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 Name	Package	In v5	Release Plan	Notes
1	asFactorDS.R	dsBase	N	Delete
2	asListDS.R	dsBase	N	Replace with dsBetaTest asListDS.o.R
3	asMatrixDS.R	dsBase	N	Replace with dsBetaTest asMatrixDS.o.R
4	cDS.R	dsBase	Y	Keep as is
5	changeRefGroupDS.R	dsBase	Y	Keep as is
6	dataframeDS.R	dsBase	N	Replace with dsBetaTest dataframeDS.o.R
7	extract.R	dsBase	Y	Keep as is
8	isNaDS.R	dsBase	Y	Keep as is
9	isValidDS.R	dsBase	Y	Keep as is
10	listDS.R	dsBase	Y	Keep as is
11	meanDS.R	dsBase	N	Replace with dsBetaTest meanDS.o.R
12	namesDS.R	dsBase	Y	Keep as is
13	numNaDS.R	dsBase	Y	Keep as is
14	quantileMeanDS.R	dsBase	Y	Keep as is
15	recodeLevelsDS.R	dsBase	Y	Keep as is
16	replaceNaDS.R	dsBase	Y	Keep as is
17	rowColCalcDS.R	dsBase	Y	Keep as is
18	setFilterDS.R	dsBase
19	subsetByClassDS.R	dsBase	Y	Keep as is
20	subsetByClassHelper1.R	dsBase	Y	Keep as is
21	subsetByClassHelper2.R	dsBase	Y	Keep as is
22	subsetByClassHelper3.R	dsBase	Y	Keep as is
23	subsetDS.R	dsBase	Y	Keep as is
24	table1dDS.R	dsBase	Y	Keep as is
25	table2dDS.R	dsBase	N	Replace with dsBetaTest table2dDS.o.R
26	varDS.R	dsBase	N	Replace with dsBetaTest varDS.o.R
27	BooleDS.o.R	dsBetaTest	Y	Move to dsBase
28	asCharacterDS.o.R	dsBetaTest	Y	Move to dsBase
29	asDataMatrix.o.R	dsBetaTest	Y	Move to dsBase
30	asFactorDS1.o.R	dsBetaTest	Y	Move to dsBase
31	asFactorDS2.o.R	dsBetaTest	Y	Move to dsBase
32	asIntegerDS.o.R	dsBetaTest	Y	Move to dsBase
33	asListDS.o.R	dsBetaTest	Y	Move to dsBase
34	asLogicalDS.o.R	dsBetaTest	Y	Move to dsBase
35	asMatrixDS.o.R	dsBetaTest	Y	Move to dsBase
36	asNumericDS.o.R	dsBetaTest	Y	Move to dsBase
37	cbindDS.o.R	dsBetaTest	Y	Move to dsBase
38	covDS.o.R	dsBetaTest	Y	Move to dsBase
39	dataFrameDS.o.R	dsBetaTest	Y	Move to dsBase
40	dataFrameSortDS.o.R	dsBetaTest	Y	Move to dsBase
41	dataFrameSubsetDS1.o.R	dsBetaTest	Y	Move to dsBase
42	dataFrameSubsetDS2.o.R	dsBetaTest	Y	Move to dsBase
43	dimDS.o.R	dsBetaTest	Y	Move to dsBase
44	glmDS1.o.R	dsBetaTest	Y	Move to dsBase
45	glmDS2.o.R	dsBetaTest	Y	Move to dsBase
46	glmSLMADS2.o.R	dsBetaTest	Y	Move to dsBase
47	histogramDS.o.R	dsBetaTest	Y	Move to dsBase
48	lengthDS.o.R	dsBetaTest	Y	Move to dsBase
49	lexisDS1.o.R	dsBetaTest	Y	Move to dsBase
50	lexisDS2.o.R	dsBetaTest	Y	Move to dsBase
51	lexisDS3.o.R	dsBetaTest	Y	Move to dsBase
52	listDisclosureSettingsDS.o.R	dsBetaTest	Y	Move to dsBase
53	matrixDS.R	dsBetaTest	Y	Move to dsBase
54	matrixDetDS1.R	dsBetaTest	Y	Move to dsBase
55	matrixDetDS2.R	dsBetaTest	Y	Move to dsBase
56	matrixDiagDS.R	dsBetaTest	Y	Move to dsBase
57	matrixDimnamesDS.R	dsBetaTest	Y	Move to dsBase
58	matrixInvertDS.R	dsBetaTest	Y	Move to dsBase
59	matrixMultDS.R	dsBetaTest	Y	Move to dsBase
60	matrixTransposeDS.R	dsBetaTest	Y	Move to dsBase
61	meanDS.o.R	dsBetaTest	Y	Move to dsBase
62	meanSdGpDS.R	dsBetaTest	Y	Move to dsBase
63	mergeDS.o.R	dsBetaTest	Y	Move to dsBase
64	messageDS.o.R	dsBetaTest	Y	Move to dsBase
65	rBinomDS.o.R	dsBetaTest	Y	Move to dsBase
66	rNormDS.o.R	dsBetaTest	Y	Move to dsBase
67	rPoisDS.o.R	dsBetaTest	Y	Move to dsBase
68	rUnifDS.o.R	dsBetaTest	Y	Move to dsBase
69	rbindDS.o.R	dsBetaTest	Y	Move to dsBase
70	reShapeDS.o.R	dsBetaTest	Y	Move to dsBase
71	recodeValuesDS1.o.R	dsBetaTest	Y	Move to dsBase
72	recodeValuesDS2.o.R	dsBetaTest	Y	Move to dsBase
73	rilmDS.b.R	dsBetaTest	N	Not ready for this release
74	rmDS.o.R	dsBetaTest	Y	Move to dsBase
75	scatterPlotDS.o.R	dsBetaTest	Y	Move to dsBase
76	seqDS.o.R	dsBetaTest	Y	Move to dsBase
77	setSeedDS.o.R	dsBetaTest	Y	Move to dsBase
78	tTestFDS2.R	dsBetaTest	N	Not ready for this release
79	table2dDS.o.R	dsBetaTest	Y	Move to dsBase
80	tapplyDS.assign.o.R	dsBetaTest	Y	Move to dsBase
81	tapplyDS.o.R	dsBetaTest	Y	Move to dsBase
82	testObjExistsDS.o.R	dsBetaTest	Y	Move to dsBase
83	unListDS.o.R	dsBetaTest	Y	Move to dsBase
84	varDS.o.R	dsBetaTest	Y	Move to dsBase
85	corDS.R	dsStats	Y	Move to dsBase
86	covDS.R	dsStats	N	Replace with dsBetaTest covDS.o.R
87	extract.R	dsStats	N	Delete	Identical to dsBase version
88	isValidDS.R	dsStats	N	Delete	Identical to dsBase version
89	setFilterDS.R	dsStats			setFilter in dsBase may not always guarantee a numeric value whereas in dsStats and dsGraphics it returns a numeric value.
90	varDS.R	dsStats	N	Delete	Identical to dsBase version
91	alphaPhiDS.R	dsModelling	Y	Move to dsBase
92	checkNegValuesDS.R	dsModelling	Y	Move to dsBase
93	glmDS1.R	dsModelling	N	Replace with dsBetaTest glmDS1.o.R
94	glmDS2.R	dsModelling	N	Replace with dsBetaTest glmDS2.o.r
95	lexisDS.R	dsModelling	N	Delete
96	lexishelper1.R	dsModelling	N	Delete
97	lexishelper2.R	dsModelling	N	Delete
98	scoreVectDS.R	dsModelling	Y	Move to dsBase
99	densityGridDS.R	dsGraphics	Y	Move to dsBase
100	extract.R	dsGraphics	N	Delete	Identical to dsBase version
101	histogramDS.R	dsGraphics	N	Replace with dsBetaTest histogramDS.o.R
102	rangeDS.R	dsGraphics	Y	Move to dsBase
103	setFilterDS.R	dsGraphics			setFilter in dsBase may not always guarantee a numeric value whereas in dsStats and dsGraphics it returns a numeric value.

