++++++++- docs/reference/ds.boxPlotGG.html | 2 +- .../ds.boxPlotGG_data_Treatment.html | 2 +- .../ds.boxPlotGG_data_Treatment_numeric.html | 2 +- docs/reference/ds.boxPlotGG_numeric.html | 2 +- docs/reference/ds.boxPlotGG_table.html | 2 +- docs/reference/ds.bp_standards.html | 2 +- docs/reference/ds.c.html | 2 +- docs/reference/ds.cbind.html | 2 +- docs/reference/ds.changeRefGroup.html | 2 +- docs/reference/ds.class.html | 2 +- docs/reference/ds.colnames.html | 2 +- docs/reference/ds.completeCases.html | 2 +- docs/reference/ds.contourPlot.html | 2 +- docs/reference/ds.cor.html | 2 +- docs/reference/ds.corTest.html | 2 +- docs/reference/ds.cov.html | 2 +- docs/reference/ds.dataFrame.html | 2 +- docs/reference/ds.dataFrameFill.html | 2 +- docs/reference/ds.dataFrameSort.html | 2 +- docs/reference/ds.dataFrameSubset.html | 2 +- docs/reference/ds.densityGrid.html | 56 ++++++++- docs/reference/ds.dim.html | 2 +- docs/reference/ds.dmtC2S.html | 2 +- docs/reference/ds.elspline.html | 2 +- docs/reference/ds.exists.html | 2 +- docs/reference/ds.exp.html | 2 +- docs/reference/ds.extractQuantiles.html | 2 +- docs/reference/ds.forestplot.html | 6 +- docs/reference/ds.gamlss.html | 2 +- docs/reference/ds.getWGSR.html | 2 +- docs/reference/ds.glm.html | 2 +- docs/reference/ds.glmPredict.html | 2 +- docs/reference/ds.glmSLMA.html | 2 +- docs/reference/ds.glmSummary.html | 2 +- docs/reference/ds.glmerSLMA.html | 2 +- docs/reference/ds.heatmapPlot.html | 62 +++++++++- docs/reference/ds.hetcor.html | 2 +- docs/reference/ds.histogram.html | 69 ++++++++++- docs/reference/ds.igb_standards.html | 2 +- docs/reference/ds.isNA.html | 2 +- docs/reference/ds.isValid.html | 2 +- docs/reference/ds.kurtosis.html | 2 +- docs/reference/ds.length.html | 2 +- docs/reference/ds.levels.html | 2 +- docs/reference/ds.lexis.html | 2 +- docs/reference/ds.list.html | 2 +- .../reference/ds.listClientsideFunctions.html | 2 +- docs/reference/ds.listDisclosureSettings.html | 2 +- docs/reference/ds.listOpals.html | 2 +- .../reference/ds.listServersideFunctions.html | 2 +- docs/reference/ds.lmerSLMA.html | 2 +- docs/reference/ds.log.html | 2 +- docs/reference/ds.look.html | 2 +- docs/reference/ds.ls.html | 2 +- docs/reference/ds.lspline.html | 2 +- docs/reference/ds.make.html | 2 +- docs/reference/ds.matrix.html | 2 +- docs/reference/ds.matrixDet.html | 2 +- docs/reference/ds.matrixDet.report.html | 2 +- docs/reference/ds.matrixDiag.html | 115 +++++++++++++++++- docs/reference/ds.matrixDimnames.html | 2 +- docs/reference/ds.matrixInvert.html | 2 +- docs/reference/ds.matrixMult.html | 2 +- docs/reference/ds.matrixTranspose.html | 2 +- docs/reference/ds.mdPattern.html | 2 +- docs/reference/ds.mean.html | 2 +- docs/reference/ds.meanByClass.html | 2 +- docs/reference/ds.meanSdGp.html | 2 +- docs/reference/ds.merge.html | 2 +- docs/reference/ds.message.html | 2 +- docs/reference/ds.metadata.html | 2 +- docs/reference/ds.mice.html | 2 +- docs/reference/ds.names.html | 2 +- docs/reference/ds.ns.html | 2 +- docs/reference/ds.numNA.html | 2 +- docs/reference/ds.qlspline.html | 2 +- docs/reference/ds.quantileMean.html | 2 +- docs/reference/ds.rBinom.html | 2 +- docs/reference/ds.rNorm.html | 2 +- docs/reference/ds.rPois.html | 2 +- docs/reference/ds.rUnif.html | 2 +- docs/reference/ds.ranksSecure.html | 2 +- docs/reference/ds.rbind.html | 2 +- docs/reference/ds.reShape.html | 2 +- docs/reference/ds.recodeLevels.html | 2 +- docs/reference/ds.recodeValues.html | 50 +++++++- docs/reference/ds.rep.html | 2 +- docs/reference/ds.replaceNA.html | 2 +- docs/reference/ds.rm.html | 2 +- docs/reference/ds.rowColCalc.html | 2 +- docs/reference/ds.sample.html | 2 +- docs/reference/ds.scatterPlot.html | 2 +- docs/reference/ds.seq.html | 2 +- docs/reference/ds.setDefaultOpals.html | 2 +- docs/reference/ds.setSeed.html | 2 +- docs/reference/ds.skewness.html | 2 +- docs/reference/ds.sqrt.html | 2 +- docs/reference/ds.subset.html | 2 +- docs/reference/ds.subsetByClass.html | 2 +- docs/reference/ds.summary.html | 2 +- docs/reference/ds.table.html | 2 +- docs/reference/ds.table1D.html | 2 +- docs/reference/ds.table2D.html | 57 ++++++++- docs/reference/ds.tapply.assign.html | 2 +- docs/reference/ds.tapply.html | 2 +- docs/reference/ds.testObjExists.html | 2 +- docs/reference/ds.unList.html | 2 +- docs/reference/ds.unique.html | 2 +- docs/reference/ds.var.html | 2 +- docs/reference/ds.vectorCalc.html | 2 +- docs/reference/extract.html | 2 +- docs/reference/getPooledMean.html | 2 +- docs/reference/getPooledVar.html | 2 +- docs/reference/glmChecks.html | 2 +- docs/reference/index.html | 6 +- docs/reference/isAssigned.html | 2 +- docs/reference/isDefined.html | 2 +- docs/reference/logical2int.html | 2 +- docs/reference/meanByClassHelper0a.html | 2 +- docs/reference/meanByClassHelper0b.html | 2 +- docs/reference/meanByClassHelper1.html | 2 +- docs/reference/meanByClassHelper2.html | 2 +- docs/reference/meanByClassHelper3.html | 2 +- docs/reference/meanByClassHelper4.html | 2 +- docs/reference/rowPercent.html | 2 +- docs/reference/subsetHelper.html | 2 +- man/ds.boxPlot.Rd | 18 +-- 150 files changed, 626 insertions(+), 172 deletions(-) diff --git a/docs/404.html b/docs/404.html index 76de734e6..c37c451a9 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.5-9000 + 6.3.5 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index e721df6e3..b18449a17 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 6.3.5 diff --git a/docs/authors.html b/docs/authors.html index ea2155cdc..827877cec 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 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 (????). dsBaseClient: 'DataSHIELD' Client Side Base Functions. -R package version 6.3.5-9000. +R package version 6.3.5. 

@Manual{,
   title = {dsBaseClient: 'DataSHIELD' Client 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 f76381f01..b3d66be0a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - +