Refactor and rename file and methods

NAMESPACE

@@ -1,18 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
-export(BooleDS)
 export(absDS)
 export(asCharacterDS)
 export(asDataMatrixDS)
-export(asFactorDS1)
-export(asFactorDS2)
+export(asFactor1DS)
+export(asFactor2DS)
 export(asFactorSimpleDS)
 export(asIntegerDS)
 export(asListDS)
 export(asLogicalDS)
 export(asMatrixDS)
 export(asNumericDS)
 export(aucDS)
+export(booleDS)
 export(boxPlotGGDS)
 export(boxPlotGG_data_TreatmentDS)
 export(boxPlotGG_data_Treatment_numericDS)
@@ -30,8 +30,8 @@ export(corTestDS)
 export(covDS)
 export(dataFrameDS)
 export(dataFrameSortDS)
-export(dataFrameSubsetDS1)
-export(dataFrameSubsetDS2)
+export(dataFrameSubset1DS)
+export(dataFrameSubset2DS)
 export(densityGridDS)
 export(dimDS)
 export(dmtC2SDS)
@@ -44,41 +44,41 @@ export(gamlssDS)
 export(getAllLevelsDS)
 export(getClassAllColsDS)
 export(getWGSRDS)
-export(glmDS1)
-export(glmDS2)
+export(glm1DS)
+export(glm2DS)
 export(glmPredictDS.ag)
 export(glmPredictDS.as)
+export(glmSLMA1DS)
+export(glmSLMA2DS)
 export(glmSLMADS.assign)
-export(glmSLMADS1)
-export(glmSLMADS2)
 export(glmSummaryDS.ag)
 export(glmSummaryDS.as)
+export(glmerSLMA2DS)
 export(glmerSLMADS.assign)
-export(glmerSLMADS2)
 export(heatmapPlotDS)
 export(hetcorDS)
-export(histogramDS1)
-export(histogramDS2)
+export(histogram1DS)
+export(histogram2DS)
 export(igb_standardsDS)
 export(isNaDS)
 export(isValidDS)
-export(kurtosisDS1)
-export(kurtosisDS2)
+export(kurtosis1DS)
+export(kurtosis2DS)
 export(lengthDS)
 export(levelsDS)
-export(lexisDS1)
-export(lexisDS2)
-export(lexisDS3)
+export(lexis1DS)
+export(lexis2DS)
+export(lexis3DS)
 export(listDS)
 export(listDisclosureSettingsDS)
+export(lmerSLMA2DS)
 export(lmerSLMADS.assign)
-export(lmerSLMADS2)
 export(logDS)
 export(lsDS)
 export(lsplineDS)
 export(matrixDS)
-export(matrixDetDS1)
-export(matrixDetDS2)
+export(matrixDet1DS)
+export(matrixDet2DS)
 export(matrixDiagDS)
 export(matrixDimnamesDS)
 export(matrixInvertDS)
@@ -111,13 +111,13 @@ export(sampleDS)
 export(scatterPlotDS)
 export(seqDS)
 export(setSeedDS)
-export(skewnessDS1)
-export(skewnessDS2)
+export(skewness1DS)
+export(skewness2DS)
 export(sqrtDS)
 export(table1DDS)
+export(table2DS)
 export(tableDS)
 export(tableDS.assign)
-export(tableDS2)
 export(tapplyDS)
 export(tapplyDS.assign)
 export(unListDS)

R/asFactorDS1.R → R/asFactor1DS.R

@@ -10,7 +10,7 @@
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
-asFactorDS1 <- function(input.var.name=NULL){
+asFactor1DS <- function(input.var.name=NULL){
   ##################################################################
   #MODULE 1: CAPTURE THE nfilter SETTINGS                          #
   thr<-dsBase::listDisclosureSettingsDS()                          #
@@ -49,5 +49,5 @@ asFactorDS1 <- function(input.var.name=NULL){
 
 }
 #AGGREGATE FUNCTION
-# asFactorDS1
+# asFactor1DS
 

R/asFactorDS2.R → R/asFactor2DS.R

@@ -18,7 +18,7 @@
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
-asFactorDS2 <- function(input.var.name=NULL, all.unique.levels.transmit=NULL, fixed.dummy.vars=NULL, baseline.level=NULL){
+asFactor2DS <- function(input.var.name=NULL, all.unique.levels.transmit=NULL, fixed.dummy.vars=NULL, baseline.level=NULL){
 
   input.var <- .loadServersideObject(input.var.name)
 
@@ -48,4 +48,4 @@ asFactorDS2 <- function(input.var.name=NULL, all.unique.levels.transmit=NULL, fi
 
 }
 #ASSIGN FUNCTION
-# asFactorDS2
+# asFactor2DS

R/BooleDS.R → R/booleDS.R

@@ -1,5 +1,5 @@
 #' 
-#' @title BooleDS
+#' @title booleDS
 #' @description Converts the individual elements of a vector or other object into
 #' Boolean indicators.
 #' @details The function converts the input vector into Boolean indicators.
@@ -26,7 +26,7 @@
 #' @return the levels of the input variable.
 #' @export
 #'
-BooleDS <- function(V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL, na.assign.text, numeric.output=TRUE){
+booleDS <- function(V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL, na.assign.text, numeric.output=TRUE){
 
   # Check Permissive Privacy Control Level.
   dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot'))

R/dataFrameSubsetDS1.R → R/dataFrameSubset1DS.R

@@ -1,54 +1,54 @@
 #'
-#' @title dataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubset
+#' @title dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset
 #' @description First serverside function for subsetting a data frame by row or by column.
 #' @details A data frame is a list of variables all with the same number of rows,
 #' which is of class 'data.frame'. For all details see the help header for ds.dataFrameSubset
 #' @param df.name a character string providing the name for the data.frame
 #' to be sorted. <df.name> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @param V1.name A character string specifying the name of a subsetting vector
 #' to which a Boolean operator will be applied to define the subset to be created.
 #' <V1.name> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @param V2.name A character string specifying the name of the vector
 #' or scalar to which the values in the vector specified by the argument <V1.name>
 #' is to be compared.
 #' <V2.name> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @param Boolean.operator.n A character string specifying one of six possible Boolean operators:
 #' '==', '!=', '>', '>=', '<', '<='
 #' <Boolean.operator.n> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @param keep.cols a numeric vector specifying the numbers of the columns to be kept in the
 #' final subset when subsetting by column. For example: keep.cols=c(2:5,7,12) will keep
 #' columns 2,3,4,5,7 and 12.
 #' <keep.cols> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @param rm.cols a numeric vector specifying the numbers of the columns to be removed before
 #' creating the final subset when subsetting by column. For example: rm.cols=c(2:5,7,12)
 #' will remove columns 2,3,4,5,7 and 12.
 #' <rm.cols> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @param keep.NAs logical, if TRUE any NAs in the vector holding the final Boolean vector
 #' indicating whether a given row should be included in the subset will be converted into
 #' 1s and so they will be included in the subset. Such NAs could be caused by NAs in
 #' either <V1.name> or <V2.name>. If FALSE or NULL NAs in the final Boolean vector will
 #' be converted to 0s and the corresponding row will therefore be excluded from the subset.
 #' <keep.NAs> argument generated and passed directly to
-#' dataFrameSubsetDS1 by ds.dataFrameSubset
+#' dataFrameSubset1DS by ds.dataFrameSubset
 #' @return This first serverside function called by ds.dataFrameSubset provides
 #' first level traps for a comprehensive series of disclosure risks which can be
-#' returned directly to the clientside because dataFrameSubsetDS1 is an aggregate
+#' returned directly to the clientside because dataFrameSubset1DS is an aggregate
 #' function. The second serverside function called by ds.dataFrameSubset
-#' (dataFrameSubsetDS2) carries out most of the same disclosure tests, but it is
+#' (dataFrameSubset2DS) carries out most of the same disclosure tests, but it is
 #' an assign function because it writes the subsetted data.frame to the serverside.
 #' In consequence, it records error messages as studysideMessages which can only be
 #' retrieved using ds.message
 #' @author Paul Burton
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
-dataFrameSubsetDS1 <- function(df.name=NULL,V1.name=NULL,V2.name=NULL,Boolean.operator.n=NULL,keep.cols=NULL,rm.cols=NULL,keep.NAs=NULL){
+dataFrameSubset1DS <- function(df.name=NULL,V1.name=NULL,V2.name=NULL,Boolean.operator.n=NULL,keep.cols=NULL,rm.cols=NULL,keep.NAs=NULL){
 
