diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 00b230a4..2a8fa619 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -13,7 +13,6 @@ name: dsBase tests' suite on: push: - branches: [master, v6.3.4-dev] schedule: - cron: '0 0 * * 0' # Weekly - cron: '0 1 * * *' # Nightly @@ -153,10 +152,9 @@ jobs: working-directory: dsBase - name: Commit results to testStatus - # if: github.repository == 'villegar/dsBase' && github.event_name != 'pull_request' run: | - git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com" - git config --global user.name "$GITHUB_ACTOR" + git config --global user.email "github-actions[bot]@users.noreply.github.com" + git config --global user.name "github-actions[bot]" cd testStatus git checkout master git pull diff --git a/DESCRIPTION b/DESCRIPTION index 2732c4db..756074fb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -73,6 +73,8 @@ Imports: mice, childsds Suggests: + spelling, testthat RoxygenNote: 7.3.2 Encoding: UTF-8 +Language: en-GB diff --git a/R/dsBase-package.R b/R/dsBase-package.R new file mode 100644 index 00000000..a65cf643 --- /dev/null +++ b/R/dsBase-package.R @@ -0,0 +1,6 @@ +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +## usethis namespace: end +NULL diff --git a/README.md b/README.md index b844fcfe..c6a1ad5f 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ Detailed instructions on how to install DataSHIELD are at https://wiki.datashiel [1] 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 (2025). _dsBase: 'DataSHIELD' Server Side Base Functions_. R - package version 6.3.3. . + package version 6.3.4. . [2] 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, diff --git a/docs/404.html b/docs/404.html index 8ba2804e..bd9ca2cd 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,5 +1,5 @@ - + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 39bf3d39..f075675a 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,5 +1,5 @@ -NA • dsBaseNA • dsBase diff --git a/docs/authors.html b/docs/authors.html index ce342a9f..0b165dc3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • dsBaseAuthors and Citation • dsBase diff --git a/docs/index.html b/docs/index.html index 41a8674e..3bed0dab 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,5 +1,5 @@ - + @@ -86,20 +86,20 @@

About - + Location What is it? - + obiba CRAN Where you probably should install DataSHIELD from. - + releases Stable releases. - + master branch Mostly in sync with the latest release, changes rarely. diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index cc41cd15..9659989b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 3.1.3 +pandoc: '3.4' pkgdown: 2.1.3 pkgdown_sha: ~ articles: {} -last_built: 2025-08-20T16:17Z +last_built: 2025-08-21T06:49Z diff --git a/docs/reference/BooleDS.html b/docs/reference/BooleDS.html index bb394a66..e99c093a 100644 --- a/docs/reference/BooleDS.html +++ b/docs/reference/BooleDS.html @@ -1,5 +1,5 @@ -BooleDS — BooleDS • dsBaseBooleDS — BooleDS • dsBaseComputes the absolute values of the input variable — absDS • dsBaseComputes the absolute values of the input variable — absDS • dsBase diff --git a/docs/reference/asCharacterDS.html b/docs/reference/asCharacterDS.html index 51833330..ad7fee82 100644 --- a/docs/reference/asCharacterDS.html +++ b/docs/reference/asCharacterDS.html @@ -1,5 +1,5 @@ -Coerces an R object into class character — asCharacterDS • dsBaseCoerces an R object into class character — asCharacterDS • dsBase diff --git a/docs/reference/asDataMatrixDS.html b/docs/reference/asDataMatrixDS.html index 6129cec8..043d39ca 100644 --- a/docs/reference/asDataMatrixDS.html +++ b/docs/reference/asDataMatrixDS.html @@ -1,5 +1,5 @@ -asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS • dsBaseasDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS • dsBaseDetermines the levels of the input variable in each single study — asFactorDS1 • dsBaseDetermines the levels of the input variable in each single study — asFactorDS1 • dsBaseConverts a numeric vector into a factor — asFactorDS2 • dsBaseConverts a numeric vector into a factor — asFactorDS2 • dsBaseConverts a numeric vector into a factor — asFactorSimpleDS • dsBaseConverts a numeric vector into a factor — asFactorSimpleDS • dsBaseCoerces an R object into class integer — asIntegerDS • dsBaseCoerces an R object into class integer — asIntegerDS • dsBase diff --git a/docs/reference/asListDS.html b/docs/reference/asListDS.html index ee8394dd..65cdc968 100644 --- a/docs/reference/asListDS.html +++ b/docs/reference/asListDS.html @@ -1,5 +1,5 @@ -asListDS a serverside aggregate function called by ds.asList — asListDS • dsBaseasListDS a serverside aggregate function called by ds.asList — asListDS • dsBase diff --git a/docs/reference/asLogicalDS.html b/docs/reference/asLogicalDS.html index 4c7a59d7..1f6ab041 100644 --- a/docs/reference/asLogicalDS.html +++ b/docs/reference/asLogicalDS.html @@ -1,5 +1,5 @@ -Coerces an R object into class numeric — asLogicalDS • dsBaseCoerces an R object into class numeric — asLogicalDS • dsBase diff --git a/docs/reference/asMatrixDS.html b/docs/reference/asMatrixDS.html index 90654e71..24e13348 100644 --- a/docs/reference/asMatrixDS.html +++ b/docs/reference/asMatrixDS.html @@ -1,5 +1,5 @@ -Coerces an R object into a matrix — asMatrixDS • dsBaseCoerces an R object into a matrix — asMatrixDS • dsBase diff --git a/docs/reference/asNumericDS.html b/docs/reference/asNumericDS.html index 844e98de..9f8e3871 100644 --- a/docs/reference/asNumericDS.html +++ b/docs/reference/asNumericDS.html @@ -1,5 +1,5 @@ -Coerces an R object into class numeric — asNumericDS • dsBaseCoerces an R object into class numeric — asNumericDS • dsBase diff --git a/docs/reference/aucDS.html b/docs/reference/aucDS.html index 91866482..d031f39e 100644 --- a/docs/reference/aucDS.html +++ b/docs/reference/aucDS.html @@ -1,5 +1,5 @@ -aucDS an aggregate function called by ds.auc — aucDS • dsBaseaucDS an aggregate function called by ds.auc — aucDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — blackBoxDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — blackBoxDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — blackBoxRanksDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — blackBoxRanksDS • dsBaseCreate the identity stats and necessary data to draw a plot on the client — boxPlotGGDS • dsBaseCreate the identity stats and necessary data to draw a plot on the client — boxPlotGGDS • dsBaseArrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS • dsBaseArrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS • dsBase diff --git a/docs/reference/boxPlotGG_data_Treatment_numericDS.html b/docs/reference/boxPlotGG_data_Treatment_numericDS.html index 3cdb19eb..7d6902ab 100644 --- a/docs/reference/boxPlotGG_data_Treatment_numericDS.html +++ b/docs/reference/boxPlotGG_data_Treatment_numericDS.html @@ -1,5 +1,5 @@ -Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS • dsBaseArrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS • dsBase diff --git a/docs/reference/bp_standardsDS.html b/docs/reference/bp_standardsDS.html index b2d91c0a..18406769 100644 --- a/docs/reference/bp_standardsDS.html +++ b/docs/reference/bp_standardsDS.html @@ -1,5 +1,5 @@ -Calculates Blood pressure z-scores — bp_standardsDS • dsBaseCalculates Blood pressure z-scores — bp_standardsDS • dsBaseConcatenates objects into a vector or list — cDS • dsBaseConcatenates objects into a vector or list — cDS • dsBase diff --git a/docs/reference/cbindDS.html b/docs/reference/cbindDS.html index 0e7ecd7c..c4be7c18 100644 --- a/docs/reference/cbindDS.html +++ b/docs/reference/cbindDS.html @@ -1,5 +1,5 @@ -cbindDS called by ds.cbind — cbindDS • dsBasecbindDS called by ds.cbind — cbindDS • dsBaseChanges a reference level of a factor — changeRefGroupDS • dsBaseChanges a reference level of a factor — changeRefGroupDS • dsBase diff --git a/docs/reference/checkNegValueDS.html b/docs/reference/checkNegValueDS.html index b40e7520..f96f4e41 100644 --- a/docs/reference/checkNegValueDS.html +++ b/docs/reference/checkNegValueDS.html @@ -1,5 +1,5 @@ -Checks if a numeric variable has negative values — checkNegValueDS • dsBaseChecks if a numeric variable has negative values — checkNegValueDS • dsBase diff --git a/docs/reference/checkPermissivePrivacyControlLevel.html b/docs/reference/checkPermissivePrivacyControlLevel.html index 0600bbdd..e6efd045 100644 --- a/docs/reference/checkPermissivePrivacyControlLevel.html +++ b/docs/reference/checkPermissivePrivacyControlLevel.html @@ -1,5 +1,5 @@ -checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel • dsBasecheckPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel • dsBase diff --git a/docs/reference/classDS.html b/docs/reference/classDS.html index 8deec4b1..71412168 100644 --- a/docs/reference/classDS.html +++ b/docs/reference/classDS.html @@ -1,5 +1,5 @@ -Returns the class of an object — classDS • dsBaseReturns the class of an object — classDS • dsBase diff --git a/docs/reference/colnamesDS.html b/docs/reference/colnamesDS.html index 4a28c26c..e1132722 