DataSHIELD functions in v5

Overview

The tables below outline all of the functions in DataSHIELD (i.e. in the base, betaTest, graphics, modelling and stats packages), and what their status will be in the v5 release. In summary we are:

  • Moving everything from the graphics, modelling and stats packages into the base packages.
  • Where an existing function has been updated with a new function in the betaTest packages it is probably* being moved to the base packages where it will replace the v4 function.
  • Where a new function has been developed in the betaTest packages it is probably* being moved to the base packages.
  • Where there are duplicates after this (e.g. where the same helper functions exist in multiple packages) we keep one of them.
  • *There are a couple of functions in betaTest we are not planning on releasing in v5, these will remain in the betaTest packages and continue to be developed & tested.

Server side functions


Function NamePackageIn v5Release PlanNotes
1asFactorDS.RdsBaseNDelete
2asListDS.RdsBaseNReplace with dsBetaTest asListDS.o.R
3asMatrixDS.RdsBaseNReplace with dsBetaTest asMatrixDS.o.R
4cDS.RdsBaseYKeep as is
5changeRefGroupDS.RdsBaseYKeep as is
6dataframeDS.RdsBaseNReplace with dsBetaTest dataframeDS.o.R
7extract.RdsBaseYKeep as is
8isNaDS.RdsBaseYKeep as is
9isValidDS.RdsBaseYKeep as is
10listDS.RdsBaseYKeep as is
11meanDS.RdsBaseNReplace with dsBetaTest meanDS.o.R
12namesDS.RdsBaseYKeep as is
13numNaDS.RdsBaseYKeep as is
14quantileMeanDS.RdsBaseYKeep as is
15recodeLevelsDS.RdsBaseYKeep as is
16replaceNaDS.RdsBaseYKeep as is
17rowColCalcDS.RdsBaseYKeep as is
18setFilterDS.RdsBase


19subsetByClassDS.RdsBaseYKeep as is
20subsetByClassHelper1.RdsBaseYKeep as is
21subsetByClassHelper2.RdsBaseYKeep as is
22subsetByClassHelper3.RdsBaseYKeep as is
23subsetDS.RdsBaseYKeep as is
24table1dDS.RdsBaseYKeep as is
25table2dDS.RdsBaseNReplace with dsBetaTest table2dDS.o.R
26varDS.RdsBaseNReplace with dsBetaTest varDS.o.R
27BooleDS.o.RdsBetaTestYMove to dsBase
28asCharacterDS.o.RdsBetaTestYMove to dsBase
29asDataMatrix.o.RdsBetaTestYMove to dsBase
30asFactorDS1.o.RdsBetaTestYMove to dsBase
31asFactorDS2.o.RdsBetaTestYMove to dsBase
32asIntegerDS.o.RdsBetaTestYMove to dsBase
33asListDS.o.RdsBetaTestYMove to dsBase
34asLogicalDS.o.RdsBetaTestYMove to dsBase