   # Check Permissive Privacy Control Level.
   dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot'))
@@ -303,4 +303,4 @@ if(sum(is.na(keep.code.n))>0){
 
 }
 # AGGREGATE FUNCTION
-# dataFrameSubsetDS1
+# dataFrameSubset1DS

R/dataFrameSubsetDS2.R → R/dataFrameSubset2DS.R

@@ -1,50 +1,49 @@
-###############################################################################|###################| 80 and 100
-
-#' @title dataFrameSubsetDS2 an assign function called by ds.dataFrameSubset
+#'
+#' @title dataFrameSubset2DS an assign function called by ds.dataFrameSubset
 #' @description Second serverside function for subsetting a data frame by row or by column.
 #' @details A data frame is a list of variables all with the same number of rows,
 #' which is of class 'data.frame'. For all details see the help header for ds.dataFrameSubset
 #' @param df.name a character string providing the name for the data.frame
 #' to be sorted. <df.name> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @param V1.name A character string specifying the name of a subsetting vector
 #' to which a Boolean operator will be applied to define the subset to be created.
 #' <V1.name> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @param V2.name A character string specifying the name of the vector
 #' or scalar to which the values in the vector specified by the argument <V1.name>
 #' is to be compared.
 #' <V2.name> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @param Boolean.operator.n A character string specifying one of six possible Boolean operators:
 #' '==', '!=', '>', '>=', '<', '<='
 #' <Boolean.operator.n> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @param keep.cols a numeric vector specifying the numbers of the columns to be kept in the
 #' final subset when subsetting by column. For example: keep.cols=c(2:5,7,12) will keep
 #' columns 2,3,4,5,7 and 12.
 #' <keep.cols> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @param rm.cols a numeric vector specifying the numbers of the columns to be removed before
 #' creating the final subset when subsetting by column. For example: rm.cols=c(2:5,7,12)
 #' will remove columns 2,3,4,5,7 and 12.
 #' <rm.cols> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @param keep.NAs logical, if TRUE any NAs in the vector holding the final Boolean vector
 #' indicating whether a given row should be included in the subset will be converted into
 #' 1s and so they will be included in the subset. Such NAs could be caused by NAs in
 #' either <V1.name> or <V2.name>. If FALSE or NULL NAs in the final Boolean vector will
 #' be converted to 0s and the corresponding row will therefore be excluded from the subset.
 #' <keep.NAs> argument generated and passed directly to
-#' dataFrameSubsetDS2 by ds.dataFrameSubset
+#' dataFrameSubset2DS by ds.dataFrameSubset
 #' @return the object specified by the <newobj> argument (or default name '<df.name>_subset')
 #' initially specified in calling ds.dataFrameSubset. The output object (the required
 #' subsetted data.frame called <newobj> is written to the serverside. In addition,
 #' two validity messages are returned via ds.dataFrameSubset
 #' indicating whether <newobj> has been created in each data source and if so whether
 #' it is in a valid form. If its form is not valid in at least one study - e.g. because
 #' a disclosure trap was tripped and creation of the full output object was blocked -
-#' dataFrameSubsetDS2 (via ds.dataFrame()) also returns any studysideMessages
+#' dataFrameSubset2DS (via ds.dataFrame()) also returns any studysideMessages
 #' that can explain the error in creating
 #' the full output object. As well as appearing on the screen at run time,if you wish to
 #' see the relevant studysideMessages at a later date you can use the \code{ds.message}
@@ -57,7 +56,7 @@
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
-dataFrameSubsetDS2<-function(df.name=NULL,V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL,keep.cols=NULL, rm.cols=NULL, keep.NAs=NULL){
+dataFrameSubset2DS<-function(df.name=NULL,V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL,keep.cols=NULL, rm.cols=NULL, keep.NAs=NULL){
 