100644 --- a/docs/reference/colnamesDS.html +++ b/docs/reference/colnamesDS.html @@ -1,5 +1,5 @@ -Returns the column names of a data frame or matrix — colnamesDS • dsBaseReturns the column names of a data frame or matrix — colnamesDS • dsBase diff --git a/docs/reference/completeCasesDS.html b/docs/reference/completeCasesDS.html index 01ab8569..56845bf1 100644 --- a/docs/reference/completeCasesDS.html +++ b/docs/reference/completeCasesDS.html @@ -1,5 +1,5 @@ -completeCasesDS: an assign function called by ds.completeCases — completeCasesDS • dsBasecompleteCasesDS: an assign function called by ds.completeCases — completeCasesDS • dsBaseComputes the sum of each variable and the sum of products for each pair of variables — corDS • dsBaseComputes the sum of each variable and the sum of products for each pair of variables — corDS • dsBaseTests for correlation between paired samples — corTestDS • dsBaseTests for correlation between paired samples — corTestDS • dsBase diff --git a/docs/reference/covDS.html b/docs/reference/covDS.html index 0fde5f83..63be57ee 100644 --- a/docs/reference/covDS.html +++ b/docs/reference/covDS.html @@ -1,5 +1,5 @@ -Computes the sum of each variable and the sum of products for each pair of variables — covDS • dsBaseComputes the sum of each variable and the sum of products for each pair of variables — covDS • dsBasedataFrameDS called by ds.dataFrame — dataFrameDS • dsBasedataFrameDS called by ds.dataFrame — dataFrameDS • dsBasedataFrameFillDS — dataFrameFillDS • dsBasedataFrameFillDS — dataFrameFillDS • dsBase diff --git a/docs/reference/dataFrameSortDS.html b/docs/reference/dataFrameSortDS.html index 61c03840..47246150 100644 --- a/docs/reference/dataFrameSortDS.html +++ b/docs/reference/dataFrameSortDS.html @@ -1,5 +1,5 @@ -Sorting and reordering data frames, vectors or matrices — dataFrameSortDS • dsBaseSorting and reordering data frames, vectors or matrices — dataFrameSortDS • dsBase diff --git a/docs/reference/dataFrameSubsetDS1.html b/docs/reference/dataFrameSubsetDS1.html index 2af88052..cd201b50 100644 --- a/docs/reference/dataFrameSubsetDS1.html +++ b/docs/reference/dataFrameSubsetDS1.html @@ -1,5 +1,5 @@ -dataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubset — dataFrameSubsetDS1 • dsBasedataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubset — dataFrameSubsetDS1 • dsBase diff --git a/docs/reference/dataFrameSubsetDS2.html b/docs/reference/dataFrameSubsetDS2.html index 13fa4212..66dc97f6 100644 --- a/docs/reference/dataFrameSubsetDS2.html +++ b/docs/reference/dataFrameSubsetDS2.html @@ -1,5 +1,5 @@ -dataFrameSubsetDS2 an assign function called by ds.dataFrameSubset — dataFrameSubsetDS2 • dsBasedataFrameSubsetDS2 an assign function called by ds.dataFrameSubset — dataFrameSubsetDS2 • dsBase diff --git a/docs/reference/densityGridDS.html b/docs/reference/densityGridDS.html index 6bd9d93d..14c4e7b2 100644 --- a/docs/reference/densityGridDS.html +++ b/docs/reference/densityGridDS.html @@ -1,5 +1,5 @@ -Generates a density grid with or without a priori defined limits — densityGridDS • dsBaseGenerates a density grid with or without a priori defined limits — densityGridDS • dsBase diff --git a/docs/reference/dimDS.html b/docs/reference/dimDS.html index ff787a02..ccda6820 100644 --- a/docs/reference/dimDS.html +++ b/docs/reference/dimDS.html @@ -1,5 +1,5 @@ -Returns the dimension of a data frame or matrix — dimDS • dsBaseReturns the dimension of a data frame or matrix — dimDS • dsBase diff --git a/docs/reference/dmtC2SDS.html b/docs/reference/dmtC2SDS.html index 27c7f867..df76184d 100644 --- a/docs/reference/dmtC2SDS.html +++ b/docs/reference/dmtC2SDS.html @@ -1,5 +1,5 @@ -Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS • dsBaseCopy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS • dsBasedsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package • dsBase + + +
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dsBase: 'DataSHIELD' Server Side Base Functions

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Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'.

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Author

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Maintainer: Stuart Wheater stuart.wheater@arjuna.com (ORCID)

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Authors:

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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.

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Site built with pkgdown 2.1.3.