Client side functions

	Function Name	Package	In v5	Release Plan	Notes
1	checkClass.R	dsBaseClient	Y	Keep as is
2	colPercent.R	dsBaseClient	N	Replace with dsBetaTestClient colPercent.R
3	ds.asCharacter.R	dsBaseClient	N	Replace with dsBetaTestClient ds.asCharacter.o.R
4	ds.asFactor.R	dsBaseClient	N	Replace with dsBetaTestClient ds.asFactor.o.R
5	ds.asList.R	dsBaseClient	N	Replace with dsBetaTestClient ds.asList.o.R
6	ds.asMatrix.R	dsBaseClient	N	Replace with dsBetaTestClient ds.asMatrix.o.R
7	ds.asNumeric.R	dsBaseClient	N	Replace with dsBetaTestClient ds.asNumeric.o.R
8	ds.assign.R	dsBaseClient	Y	Keep as is
9	ds.c.R	dsBaseClient	Y	Keep as is
10	ds.cbind.R	dsBaseClient	N	Replace with dsBetaTestClient ds.cbind.o.R
11	ds.changeRefGroup.R	dsBaseClient	Y	Keep as is
12	ds.class.R	dsBaseClient	Y	Keep as is
13	ds.colnames.R	dsBaseClient	Y	Keep as is
14	ds.dataframe.R	dsBaseClient	N	Replace with dsBetaTestClient ds.dataframe.o.R
15	ds.dim.R	dsBaseClient	N	Replace with dsBetaTestClient ds.dim.o.R
16	ds.exists.R	dsBaseClient	Y	Keep as is
17	ds.exp.R	dsBaseClient	Y	Keep as is
18	ds.isNA.R	dsBaseClient	Y	Keep as is
19	ds.isValid.R	dsBaseClient	Y	Keep as is
20	ds.length.R	dsBaseClient	N	Replace with dsBetaTestClient ds.length.o.R
21	ds.levels.R	dsBaseClient	Y	Keep as is
22	ds.list.R	dsBaseClient	Y	Keep as is
23	ds.log.R	dsBaseClient	Y	Keep as is
24	ds.ls.R	dsBaseClient	Y	Keep as is
25	ds.mean.R	dsBaseClient	N	Replace with dsBetaTestClient ds.mean.o.R
26	ds.meanByClass.R	dsBaseClient	Y	Keep as is
27	ds.names.R	dsBaseClient	Y	Keep as is
28	ds.numNA.R	dsBaseClient	Y	Keep as is
29	ds.quantileMean.R	dsBaseClient	Y	Keep as is
30	ds.recodeLevels.R	dsBaseClient	Y	Keep as is
31	ds.replaceNA.R	dsBaseClient	Y	Keep as is
32	ds.rowColCalc.R	dsBaseClient	Y	Keep as is
33	ds.subset.R	dsBaseClient	Y	Keep as is
34	ds.subsetByClass.R	dsBaseClient	Y	Keep as is
35	ds.summary.R	dsBaseClient	Y	Keep as is
36	ds.table1D.R	dsBaseClient	Y	Keep as is
37	ds.table2D.R	dsBaseClient	N	Replace with dsBetaTestClient ds.table.2D.o.R
38	ds.vectorCalc.R	dsBaseClient	Y	Keep as is
39	extract.R	dsBaseClient	Y	Keep as is
40	findLoginObjects.R	dsBaseClient	Y	Keep as is
41	getOpals.R	dsBaseClient	Y	Keep as is
42	getPooledMean.R	dsBaseClient	Y	Keep as is	dsBaseClient & 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.