35asMatrixDS.o.RdsBetaTestYMove to dsBase
36asNumericDS.o.RdsBetaTestYMove to dsBase
37cbindDS.o.RdsBetaTestYMove to dsBase
38covDS.o.RdsBetaTestYMove to dsBase
39dataFrameDS.o.RdsBetaTestYMove to dsBase
40dataFrameSortDS.o.RdsBetaTestYMove to dsBase
41dataFrameSubsetDS1.o.RdsBetaTestYMove to dsBase
42dataFrameSubsetDS2.o.RdsBetaTestYMove to dsBase
43dimDS.o.RdsBetaTestYMove to dsBase
44glmDS1.o.RdsBetaTestYMove to dsBase
45glmDS2.o.RdsBetaTestYMove to dsBase
46glmSLMADS2.o.RdsBetaTestYMove to dsBase
47histogramDS.o.RdsBetaTestYMove to dsBase
48lengthDS.o.RdsBetaTestYMove to dsBase
49lexisDS1.o.RdsBetaTestYMove to dsBase
50lexisDS2.o.RdsBetaTestYMove to dsBase
51lexisDS3.o.RdsBetaTestYMove to dsBase
52listDisclosureSettingsDS.o.RdsBetaTestYMove to dsBase
53matrixDS.RdsBetaTestYMove to dsBase
54matrixDetDS1.RdsBetaTestYMove to dsBase
55matrixDetDS2.RdsBetaTestYMove to dsBase
56matrixDiagDS.RdsBetaTestYMove to dsBase
57matrixDimnamesDS.RdsBetaTestYMove to dsBase
58matrixInvertDS.RdsBetaTestYMove to dsBase
59matrixMultDS.RdsBetaTestYMove to dsBase
60matrixTransposeDS.RdsBetaTestYMove to dsBase
61meanDS.o.RdsBetaTestYMove to dsBase
62meanSdGpDS.RdsBetaTestYMove to dsBase
63mergeDS.o.RdsBetaTestYMove to dsBase
64messageDS.o.RdsBetaTestYMove to dsBase
65rBinomDS.o.RdsBetaTestYMove to dsBase
66rNormDS.o.RdsBetaTestYMove to dsBase
67rPoisDS.o.RdsBetaTestYMove to dsBase
68rUnifDS.o.RdsBetaTestYMove to dsBase
69rbindDS.o.RdsBetaTestYMove to dsBase
70reShapeDS.o.RdsBetaTestYMove to dsBase
71recodeValuesDS1.o.RdsBetaTestYMove to dsBase
72recodeValuesDS2.o.RdsBetaTestYMove to dsBase
73rilmDS.b.RdsBetaTestNNot ready for this release
74rmDS.o.RdsBetaTestYMove to dsBase
75scatterPlotDS.o.RdsBetaTestYMove to dsBase
76seqDS.o.RdsBetaTestYMove to dsBase
77setSeedDS.o.RdsBetaTestYMove to dsBase
78tTestFDS2.RdsBetaTestNNot ready for this release
79table2dDS.o.RdsBetaTestYMove to dsBase
80tapplyDS.assign.o.RdsBetaTestYMove to dsBase
81tapplyDS.o.RdsBetaTestYMove to dsBase
82testObjExistsDS.o.RdsBetaTestYMove to dsBase
83unListDS.o.RdsBetaTestYMove to dsBase
84varDS.o.RdsBetaTestYMove to dsBase
85corDS.RdsStatsYMove to dsBase
86covDS.RdsStatsNReplace with dsBetaTest covDS.o.R
87extract.RdsStatsNDeleteIdentical to dsBase version
88isValidDS.RdsStatsNDeleteIdentical to dsBase version
89setFilterDS.RdsStats