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+ + + + + + + + diff --git a/docs/reference/elsplineDS.html b/docs/reference/elsplineDS.html index 246ef707..190483ae 100644 --- a/docs/reference/elsplineDS.html +++ b/docs/reference/elsplineDS.html @@ -1,5 +1,5 @@ -Basis for a piecewise linear spline with meaningful coefficients — elsplineDS • dsBaseBasis for a piecewise linear spline with meaningful coefficients — elsplineDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies — extractQuantilesDS1 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies — extractQuantilesDS1 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies — extractQuantilesDS2 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies — extractQuantilesDS2 • dsBasegamlssDS an aggregate function called by ds.gamlss — gamlssDS • dsBase -Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS • dsBaseComputes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS • dsBaseglmDS1 called by ds.glm — glmDS1 • dsBaseglmDS1 called by ds.glm — glmDS1 • dsBase diff --git a/docs/reference/glmDS2.html b/docs/reference/glmDS2.html index e3a9088b..71ccd910 100644 --- a/docs/reference/glmDS2.html +++ b/docs/reference/glmDS2.html @@ -1,5 +1,5 @@ -glmDS2 called by ds.glm — glmDS2 • dsBaseglmDS2 called by ds.glm — glmDS2 • dsBase diff --git a/docs/reference/glmPredictDS.ag.html b/docs/reference/glmPredictDS.ag.html index 88224724..f99f1f21 100644 --- a/docs/reference/glmPredictDS.ag.html +++ b/docs/reference/glmPredictDS.ag.html @@ -1,5 +1,5 @@ -predict regression responses from a glm object — glmPredictDS.ag • dsBasepredict regression responses from a glm object — glmPredictDS.ag • dsBasepredict regression responses from a glm object — glmPredictDS.as • dsBasepredict regression responses from a glm object — glmPredictDS.as • dsBaseFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign • dsBaseFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign • dsBaseFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS1 • dsBaseFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS1 • dsBaseFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS2 • dsBaseFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS2 • dsBasesummarize a glm object on the serverside — glmSummaryDS.ag • dsBasesummarize a glm object on the serverside — glmSummaryDS.ag • dsBasesummarize a glm object on the serverside — glmSummaryDS.as • dsBasesummarize a glm object on the serverside — glmSummaryDS.as • dsBaseFitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign • dsBaseFitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign • dsBaseFitting generalized linear mixed effect models - serverside function — glmerSLMADS2 • dsBaseFitting generalized linear mixed effect models - serverside function — glmerSLMADS2 • dsBaseCalculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS • dsBaseCalculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS • dsBase diff --git a/docs/reference/hetcorDS.html b/docs/reference/hetcorDS.html index d12ec828..ac02df16 100644 --- a/docs/reference/hetcorDS.html +++ b/docs/reference/hetcorDS.html @@ -1,5 +1,5 @@ -Heterogeneous Correlation Matrix — hetcorDS • dsBaseHeterogeneous Correlation Matrix — hetcorDS • dsBase diff --git a/docs/reference/histogramDS1.html b/docs/reference/histogramDS1.html index a9e7b356..dfae6675 100644 --- a/docs/reference/histogramDS1.html +++ b/docs/reference/histogramDS1.html @@ -1,5 +1,5 @@ -returns the minimum and the maximum of the input numeric vector — histogramDS1 • dsBasereturns the minimum and the maximum of the input numeric vector — histogramDS1 • dsBaseComputes a histogram of the input variable without plotting. — histogramDS2 • dsBaseComputes a histogram of the input variable without plotting. — histogramDS2 • dsBaseConverts birth measurements to intergrowth z-scores/centiles — igb_standardsDS • dsBaseConverts birth measurements to intergrowth z-scores/centiles — igb_standardsDS • dsBase diff --git a/docs/reference/index.html b/docs/reference/index.html index 7c6dd126..59255ef6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ -Package index • dsBasePackage index • dsBase diff --git a/docs/reference/isNaDS.html b/docs/reference/isNaDS.html index dbfb140c..06080e50 100644 --- a/docs/reference/isNaDS.html +++ b/docs/reference/isNaDS.html @@ -1,5 +1,5 @@ -Checks if a vector is empty — isNaDS • dsBaseChecks if a vector is empty — isNaDS • dsBaseChecks if an input is valid — isValidDS • dsBaseChecks if an input is valid — isValidDS • dsBase diff --git a/docs/reference/kurtosisDS1.html b/docs/reference/kurtosisDS1.html index 18f70f62..d65a39fb 100644 --- a/docs/reference/kurtosisDS1.html +++ b/docs/reference/kurtosisDS1.html @@ -1,5 +1,5 @@ -Calculates the kurtosis of a