   # Check Permissive Privacy Control Level.
   dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot'))
@@ -327,4 +326,4 @@ return(df.subset)
 
 }
 #ASSIGN FUNCTION
-# dataFrameSubsetDS2
+# dataFrameSubset2DS

R/glmDS1.R → R/glm1DS.R

@@ -1,9 +1,9 @@
 #' 
-#' @title glmDS1 called by ds.glm
+#' @title glm1DS called by ds.glm
 #' @description This is the first server-side aggregate function called by ds.glm
 #' @details It is an
 #' aggregation function that sets up the model structure
-#' and creates the starting beta.vector that feeds, via ds.glm, into glmDS2 to enable
+#' and creates the starting beta.vector that feeds, via ds.glm, into glm2DS to enable
 #' iterative fitting of the generalized linear model that has been
 #' been specified. For more details please see the extensive header for ds.glm.
 #' @param formula a glm() formula consistent with R syntax eg U~x+y+Z to regress
@@ -22,7 +22,7 @@
 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
-glmDS1 <- function(formula, family, weights, offset, data){
+glm1DS <- function(formula, family, weights, offset, data){
 
 
 #############################################################
@@ -202,11 +202,11 @@ if(!is.null(offsetvar))
 	}
 }
 
-  #If y, X or w data are invalid, or the model is overparameterized, this will be detected by glmDS1
+  #If y, X or w data are invalid, or the model is overparameterized, this will be detected by glm1DS
   #and passed to ds.glm resulting in a warning and a controlled shut down of the function.
   #But in case someone modifies the client side function to circumvent the trap, so the
-  #error is only apparent once the main main iterations have started via glmDS2
-  #the equivalent tests in glmDS2 will destroy the info.matrix and score.vector in the affected study so
+  #error is only apparent once the main main iterations have started via glm2DS
+  #the equivalent tests in glm2DS will destroy the info.matrix and score.vector in the affected study so
   #the model fitting will simply terminate.
 
     if(!(y.invalid>0||w.invalid>0||o.invalid>0||sum(Xpar.invalid)>0||glm.saturation.invalid>0)){
@@ -221,6 +221,6 @@ if(!is.null(offsetvar))
 
 }
 #AGGREGATE FUNCTION
-# glmDS1
+# glm1DS
 
 

R/glmDS2.R → R/glm2DS.R

@@ -1,9 +1,9 @@
 #' 
-#' @title glmDS2 called by ds.glm
+#' @title glm2DS called by ds.glm
 #' @description This is the second server-side aggregate function called by ds.glm.
 #' @details It is an aggregate function that uses the model structure and starting
-#' beta.vector constructed by glmDS1 to iteratively fit the generalized linear model
-#' that has been specified. The function glmDS2 also carries out a series of disclosure
+#' beta.vector constructed by glm1DS to iteratively fit the generalized linear model
+#' that has been specified. The function glm2DS also carries out a series of disclosure
 #' checks and if the arguments or data fail any of those tests,
 #' model construction is blocked and an appropriate serverside error message is
 #' created and returned to ds.glm on the clientside.
@@ -25,7 +25,7 @@
 #' @return List with values from GLM model
 #' @export
 #'
-glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) {
+glm2DS <- function (formula, family, beta.vect, offset, weights, dataName) {
 
   #############################################################
   #MODULE 1: CAPTURE THE nfilter SETTINGS
@@ -266,7 +266,7 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) {
   #score.vector and information.matrix in the study with the problem.
   #So this will make model fail without explanation
 
-  #Disclosure code from glmDS1
+  #Disclosure code from glm1DS
 
   errorMessage.combined <- NULL
 
@@ -335,7 +335,7 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) {
   #CHECK W VECTOR VALIDITY
   w.invalid <- 0
 
-  #Keep same object name as in glmDS1
+  #Keep same object name as in glm1DS
   w.vect <- weightsvar
 
   unique.values.noNA.w <- unique(w.vect[stats::complete.cases(w.vect)])
@@ -390,4 +390,4 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) {
 
 }
 # AGGREGATE FUNCTION
-# glmDS2
+# glm2DS