setFilter in dsBase may not always guarantee a numeric value whereas in dsStats and dsGraphics it returns a numeric value.
90varDS.RdsStatsNDeleteIdentical to dsBase version
91alphaPhiDS.RdsModellingYMove to dsBase
92checkNegValuesDS.RdsModellingYMove to dsBase
93glmDS1.RdsModellingNReplace with dsBetaTest glmDS1.o.R
94glmDS2.RdsModellingNReplace with dsBetaTest glmDS2.o.r
95lexisDS.RdsModellingNDelete
96lexishelper1.RdsModellingNDelete
97lexishelper2.RdsModellingNDelete
98scoreVectDS.RdsModellingYMove to dsBase
99densityGridDS.RdsGraphicsYMove to dsBase
100extract.RdsGraphicsNDeleteIdentical to dsBase version
101histogramDS.RdsGraphicsNReplace with dsBetaTest histogramDS.o.R
102rangeDS.RdsGraphicsYMove to dsBase
103setFilterDS.RdsGraphics

setFilter in dsBase may not always guarantee a numeric value whereas in dsStats and dsGraphics it returns a numeric value.



Client side functions


Function NamePackageIn v5Release PlanNotes
1checkClass.RdsBaseClientYKeep as is
2colPercent.RdsBaseClientNReplace with dsBetaTestClient colPercent.R
3ds.asCharacter.RdsBaseClientNReplace with dsBetaTestClient ds.asCharacter.o.R
4ds.asFactor.RdsBaseClientNReplace with dsBetaTestClient ds.asFactor.o.R
5ds.asList.RdsBaseClientNReplace with dsBetaTestClient ds.asList.o.R
6ds.asMatrix.RdsBaseClientNReplace with dsBetaTestClient ds.asMatrix.o.R
7ds.asNumeric.RdsBaseClientNReplace with dsBetaTestClient ds.asNumeric.o.R
8ds.assign.RdsBaseClientYKeep as is
9ds.c.RdsBaseClientYKeep as is
10ds.cbind.RdsBaseClientNReplace with dsBetaTestClient ds.cbind.o.R
11ds.changeRefGroup.RdsBaseClientYKeep as is
12ds.class.RdsBaseClientYKeep as is
13ds.colnames.RdsBaseClientYKeep as is
14ds.dataframe.RdsBaseClientNReplace with dsBetaTestClient ds.dataframe.o.R
15ds.dim.RdsBaseClientNReplace with dsBetaTestClient ds.dim.o.R
16ds.exists.RdsBaseClientYKeep as is
17ds.exp.RdsBaseClientYKeep as is
18ds.isNA.RdsBaseClientYKeep as is
19ds.isValid.RdsBaseClientYKeep as is
20ds.length.RdsBaseClientNReplace with dsBetaTestClient ds.length.o.R
21ds.levels.RdsBaseClientYKeep as is
22ds.list.RdsBaseClientYKeep as is
23ds.log.RdsBaseClientYKeep as is
24ds.ls.RdsBaseClientYKeep as is
25ds.mean.RdsBaseClientNReplace with dsBetaTestClient ds.mean.o.R
26ds.meanByClass.RdsBaseClientYKeep as is
27ds.names.RdsBaseClientYKeep as is
28ds.numNA.RdsBaseClientYKeep as is
29ds.quantileMean.RdsBaseClientYKeep as is
30ds.recodeLevels.RdsBaseClientYKeep as is
31ds.replaceNA.RdsBaseClientYKeep as is
32ds.rowColCalc.RdsBaseClientYKeep as is
33ds.subset.RdsBaseClientYKeep as is
34ds.subsetByClass.RdsBaseClientYKeep as is
35ds.summary.RdsBaseClientYKeep as is
36ds.table1D.RdsBaseClientYKeep as is
37ds.table2D.RdsBaseClientNReplace with dsBetaTestClient ds.table.2D.o.R
38ds.vectorCalc.RdsBaseClientYKeep as is
39extract.RdsBaseClientYKeep as is
40findLoginObjects.RdsBaseClientYKeep as is
41getOpals.RdsBaseClientYKeep as is
42getPooledMean.RdsBaseClientYKeep as isdsBaseClient & dsBetaTestClient have the same source code. dsStatsClient does not use completeLength variable and instead just takes the length.total and sum.weighted variables to return mean.global.
43getPooledVar.RdsBaseClientYKeep as isdsBaseClient & dsBetaTestClient have the same source code. dsStatsClient does not use completeLength variable and instead just takes the length.total and sum.weighted variables to return var.global.
44isAssigned.RdsBaseClientYKeep as is
45isDefined.RdsBaseClientYKeep as is
46logical2int.RdsBaseClientYKeep as is
47meanByClassHelper0a.RdsBaseClientYKeep as is
48meanByClassHelper0b.RdsBaseClientYKeep as is
49meanByClassHelper1.RdsBaseClientYKeep as is
50meanByClassHelper2.RdsBaseClientYKeep as is
51meanByClassHelper3.RdsBaseClientYKeep as is
52meanByClassHelper4.RdsBaseClientYKeep as is
53rowPercent.RdsBaseClientNReplace with dsBetaTestClient rowPercent.R
54subsetHelper.RdsBaseClientYKeep as is
55checkClass.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