numeric variable — kurtosisDS1 • dsBaseCalculates the kurtosis of a numeric variable — kurtosisDS1 • dsBase diff --git a/docs/reference/kurtosisDS2.html b/docs/reference/kurtosisDS2.html index b43cd157..7758f44c 100644 --- a/docs/reference/kurtosisDS2.html +++ b/docs/reference/kurtosisDS2.html @@ -1,5 +1,5 @@ -Calculates the kurtosis of a numeric variable — kurtosisDS2 • dsBaseCalculates the kurtosis of a numeric variable — kurtosisDS2 • dsBaseReturns the length of a vector or list — lengthDS • dsBaseReturns the length of a vector or list — lengthDS • dsBase diff --git a/docs/reference/levelsDS.html b/docs/reference/levelsDS.html index b535bd7a..5d7163fb 100644 --- a/docs/reference/levelsDS.html +++ b/docs/reference/levelsDS.html @@ -1,5 +1,5 @@ -Returns the levels of a factor vector — levelsDS • dsBaseReturns the levels of a factor vector — levelsDS • dsBase diff --git a/docs/reference/lexisDS1.html b/docs/reference/lexisDS1.html index 65381e78..acf40341 100644 --- a/docs/reference/lexisDS1.html +++ b/docs/reference/lexisDS1.html @@ -1,5 +1,5 @@ -lexisDS1 — lexisDS1 • dsBaselexisDS1 — lexisDS1 • dsBase diff --git a/docs/reference/lexisDS2.html b/docs/reference/lexisDS2.html index 23318275..203d290c 100644 --- a/docs/reference/lexisDS2.html +++ b/docs/reference/lexisDS2.html @@ -1,5 +1,5 @@ -lexisDS2 — lexisDS2 • dsBaselexisDS2 — lexisDS2 • dsBase diff --git a/docs/reference/lexisDS3.html b/docs/reference/lexisDS3.html index c2513381..c16502f5 100644 --- a/docs/reference/lexisDS3.html +++ b/docs/reference/lexisDS3.html @@ -1,5 +1,5 @@ -@title lexisDS3 — lexisDS3 • dsBase@title lexisDS3 — lexisDS3 • dsBase diff --git a/docs/reference/listDS.html b/docs/reference/listDS.html index d6962b85..517bff8d 100644 --- a/docs/reference/listDS.html +++ b/docs/reference/listDS.html @@ -1,5 +1,5 @@ -Coerce objects into a list — listDS • dsBaseCoerce objects into a list — listDS • dsBase diff --git a/docs/reference/listDisclosureSettingsDS.html b/docs/reference/listDisclosureSettingsDS.html index 554e51cd..2f6252fa 100644 --- a/docs/reference/listDisclosureSettingsDS.html +++ b/docs/reference/listDisclosureSettingsDS.html @@ -1,5 +1,5 @@ -listDisclosureSettingsDS — listDisclosureSettingsDS • dsBaselistDisclosureSettingsDS — listDisclosureSettingsDS • dsBaseFitting linear mixed effect models - serverside function — lmerSLMADS.assign • dsBaseFitting linear mixed effect models - serverside function — lmerSLMADS.assign • dsBaseFitting linear mixed effect models - serverside function — lmerSLMADS2 • dsBaseFitting linear mixed effect models - serverside function — lmerSLMADS2 • dsBaselists all objects on a serverside environment — lsDS • dsBaselists all objects on a serverside environment — lsDS • dsBaseBasis for a piecewise linear spline with meaningful coefficients — lsplineDS • dsBaseBasis for a piecewise linear spline with meaningful coefficients — lsplineDS • dsBasematrixDS assign function called by ds.matrix — matrixDS • dsBasematrixDS assign function called by ds.matrix — matrixDS • dsBase diff --git a/docs/reference/matrixDetDS1.html b/docs/reference/matrixDetDS1.html index b4da1887..63f81b79 100644 --- a/docs/reference/matrixDetDS1.html +++ b/docs/reference/matrixDetDS1.html @@ -1,5 +1,5 @@ -matrixDetDS aggregate function called by ds.matrixDet.report — matrixDetDS1 • dsBasematrixDetDS aggregate function called by ds.matrixDet.report — matrixDetDS1 • dsBasematrixDetDS assign function called by ds.matrixDet — matrixDetDS2 • dsBasematrixDetDS assign function called by ds.matrixDet — matrixDetDS2 • dsBasematrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS • dsBasematrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS • dsBasematrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS • dsBasematrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS • dsBasematrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS • dsBasematrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS • dsBase diff --git a/docs/reference/matrixMultDS.html b/docs/reference/matrixMultDS.html index eefb7112..8bae8648 100644 --- a/docs/reference/matrixMultDS.html +++ b/docs/reference/matrixMultDS.html @@ -1,5 +1,5 @@ -matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS • dsBasematrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS • dsBase diff --git a/docs/reference/matrixTransposeDS.html b/docs/reference/matrixTransposeDS.html index a1d02f7e..fc9337f2 100644 --- a/docs/reference/matrixTransposeDS.html +++ b/docs/reference/matrixTransposeDS.html @@ -1,5 +1,5 @@ -matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS • dsBasematrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS • dsBase diff --git a/docs/reference/meanDS.html b/docs/reference/meanDS.html index 62d29d65..e8946d90 100644 --- a/docs/reference/meanDS.html +++ b/docs/reference/meanDS.html @@ -1,5 +1,5 @@ -Computes statistical mean of a vector — meanDS • dsBaseComputes statistical mean of a vector — meanDS • dsBase diff --git a/docs/reference/meanSdGpDS.html b/docs/reference/meanSdGpDS.html index bc8825d1..44cf811b 100644 --- a/docs/reference/meanSdGpDS.html +++ b/docs/reference/meanSdGpDS.html @@ -1,5 +1,5 @@ -MeanSdGpDS — meanSdGpDS • dsBaseMeanSdGpDS — meanSdGpDS • dsBase diff --git a/docs/reference/mergeDS.html b/docs/reference/mergeDS.html index f97d682c..5cbb47cc 100644 --- a/docs/reference/mergeDS.html +++ b/docs/reference/mergeDS.html @@ -1,5 +1,5 @@ -mergeDS (assign function) called by ds.merge — mergeDS • dsBasemergeDS (assign function) called by ds.merge — mergeDS • dsBasemessageDS — messageDS • dsBasemessageDS — messageDS • dsBaseReturns the metadata, if any, about the specified variable — metadataDS • dsBaseReturns the metadata, if any, about the specified variable — metadataDS • dsBase diff --git a/docs/reference/miceDS.html b/docs/reference/miceDS.html index 6f8c57b9..9457e5a8 100644 --- a/docs/reference/miceDS.html +++ b/docs/reference/miceDS.html @@ -1,5 +1,5 @@ -Aggregate function called by ds.mice — miceDS • dsBaseAggregate function called by ds.mice — miceDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — minMaxRandDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — minMaxRandDS • dsBaseReturn the names of a list object — namesDS • dsBaseReturn the names of a list object — namesDS • dsBase diff --git a/docs/reference/nsDS.html b/docs/reference/nsDS.html index 65d02e21..03822097 100644 --- a/docs/reference/nsDS.html +++ b/docs/reference/nsDS.html @@ -1,5 +1,5 @@ -Generate a Basis Matrix for Natural Cubic Splines — nsDS • dsBaseGenerate a Basis Matrix for Natural Cubic Splines — nsDS • dsBaseCounts the number of missing values — numNaDS • dsBaseCounts the number of missing values — numNaDS • dsBaseBasis for a piecewise linear spline with meaningful coefficients — qlsplineDS • dsBaseBasis for a piecewise linear spline with meaningful coefficients — qlsplineDS • dsBaseGenerates quantiles and mean information without maximum and minimum — quantileMeanDS • dsBaseGenerates quantiles and mean information without maximum and minimum — quantileMeanDS • dsBaserBinomDS serverside assign function — rBinomDS • dsBaserBinomDS serverside assign function — rBinomDS • dsBase diff --git a/docs/reference/rNormDS.html b/docs/reference/rNormDS.html index 35e47dfc..7720f286 100644 --- a/docs/reference/rNormDS.html +++ b/docs/reference/rNormDS.html @@ -1,5 +1,5 @@ -rNormDS serverside assign function — rNormDS • dsBaserNormDS serverside assign function — rNormDS • dsBase diff --git a/docs/reference/rPoisDS.html b/docs/reference/rPoisDS.html index 82595f81..c560901e 100644 --- a/docs/reference/rPoisDS.html +++ b/docs/reference/rPoisDS.html @@ -1,5 +1,5 @@ -rPoisDS serverside assign function — rPoisDS • dsBaserPoisDS serverside assign function — rPoisDS • dsBase diff --git a/docs/reference/rUnifDS.html b/docs/reference/rUnifDS.html index 77495f76..7af321e6 100644 --- a/docs/reference/rUnifDS.html +++ b/docs/reference/rUnifDS.html @@ -1,5 +1,5 @@ -rUnifDS serverside assign function — rUnifDS • dsBaserUnifDS serverside assign function — rUnifDS • dsBase diff --git a/docs/reference/rangeDS.html b/docs/reference/rangeDS.html index b5687859..fb661e2f 100644 --- a/docs/reference/rangeDS.html +++ b/docs/reference/rangeDS.html @@ -1,5 +1,5 @@ -returns the minimum and maximum of a numeric vector — rangeDS • dsBasereturns the minimum and maximum of a numeric vector — rangeDS • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS1 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS1 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS2 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS2 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS3 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS3 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS4 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS5 • dsBaseSecure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS5 • dsBaserbindDS called by ds.rbind — rbindDS • dsBaserbindDS called by ds.rbind — rbindDS • dsBasereShapeDS (assign function) called by ds.reShape — reShapeDS • dsBasereShapeDS (assign function) called by ds.reShape — reShapeDS • dsBaseRecodes the levels of a categorical variables — recodeLevelsDS • dsBaseRecodes the levels of a categorical variables — recodeLevelsDS • dsBaserecodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS • dsBaserecodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS • dsBaserepDS called by ds.rep — repDS • dsBaserepDS called by ds.rep — repDS • dsBaseReplaces the missing values in a vector — replaceNaDS • dsBaseReplaces the missing values in a vector — replaceNaDS • dsBasermDS an aggregate function called by ds.rm — rmDS • dsBasermDS an aggregate function called by ds.rm — rmDS • dsBase diff --git a/docs/reference/rowColCalcDS.html b/docs/reference/rowColCalcDS.html index ea332ea6..2e657383 100644 --- a/docs/reference/rowColCalcDS.html +++ b/docs/reference/rowColCalcDS.html @@ -1,5 +1,5 @@ -Computes sums and means of rows or columns of numeric arrays — rowColCalcDS • dsBaseComputes sums and means of rows or columns of numeric arrays — rowColCalcDS • dsBaserandom sampling and permuting of vectors, dataframes and matrices — sampleDS • dsBaserandom sampling and permuting of vectors, dataframes and matrices — sampleDS • dsBaseCalculates the coordinates of the data to be plot — scatterPlotDS • dsBaseCalculates the coordinates of the data to be plot — scatterPlotDS • dsBaseseqDS a serverside assign function called by ds.seq — seqDS • dsBaseseqDS a serverside assign function called by ds.seq — seqDS • dsBase diff --git a/docs/reference/setSeedDS.html b/docs/reference/setSeedDS.html index 525ddf79..4e49ec86 100644 --- a/docs/reference/setSeedDS.html +++ b/docs/reference/setSeedDS.html @@ -1,5 +1,5 @@ -setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS • dsBasesetSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS • dsBaseCalculates the skewness of a numeric variable — skewnessDS1 • dsBaseCalculates the skewness of a numeric variable — skewnessDS1 • dsBase diff --git a/docs/reference/skewnessDS2.html b/docs/reference/skewnessDS2.html index ef93b35e..f86c7490 100644 --- a/docs/reference/skewnessDS2.html +++ b/docs/reference/skewnessDS2.html @@ -1,5 +1,5 @@ -Calculates the skewness of a numeric variable — skewnessDS2 • dsBaseCalculates the skewness of a numeric variable — skewnessDS2 • dsBaseComputes the square root values of the input variable — sqrtDS • dsBaseComputes the square root values of the input variable — sqrtDS • dsBase diff --git a/docs/reference/subsetByClassDS.html b/docs/reference/subsetByClassDS.html index 06507b87..92b0197c 100644 --- a/docs/reference/subsetByClassDS.html +++ b/docs/reference/subsetByClassDS.html @@ -1,5 +1,5 @@ -Breaks down a dataframe or a factor into its sub-classes — subsetByClassDS • dsBaseBreaks down a dataframe or a factor into its sub-classes — subsetByClassDS • dsBaseGenerates a valid subset of a table or a vector — subsetDS • dsBaseGenerates a valid subset of a table or a vector — subsetDS • dsBaseCreates 1-dimensional contingency tables — table1DDS • dsBaseCreates 1-dimensional contingency tables — table1DDS • dsBasetable2DDS (aggregate function) called by ds.table2D — table2DDS • dsBasetable2DDS (aggregate function) called by ds.table2D — table2DDS • dsBasetableDS.assign is the serverside assign function called by ds.table — tableDS.assign • dsBasetableDS.assign is the serverside assign function called by ds.table — tableDS.assign • dsBasetableDS is the first of two serverside aggregate functions called by ds.table — tableDS • dsBasetableDS is the first of two serverside aggregate functions called by ds.table — tableDS • dsBasetableDS is the second of two serverside aggregate functions called by ds.table — tableDS2 • dsBasetableDS is the second of two serverside aggregate functions called by ds.table — tableDS2 • dsBasetapplyDS.assign called by ds.tapply.assign — tapplyDS.assign • dsBasetapplyDS.assign called by ds.tapply.assign — tapplyDS.assign • dsBasetapplyDS called by ds.tapply — tapplyDS • dsBasetapplyDS called by ds.tapply — tapplyDS • dsBasetestObjExistsDS — testObjExistsDS • dsBasetestObjExistsDS — testObjExistsDS • dsBase diff --git a/docs/reference/unListDS.html b/docs/reference/unListDS.html index 2bc79c42..d7b8aaf4 100644 --- a/docs/reference/unListDS.html +++ b/docs/reference/unListDS.html @@ -1,5 +1,5 @@ -unListDS a serverside assign function called by ds.unList — unListDS • dsBaseunListDS a serverside assign function called by ds.unList — unListDS • dsBaseApplies the unique method to a server-side variable. — uniqueDS • dsBaseApplies the unique method to a server-side variable. — uniqueDS • dsBase diff --git a/docs/reference/varDS.html b/docs/reference/varDS.html index 7e785dd6..37a4d212 100644 --- a/docs/reference/varDS.html +++ b/docs/reference/varDS.html @@ -1,5 +1,5 @@ -Computes the variance of vector — varDS • dsBaseComputes the variance of vector — varDS • dsBase diff --git a/docs/reference/vectorDS.html b/docs/reference/vectorDS.html index 4da45050..c7cca023 100644 --- a/docs/reference/vectorDS.html +++ b/docs/reference/vectorDS.html @@ -1,5 +1,5 @@ -Creates a vector on the server-side. — vectorDS • dsBaseCreates a vector on the server-side. — vectorDS • dsBase diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 