43	getPooledVar.R	dsBaseClient	Y	Keep as is	dsBaseClient & 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.
44	isAssigned.R	dsBaseClient	Y	Keep as is
45	isDefined.R	dsBaseClient	Y	Keep as is
46	logical2int.R	dsBaseClient	Y	Keep as is
47	meanByClassHelper0a.R	dsBaseClient	Y	Keep as is
48	meanByClassHelper0b.R	dsBaseClient	Y	Keep as is
49	meanByClassHelper1.R	dsBaseClient	Y	Keep as is
50	meanByClassHelper2.R	dsBaseClient	Y	Keep as is
51	meanByClassHelper3.R	dsBaseClient	Y	Keep as is
52	meanByClassHelper4.R	dsBaseClient	Y	Keep as is
53	rowPercent.R	dsBaseClient	N	Replace with dsBetaTestClient rowPercent.R
54	subsetHelper.R	dsBaseClient	Y	Keep as is
55	checkClass.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
56	colPercent.R	dsBetaTestClient	Y	Move to dsBaseClient	Difference in details required by the client function
57	ds.Boole.o.R	dsBetaTestClient	Y	Move to dsBaseClient
58	ds.asCharacter.o.R	dsBetaTestClient	Y	Move to dsBaseClient
59	ds.asDataMatrix.o.R	dsBetaTestClient	Y	Move to dsBaseClient
60	ds.asFactor.o.R	dsBetaTestClient	Y	Move to dsBaseClient
61	ds.asInteger.o.R	dsBetaTestClient	Y	Move to dsBaseClient
62	ds.asList.o.R	dsBetaTestClient	Y	Move to dsBaseClient
63	ds.asLogical.o.R	dsBetaTestClient	Y	Move to dsBaseClient
64	ds.asMatrix.o.R	dsBetaTestClient	Y	Move to dsBaseClient
65	ds.asNumeric.o.R	dsBetaTestClient	Y	Move to dsBaseClient
66	ds.cbind.o.R	dsBetaTestClient	Y	Move to dsBaseClient
67	ds.cor.o.R	dsBetaTestClient	Y	Move to dsBaseClient
68	ds.cov.o.R	dsBetaTestClient	Y	Move to dsBaseClient
69	ds.dataFrame.o.R	dsBetaTestClient	Y	Move to dsBaseClient	Renamed to "ds.dataframe.R"
70	ds.dataFrameSort.o.R	dsBetaTestClient	Y	Move to dsBaseClient	Renamed to "ds.dataframeSort.R" ?
71	ds.dataFrameSubset.o.R	dsBetaTestClient	Y	Move to dsBaseClient	Renamed to "ds.dataframeSubset.R" ?
