Merge pull request #40 from datashield/v5.1-dev

V5.1 dev

Author: OllyButters

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsBase
 Title: DataSHIELD server site base functions
-Version: 5.0.0
+Version: 5.1.0
 Author: DataSHIELD Developers <datashield@newcastle.ac.uk>
 Maintainer: DataSHIELD Developers <datashield@newcastle.ac.uk>
 License: GPL-3
@@ -17,7 +17,6 @@ AggregateMethods:
     dataFrameSubsetDS1,
     densityGridDS,
     dimDS,
-    dimDS,
     glmDS1,
     glmDS2,
     glmSLMADS1,
@@ -32,8 +31,6 @@ AggregateMethods:
     listDisclosureSettingsDS,
     matrixDetDS1,
     meanDS,
-    meanDS,
-    meanSdGpDS,
     meanSdGpDS,
     messageDS,
     namesDS,
@@ -50,10 +47,10 @@ AggregateMethods:
     tapplyDS,
     testObjExistsDS,
     tTestFDS2,
-    unListDS,
     varDS,
     class=base::class,
     colnames=base::colnames,
+    cor.test=stats::cor.test,
     dim=base::dim,
     exists=base::exists,
     is.character=base::is.character,
@@ -64,7 +61,8 @@ AggregateMethods:
     length=base::length,
     levels=base::levels,
     ls=base::ls,
-    NROW=base::NROW
+    NROW=base::NROW,
+    t.test=stats::t.test
 AssignMethods:
     asCharacterDS,
     asDataMatrixDS,
@@ -74,13 +72,13 @@ AssignMethods:
     asListDS,
     asLogicalDS,
     asMatrixDS,
-    asMatrixDS,
     asNumericDS,
     BooleDS,
     cbindDS,
     cDS,
     changeRefGroupDS,
     dataFrameDS,
+    dataFrameFillDS,
     dataFrameSortDS,
     dataFrameSubsetDS2,
     listDS,
@@ -109,9 +107,11 @@ AssignMethods:
     subsetByClassDS,
     subsetDS,
     tapplyDS.assign,
+    unListDS,
     as.character=base::as.character,
     as.null=base::as.null,
     as.numeric=base::as.numeric,
+    attach=base::attach,
     c=base::c,
     cbind=base::cbind,
     complete.cases=stats::complete.cases,
@@ -131,4 +131,4 @@ Options:
     default.nfilter.tab=3,
     default.nfilter.noise=0.25,
     default.nfilter.levels=0.33
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2

NAMESPACE

@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(BooleDS)
-export(alphaPhiDS)
 export(asCharacterDS)
 export(asDataMatrixDS)
 export(asFactorDS1)
@@ -18,6 +17,7 @@ export(checkNegValueDS)
 export(corDS)
 export(covDS)
 export(dataFrameDS)
+export(dataFrameFillDS)
 export(dataFrameSortDS)
 export(dataFrameSubsetDS1)
 export(dataFrameSubsetDS2)
@@ -67,7 +67,6 @@ export(replaceNaDS)
 export(rmDS)
 export(rowColCalcDS)
 export(scatterPlotDS)
-export(scoreVectDS)
 export(seqDS)
 export(setSeedDS)
 export(subsetByClassDS)

R/alphaPhiDS.R

@@ -9,7 +9,7 @@
 #' \code{ds.asInteger}.
 #' @return the object specified by the <newobj> argument (or its default name
 #' <x.name>.int) which is written to the serverside. For further
-#' details see help on the clientside function \type{ds.asInteger}.
+#' details see help on the clientside function \code{ds.asInteger}.
 #' @author Amadou Gaye, Paul Burton, Demetris Avraam, for DataSHIELD Development Team
 #' @export
 #'

R/asIntegerDS.R

@@ -10,12 +10,20 @@
 #' 
 cDS <- function (objs) {
   # this filter sets the minimum number of observations that are allowed 
-  nfilter <- setFilterDS()
+
+  #############################################################
+  # MODULE 1: CAPTURE THE nfilter SETTINGS
+  thr <- listDisclosureSettingsDS()
+  nfilter.tab <- as.numeric(thr$nfilter.tab)
+  #nfilter.glm <- as.numeric(thr$nfilter.glm)
+  #nfilter.subset <- as.numeric(thr$nfilter.subset)
+  #nfilter.string <- as.numeric(thr$nfilter.string)
+  #############################################################
 
   x <-  unlist(objs)
 
   # check if the output is valid and output accordingly
-  if(length(x) < nfilter){
+  if(length(x) < nfilter.tab){
     if(length(x == 0)){
       x <- c()
     }else{

R/cDS.R

@@ -0,0 +1,48 @@
+#' 
+#' @title dataFrameFillDS
+#' @description An assign function called by the clientside ds.dataFrameFill function.
+#' @details This function checks if each study has all the variables compared to the other studies
+#' in the analysis. If a study does not have some of the variables, the function generates those
+#' variables as vectors of missing values and combines them as columns to the input data frame. 
+#' Then, the "complete" in terms of the columns dataframe is saved in each server with a name
+#' specified by the argument \code{newobj} on the clientside. 
+#' @param df.name a character string representing the name of the input data frame that will be
+#' filled with extra columns with missing values if a number of variables is missing from it
+#' compared to the data frames of the other studies used in the analysis.
+#' @param allNames.transmit unique names of all the variables that are included in the input 
+#' data frames from all the used datasources. 
+#' @return Nothing is returned to the client. The generated object is written to the serverside.
+#' @author Demetris Avraam for DataSHIELD Development Team
+#' @export
+#' 
+dataFrameFillDS <- function(df.name, allNames.transmit){
+  
+  datatext <- paste0("data.frame(",df.name,")")
+  data <- eval(parse(text=datatext))
+
+  if(!is.null(allNames.transmit)){
+    allNames <- unlist(strsplit(allNames.transmit, split=","))
+  }else{
+    allNames <- NULL
+  }
+  
+  study.colnames <- colnames(data)
+  missingVars <- allNames[-which(allNames %in% study.colnames)]
+  
+  numRows <- dim(data)[1]
+  numCols <- length(missingVars)
+  
+  mat.new <- matrix(NA, ncol=numCols, nrow=numRows)
+  
+  df.new <- as.data.frame(mat.new)
+  colnames(df.new) <- missingVars
+  df.new <- lapply(df.new, as.numeric)
+
+  df.out <- cbind(data, df.new)
+  
+  return(df.out)
+
+}
+# ASSIGN FUNCTION
+# dataFrameFillDS
+