265de84e..04ef332c 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -41,6 +41,7 @@ /reference/densityGridDS.html /reference/dimDS.html /reference/dmtC2SDS.html +/reference/dsBase-package.html /reference/elsplineDS.html /reference/extract.html /reference/extractQuantilesDS1.html diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 00000000..23ca495f --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,327 @@ +Aguirre +BMI +Banerjee +Boniol +BooleDS +Bota +Budin +CG +Cederkvist +Codecov +DDS +DF +DMT +DMTs +DataSHIELD +Demir +Dibben +Doiron +Duijts +Escribà +Ferretti +Fortier +GAMLSS +Giepmans +GlobalEnv +González +Gonçalves +HC +Haakma +Hartlev +Hasenauer +Heuvel +Hiekkalinna +Huth +Hveem +Inf +Isaeva +Jaddoe +Knoppers +Kvaløy +LaFlamme +Ljøsne +MUAC +Macleod +Mayrhofer +MeanSdGpDS +Millar +Molnar +Montagut +Murtagh +Nuotio +Nybo +Perola +Poisson +Polychoric +Polyserial +R's +RS +Reischl +Ryser +SDS +SDs +SLMA +SSF +Schwarz +Serverside +Severside +Stasinopoulos +Stolk +Strandberg +Swertz +TBL +TDemetris +TSF +Tedds +WGS +Waldenberger +Welten +Woffenbuttel +Zbp +ag +asDataMatrix +asDataMatrixDS +asFactor +asFactorSimple +asList +asListDS +ascharacter +asdatamatrix +asinteger +auc +aucDS +bfa +blackBox +blackBoxDS +blackBoxRanksDS +blackbox +booleans +bp +byrow +casewise +cbind +cbindDS +cbinded +cbinding +centile +centiles +checkPermissivePrivacyControlLevel +childsds +clientside +colMeans +colSums +completeCases +completeCasesDS +crit +cs +cvar +cyc +dataFrame +dataFrameDS +dataFrameFill +dataFrameFillDS +dataFrameShort +dataFrameSort +dataFrameSortDS +dataFrameSubset +dataFrameSubsetDS +dataName +dataframesort +datashield +datasource +datasources +deKlerk +defaultMethod +df +dfdata +diag +disclosive +dmtC +ds +dsBaseClient +dups +eg +elspline +etc +extractQuantileDS +extractQuantiles +extractQuantilesDS +fixef +gamlss +gamlssDS +gd +ggplot +glm +glmDS +glmPredict +glmSLMA +glmSLMADS +glmSummary +glmSummaryDS +glme +glmer +glmerMod +glmerSLMA +glmerSLMADS +glmes +glmname +hca +hcircm +hetcor +hfa +idvar +igb +imputationSet +incomparables +inout +kendall +lencm +lexisDS +lfa +listDisclosureSettings +listDisclosureSettingsDS +lme +lmer +lmerMod +lmerSLMA +lmerSLMADS +lmerSLMDS +lmes +loess +lspline +manag +matdftbl +matrixDS +matrixDet +matrixDetDS +matrixDiag +matrixDiagDS +matrixDimnames +matrixDimnamesDS +matrixInvert +matrixInvertDS +matrixMult +matrixMultDS +matrixTranspose +matrixTransposeDS +maxit +mdata +meanSdGp +mergeDS +messageDS +messageobj +metafor +mfa +mids +misspecifications +modeling +mxn +mxp +nAGQ +namesDS +ncol +ncols +nearPD +newObj +newObject +newdataname +newobj +nfilter +nrows +num +nxp +obiba +obj +obs +param +pb +pearson +perc +poisson +polychoric +polyserial +predictorMatrix +privacyControlLevel +prob +probs +pseudodata +qlspline +quatric +rBinom +rBinomDS +rNorm +rNormDS +rPois +rPoisDS +rUnif +rUnifDS +ra +ranksSecure +ranksSecureDS +rbindDS +rbinded +rbinom +rd +reShape +reShapeDS +recodeValues +recodeValuesDS +repDS +rm +rmDS +rnorm +rowMeans +rowSums +rpois +runif +rvar +sR +samp +sampleDS +sbp +sd +sds +seedtext +sep +seq +seqDS +serverside +serversideMessage +setSeed +setSeedDS +setSeedDs +smallCellsRule +spearman +ssa +studyid +studysideMessage +studysideMessages +stvar +subtable +tableDS +tapply +tapplyDS +testObjExists +testObjExistsDS +th +tibble +timevar +tol +tsa +unList +uniques +unlist +useNA +val +vals +var +vect +wfa +wfh +wfl +wlr +wtkg +xvect +yvect +zscore +zscores diff --git a/man/dsBase-package.Rd b/man/dsBase-package.Rd new file mode 100644 index 00000000..725c4131 --- /dev/null +++ b/man/dsBase-package.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dsBase-package.R +\docType{package} +\name{dsBase-package} +\alias{dsBase} +\alias{dsBase-package} +\title{dsBase: 'DataSHIELD' Server Side Base Functions} +\description{ +Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'. +} +\author{ +\strong{Maintainer}: Stuart Wheater \email{stuart.wheater@arjuna.com} (\href{https://orcid.org/0009-0003-2419-1964}{ORCID}) + +Authors: +\itemize{ + \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}) + \item Patricia Ryser-Welch (\href{https://orcid.org/0000-0002-0070-0264}{ORCID}) + \item Alex Westerberg + \item Leire Abarrategui + \item Roberto Villegas-Diaz (\href{https://orcid.org/0000-0001-5036-8661}{ORCID}) + \item Demetris Avraam (\href{https://orcid.org/0000-0001-8908-2441}{ORCID}) + \item Yannick Marcon \email{yannick.marcon@obiba.org} (\href{https://orcid.org/0000-0003-0138-2023}{ORCID}) + \item Tom Bishop + \item Amadou Gaye (\href{https://orcid.org/0000-0002-1180-2792}{ORCID}) + \item Xavier Escribà-Montagut (\href{https://orcid.org/0000-0003-2888-8948}{ORCID}) +} + +} +\keyword{internal}