72	ds.dim.o.R	dsBetaTestClient	Y	Move to dsBaseClient
73	ds.glm.o.R	dsBetaTestClient	Y	Move to dsBaseClient
74	ds.glmSLMA.o.R	dsBetaTestClient	Y	Move to dsBaseClient
75	ds.histogram.o.R	dsBetaTestClient	Y	Move to dsBaseClient
76	ds.length.o.R	dsBetaTestClient	Y	Move to dsBaseClient
77	ds.lexis.o.R	dsBetaTestClient	Y	Move to dsBaseClient
78	ds.listClientsideFunctions.o.R	dsBetaTestClient	Y	Move to dsBaseClient
79	ds.listDisclosureSettings.o.R	dsBetaTestClient	Y	Move to dsBaseClient
80	ds.listOpals.o.R	dsBetaTestClient	Y	Move to dsBaseClient
81	ds.listServersideFunctions.o.R	dsBetaTestClient	Y	Move to dsBaseClient
82	ds.look.o.R	dsBetaTestClient	Y	Move to dsBaseClient
83	ds.make.o.R	dsBetaTestClient	Y	Move to dsBaseClient
84	ds.matrix.R	dsBetaTestClient	Y	Move to dsBaseClient
85	ds.matrixDet.R	dsBetaTestClient	Y	Move to dsBaseClient
86	dsmatrixDet.report.R	dsBetaTestClient	Y	Move to dsBaseClient
87	ds.matrixDiag.R	dsBetaTestClient	Y	Move to dsBaseClient
88	ds.matrixDimnames.R	dsBetaTestClient	Y	Move to dsBaseClient
89	ds.matrixInvert.R	dsBetaTestClient	Y	Move to dsBaseClient
90	ds.matrixMult.R	dsBetaTestClient	Y	Move to dsBaseClient
91	ds.matrixTranspose.R	dsBetaTestClient	Y	Move to dsBaseClient
92	ds.mean.o.R	dsBetaTestClient	Y	Move to dsBaseClient
93	ds.meanSdGp.R	dsBetaTestClient	Y	Move to dsBaseClient
94	ds.merge.o.R	dsBetaTestClient	Y	Move to dsBaseClient
95	ds.message.o.R	dsBetaTestClient	Y	Move to dsBaseClient
96	ds.rBinom.o.R	dsBetaTestClient	Y	Move to dsBaseClient
97	ds.rNorm.o.R	dsBetaTestClient	Y	Move to dsBaseClient
98	ds.rPois.o.R	dsBetaTestClient	Y	Move to dsBaseClient
99	ds.rUnif.o.R	dsBetaTestClient	Y	Move to dsBaseClient
100	ds.rbind.o.R	dsBetaTestClient	Y	Move to dsBaseClient
101	ds.reShape.o.R	dsBetaTestClient	Y	Move to dsBaseClient
102	ds.recodeValues.o.R	dsBetaTestClient	Y	Move to dsBaseClient
103	ds.rilm.b.R	dsBetaTestClient	N	Not ready for this release
104	ds.rm.o.R	dsBetaTestClient	Y	Move to dsBaseClient
105	ds.scatterPlot.o.R	dsBetaTestClient	Y	Move to dsBaseClient
106	ds.seq.o.R	dsBetaTestClient	Y	Move to dsBaseClient
107	ds.setDefaultOpals.o.R	dsBetaTestClient	Y	Move to dsBaseClient
108	ds.setSeed.o.R	dsBetaTestClient	Y	Move to dsBaseClient
109	ds.tTestF.R	dsBetaTestClient	N	Not ready for this release
110	ds.table2D.o.R	dsBetaTestClient	Y	Move to dsBaseClient
111	ds.tapply.assign.o.R	dsBetaTestClient	Y	Move to dsBaseClient
112	ds.tapply.o.R	dsBetaTestClient	Y	Move to dsBaseClient
113	ds.testObjExists.o.R	dsBetaTestClient	Y	Move to dsBaseClient
114	ds.unList.o.R	dsBetaTestClient	Y	Move to dsBaseClient
115	ds.var.o.R	dsBetaTestClient	Y	Move to dsBaseClient
116	extract.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
117	findLoginObjects.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
118	getOpals.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
119	getPooledMean.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
120	getPooledVar.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
121	glmChecks.R	dsBetaTestClient	Y	Move to dsBaseClient	Identical to dsBaseClient version
122	isAssigned.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
123	isDefined.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
124	logical2int.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
125	rowPercent.R	dsBetaTestClient	Y	Move to dsBaseClient	Difference in documentation and author
126	subsetHelper.R	dsBetaTestClient	N	Delete	Identical to dsBaseClient version
127	tTestHelper1.R	dsBetaTestClient	N	Not ready for this release
128	tTestHelper2.R	dsBetaTestClient	N	Not ready for this release
129	checkClass.R	dsStatsClient	N	Delete	Identical to dsBaseClient version
130	ds.cor.R	dsStatsClient	N	Replace with dsBetaTestClient ds.cor.o.R
131	ds.corTest.R	dsStatsClient	Y	Move to dsBaseClient
132	ds.cov.R	dsStatsClient	N	Replace wtih dsBetaTestClient ds.cov.o.R
133	ds.tTest.R	dsStatsClient	Y	Move to dsBaseClient
134	ds.var.R	dsStatsClient	N	Replace with dsBetaTestClient ds.var.o.R
135	extract.R	dsStatsClient	N	Delete	Identical to dsBaseClient version
136	findLoginObjects.R	dsStatsClient	N	Delete	Identical to dsBaseClient version
137	getOpals.R	dsStatsClient	N	Delete	The 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.