56colPercent.RdsBetaTestClientYMove to dsBaseClientDifference in details required by the client function
57ds.Boole.o.RdsBetaTestClientYMove to dsBaseClient
58ds.asCharacter.o.RdsBetaTestClientYMove to dsBaseClient
59ds.asDataMatrix.o.RdsBetaTestClientYMove to dsBaseClient
60ds.asFactor.o.RdsBetaTestClientYMove to dsBaseClient
61ds.asInteger.o.RdsBetaTestClientYMove to dsBaseClient
62ds.asList.o.RdsBetaTestClientYMove to dsBaseClient
63ds.asLogical.o.RdsBetaTestClientYMove to dsBaseClient
64ds.asMatrix.o.RdsBetaTestClientYMove to dsBaseClient
65ds.asNumeric.o.RdsBetaTestClientYMove to dsBaseClient
66ds.cbind.o.RdsBetaTestClientYMove to dsBaseClient
67ds.cor.o.RdsBetaTestClientYMove to dsBaseClient
68ds.cov.o.RdsBetaTestClientYMove to dsBaseClient
69ds.dataFrame.o.RdsBetaTestClientYMove to dsBaseClientRenamed to "ds.dataframe.R"
70ds.dataFrameSort.o.RdsBetaTestClientYMove to dsBaseClientRenamed to "ds.dataframeSort.R" ?
71ds.dataFrameSubset.o.RdsBetaTestClientYMove to dsBaseClientRenamed to "ds.dataframeSubset.R" ?
72ds.dim.o.RdsBetaTestClientYMove to dsBaseClient
73ds.glm.o.RdsBetaTestClientYMove to dsBaseClient
74ds.glmSLMA.o.RdsBetaTestClientYMove to dsBaseClient
75ds.histogram.o.RdsBetaTestClientYMove to dsBaseClient
76ds.length.o.RdsBetaTestClientYMove to dsBaseClient
77ds.lexis.o.RdsBetaTestClientYMove to dsBaseClient
78ds.listClientsideFunctions.o.RdsBetaTestClientYMove to dsBaseClient
79ds.listDisclosureSettings.o.RdsBetaTestClientYMove to dsBaseClient
80ds.listOpals.o.RdsBetaTestClientYMove to dsBaseClient
81ds.listServersideFunctions.o.RdsBetaTestClientYMove to dsBaseClient
82ds.look.o.RdsBetaTestClientYMove to dsBaseClient
83ds.make.o.RdsBetaTestClientYMove to dsBaseClient
84ds.matrix.RdsBetaTestClientYMove to dsBaseClient
85ds.matrixDet.RdsBetaTestClientYMove to dsBaseClient
86dsmatrixDet.report.RdsBetaTestClientYMove to dsBaseClient
87ds.matrixDiag.RdsBetaTestClientYMove to dsBaseClient
88ds.matrixDimnames.RdsBetaTestClientYMove to dsBaseClient
89ds.matrixInvert.RdsBetaTestClientYMove to dsBaseClient
90ds.matrixMult.RdsBetaTestClientYMove to dsBaseClient
91ds.matrixTranspose.RdsBetaTestClientYMove to dsBaseClient
92ds.mean.o.RdsBetaTestClientYMove to dsBaseClient
93ds.meanSdGp.RdsBetaTestClientYMove to dsBaseClient
94ds.merge.o.RdsBetaTestClientYMove to dsBaseClient
95ds.message.o.RdsBetaTestClientYMove to dsBaseClient
96ds.rBinom.o.RdsBetaTestClientYMove to dsBaseClient
97ds.rNorm.o.RdsBetaTestClientYMove to dsBaseClient
98ds.rPois.o.RdsBetaTestClientYMove to dsBaseClient
99ds.rUnif.o.RdsBetaTestClientYMove to dsBaseClient
100ds.rbind.o.RdsBetaTestClientYMove to dsBaseClient
101ds.reShape.o.RdsBetaTestClientYMove to dsBaseClient
102ds.recodeValues.o.RdsBetaTestClientYMove to dsBaseClient
103ds.rilm.b.RdsBetaTestClientNNot ready for this release
104ds.rm.o.RdsBetaTestClientYMove to dsBaseClient
105ds.scatterPlot.o.RdsBetaTestClientYMove to dsBaseClient
106ds.seq.o.RdsBetaTestClientYMove to dsBaseClient
107ds.setDefaultOpals.o.RdsBetaTestClientYMove to dsBaseClient
108ds.setSeed.o.RdsBetaTestClientYMove to dsBaseClient
109ds.tTestF.RdsBetaTestClientNNot ready for this release
110ds.table2D.o.RdsBetaTestClientYMove to dsBaseClient
111ds.tapply.assign.o.RdsBetaTestClientYMove to dsBaseClient
112ds.tapply.o.RdsBetaTestClientYMove to dsBaseClient
113ds.testObjExists.o.RdsBetaTestClientYMove to dsBaseClient
114ds.unList.o.RdsBetaTestClientYMove to dsBaseClient
115ds.var.o.RdsBetaTestClientYMove to dsBaseClient
116extract.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
117findLoginObjects.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
118getOpals.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
119getPooledMean.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
120getPooledVar.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
121glmChecks.RdsBetaTestClientYMove to dsBaseClientIdentical to dsBaseClient version