138	getPooledMean.R	dsStatsClient	N	Delete	Not called anywhere, looks like old buggy version.
139	getPooledVar.R	dsStatsClient	N	Delete	Not called anywhere, looks like old buggy version.
140	isAssigned.R	dsStatsClient	N	Delete	Identical to dsBaseClient version
141	isDefined.R	dsStatsClient	N	Delete	Identical to dsBaseClient version
142	logical2int.R	dsStatsClient	N	Delete	Identical to dsBaseClient version
143	tTestHelper1.R	dsStatsClient	N	Not ready for this release	Call to server changed, differences in: length.local, mean.local, var.local, null.y, length.local.y, pval, cint, results (from BetaTestClient)
144	tTestHelper2.R	dsStatsClient	N	Not ready for this release	Differences in levels_all, formula, study.summary, pval.vect.final, ci.mult (compared to dsBetaTestClient)
145	checkClass.R	dsModellingClient	N	Delete	Identical to dsBaseClient version
146	ds.gee.R	dsModellingClient	Y	Move to dsBaseClient
147	ds.glm.R	dsModellingClient	N	Replace with dsBetaTestClient ds.glm.o.R
148	ds.lexis.R	dsModellingClient	N	Delete
149	extract.R	dsModellingClient	N	Delete	Identical to dsBaseClient version
150	findLoginObjects.R	dsModellingClient	N	Delete	Identical to dsBaseClient version
151	geeChecks.R	dsModellingClient	Y	Move to dsBaseClient
152	geehelper1.R	dsModellingClient	Y	Move to dsBaseClient
153	geehelper2.R	dsModellingClient	Y	Move to dsBaseClient
154	getOpals.R	dsModellingClient	N	Delete	The 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.
155	glmChecks.R	dsModellingClient	N	Delete	Identical to dsBetaTestClient version
156	isAssigned.R	dsModellingClient	N	Delete	Identical to dsBaseClient version
157	isDefined.R	dsModellingClient	N	Delete	Identical to dsBaseClient version
158	lexisHelper1.R	dsModellingClient	N	Delete
159	logical2int.R	dsModellingClient	N	Delete	Identical to dsBaseClient version
160	checkClass.R	dsGraphicsClient	N	Delete	Identical to dsBaseClient version
161	ds.contourPlot.R	dsGraphicsClient	Y	Move to dsBaseClient
162	ds.densityGrid.R	dsGraphicsClient	Y	Move to dsBaseClient
163	ds.heatmapPlot.R	dsGraphicsClient	Y	Move to dsBaseClient
164	ds.histogram.R	dsGraphicsClient	N	Replace with dsBetaTestClient ds.histogram.o.R
165	extract.R	dsGraphicsClient	N	Delete	Identical to dsBaseClient version
166	findLoginObjects.R	dsGraphicsClient	N	Delete	Identical to dsBaseClient version
167	getOpals.R	dsGraphicsClient	N	Delete	The 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.
168	isAssigned.R	dsGraphicsClient	N	Delete	Identical to dsBaseClient version
169	isDefined.R	dsGraphicsClient	N	Delete	Identical to dsBaseClient version

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