122isAssigned.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
123isDefined.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
124logical2int.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
125rowPercent.RdsBetaTestClientYMove to dsBaseClientDifference in documentation and author
126subsetHelper.RdsBetaTestClientNDeleteIdentical to dsBaseClient version
127tTestHelper1.RdsBetaTestClientNNot ready for this release
128tTestHelper2.RdsBetaTestClientNNot ready for this release
129checkClass.RdsStatsClientNDeleteIdentical to dsBaseClient version
130ds.cor.RdsStatsClientNReplace with dsBetaTestClient ds.cor.o.R
131ds.corTest.RdsStatsClientYMove to dsBaseClient
132ds.cov.RdsStatsClientNReplace wtih dsBetaTestClient ds.cov.o.R
133ds.tTest.RdsStatsClientYMove to dsBaseClient
134ds.var.RdsStatsClientNReplace with dsBetaTestClient ds.var.o.R
135extract.RdsStatsClientNDeleteIdentical to dsBaseClient version
136findLoginObjects.RdsStatsClientNDeleteIdentical to dsBaseClient version
137getOpals.RdsStatsClientNDeleteThe function has been extended to support the global environment used by datashield calls and the test environment used by test_that. It has been refactored with some helper function for clarity.
138getPooledMean.RdsStatsClientNDeleteNot called anywhere, looks like old buggy version.
139getPooledVar.RdsStatsClientNDeleteNot called anywhere, looks like old buggy version.
140isAssigned.RdsStatsClientNDeleteIdentical to dsBaseClient version
141isDefined.RdsStatsClientNDeleteIdentical to dsBaseClient version
142logical2int.RdsStatsClientNDeleteIdentical to dsBaseClient version
143tTestHelper1.RdsStatsClientNNot ready for this releaseCall to server changed, differences in: length.local, mean.local, var.local, null.y, length.local.y, pval, cint, results (from BetaTestClient)
144tTestHelper2.RdsStatsClientNNot ready for this releaseDifferences in levels_all, formula, study.summary, pval.vect.final, ci.mult (compared to dsBetaTestClient)
145checkClass.RdsModellingClientNDeleteIdentical to dsBaseClient version
146ds.gee.RdsModellingClientYMove to dsBaseClient
147ds.glm.RdsModellingClientNReplace with dsBetaTestClient ds.glm.o.R
148ds.lexis.RdsModellingClientNDelete
149extract.RdsModellingClientNDeleteIdentical to dsBaseClient version
150findLoginObjects.RdsModellingClientNDeleteIdentical to dsBaseClient version
151geeChecks.RdsModellingClientYMove to dsBaseClient
152geehelper1.RdsModellingClientYMove to dsBaseClient
153geehelper2.RdsModellingClientYMove to dsBaseClient
154getOpals.RdsModellingClientNDeleteThe function has been extended to support the global environment used by datashield calls and the test environment used by test_that. It has been refactored with some helper function for clarity.
155glmChecks.RdsModellingClientNDeleteIdentical to dsBetaTestClient version
156isAssigned.RdsModellingClientNDeleteIdentical to dsBaseClient version
157isDefined.RdsModellingClientNDeleteIdentical to dsBaseClient version
158lexisHelper1.RdsModellingClientNDelete
159logical2int.RdsModellingClientNDeleteIdentical to dsBaseClient version
160checkClass.RdsGraphicsClientNDeleteIdentical to dsBaseClient version
161ds.contourPlot.RdsGraphicsClientYMove to dsBaseClient
162ds.densityGrid.RdsGraphicsClientYMove to dsBaseClient
163ds.heatmapPlot.RdsGraphicsClientYMove to dsBaseClient
164ds.histogram.RdsGraphicsClientN

Replace with dsBetaTestClient ds.histogram.o.R


165extract.RdsGraphicsClientNDeleteIdentical to dsBaseClient version
166findLoginObjects.RdsGraphicsClientNDeleteIdentical to dsBaseClient version
167getOpals.RdsGraphicsClientNDeleteThe function has been extended to support the global environment used by datashield calls and the test environment used by test_that. It has been refactored with some helper function for clarity.
168isAssigned.RdsGraphicsClientNDeleteIdentical to dsBaseClient version
169isDefined.RdsGraphicsClientNDeleteIdentical to dsBaseClient version