Merge pull request #61 from StuartWheater/temp_cran-version-fix

Updates for CRAN

Author: StuartWheater

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: dsBaseClient
 Title: 'DataSHIELD' Client Side Base Functions
-Version: 7.0.0-9000
+Version: 7.0.0.9000
 Description: Base 'DataSHIELD' functions for the client 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("dsBaseClient")'.
+    the automated output checks. For more details, see citation("dsBaseClient").
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
                     role = c("aut"),

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(computeWeightedMeans)
 export(ds.Boole)
 export(ds.abs)
 export(ds.asCharacter)

R/computeWeightedMeans.R

@@ -9,9 +9,11 @@
 #' @param variables character name of the variable(s) to focus on. The variables must be in the data.table
 #' @param weight character name of the data.table column that contains a weight. 
 #' @param by character vector of the columns to group by
+#' @return Returns a data table object with computed weighted means.
+#'
 #' @import data.table
 #' @importFrom stats as.formula na.omit ts weighted.mean
-#' @export
+#' @keywords internal
 computeWeightedMeans <- function(data_table, variables, weight, by) {
 
   if (is.null(weight)) {

R/ds.cbind.R

@@ -157,7 +157,7 @@ ds.cbind <- function(x=NULL, DataSHIELD.checks=FALSE, force.colnames=NULL, newob
         }
         colNames <- unlist(colNames)
         if(anyDuplicated(colNames) != 0){
-          cat("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n")
+          message("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n")
         }  
       }  
     } 
@@ -198,30 +198,30 @@ ds.cbind <- function(x=NULL, DataSHIELD.checks=FALSE, force.colnames=NULL, newob
       next.class <- DSI::datashield.aggregate(datasources[std], calltext1)
       class.vector <- c(class.vector, next.class[[1]])
       if (notify.of.progress){
-        cat("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n")
+        message("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n")
       }  
     }
     for(j in 1:length(x)){
       test.df <- x[j]
       if(class.vector[j]!="data.frame" && class.vector[j]!="matrix"){
         colname.vector <- c(colname.vector, test.df)
         if (notify.of.progress){
-          cat("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
+          message("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
         }  
       }else{
         calltext2 <- call('colnamesDS', test.df)
         df.names <- DSI::datashield.aggregate(datasources[std], calltext2)
         colname.vector <- c(colname.vector, df.names[[1]])
         if (notify.of.progress){
-          cat("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
+          message("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
         }  
       }
     }
     colname.list[[std]] <- colname.vector
   }
 
   if (notify.of.progress){
-    cat("\nBoth steps in all studies completed\n")
+    message("\nBoth steps in all studies completed\n")
   }
 
   # prepare name vectors for transmission

R/ds.contourPlot.R

@@ -120,6 +120,10 @@ ds.contourPlot <- function(x=NULL, y=NULL, type='combine', show='all', numints=2
     stop("y=NULL. Please provide the names of two numeric vectors!", call.=FALSE)
   }
 
+  # Save par and setup reseting of par values
+  old_par <- graphics::par(no.readonly = TRUE)
+  on.exit(graphics::par(old_par), add = TRUE)
+
   # check if the input objects are defined in all the studies
   isDefined(datasources, x)
   isDefined(datasources, y)

R/ds.dataFrame.R

@@ -137,7 +137,7 @@ ds.dataFrame <- function(x=NULL, row.names=NULL, check.rows=FALSE, check.names=T
         }
         colNames <- unlist(colNames)
         if(anyDuplicated(colNames) != 0){
-          cat("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n")
+          message("\n Warning: Some column names in study", j, "are duplicated and a suffix '.k' will be added to the kth replicate \n")
         }  
       }  
     } 
@@ -178,30 +178,30 @@ ds.dataFrame <- function(x=NULL, row.names=NULL, check.rows=FALSE, check.names=T
       next.class <- DSI::datashield.aggregate(datasources[std], calltext1)
       class.vector <- c(class.vector, next.class[[1]])
       if (notify.of.progress){
-        cat("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n")
+        message("\n",j," of ", length(x), " elements to combine in step 1 of 2 in study ", std, "\n")
       }  
     }
     for(j in 1:length(x)){
       test.df <- x[j]
       if(class.vector[j]!="data.frame" && class.vector[j]!="matrix"){
         colname.vector <- c(colname.vector, test.df)
         if (notify.of.progress){
-          cat("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
+          message("\n",j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
         }  
       }else{
         calltext2 <- call('colnamesDS', test.df)
         df.names <- DSI::datashield.aggregate(datasources[std], calltext2)
         colname.vector <- c(colname.vector, df.names[[1]])
         if (notify.of.progress){
-          cat("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
+          message("\n", j," of ", length(x), " elements to combine in step 2 of 2 in study ", std, "\n")
         }  
       }
     }
     colname.list[[std]] <- colname.vector
   }
 
   if (notify.of.progress){
-    cat("\nBoth steps in all studies completed\n")
+    message("\nBoth steps in all studies completed\n")
   }
 
   # prepare vectors for transmission

R/ds.dataFrameSubset.R

@@ -231,13 +231,13 @@ if(!is.null(rm.cols)){
         if (notify.of.progress)
 	{
             if(num.messages==1){
-	        cat("\nSource",s,"\n",return.warning.message[[s]][[1]],"\n")
+	        message("\nSource",s,"\n",return.warning.message[[s]][[1]],"\n")
 	    }else{
-	        cat("\nSource",s,"\n")
+	        message("\nSource",s,"\n")
 		for(m in 1:(num.messages-1)){
-		    cat(return.warning.message[[s]][[m]],"\n")
+		    message(return.warning.message[[s]][[m]],"\n")
                 }
-                cat(return.warning.message[[s]][[num.messages]],"\n")
+                message(return.warning.message[[s]][[num.messages]],"\n")
 	    }
         }
     }

R/ds.dmtC2S.R

@@ -93,7 +93,7 @@ if(dplyr::is.tbl(dfdata))
 
   if(!is.matrix(dfdata) && !is.data.frame(dfdata) && !dplyr::is.tbl(dfdata))
 	{
-	   cat("\n            FAILED: <dfdata> must either be a data.frame, matrix or tibble")	
+	   message("\n            FAILED: <dfdata> must either be a data.frame, matrix or tibble")	
        return('Please respecify')
 	}
 

R/ds.extractQuantiles.R

@@ -224,7 +224,7 @@ datasources.in.current.function<-datasources
   #CALL CLIENTSIDE FUNCTION ds.dmtC2S TO RETURN final.quantile.df TO SERVERSIDE
   dsBaseClient::ds.dmtC2S(dfdata=final.quantile.df,newobj="final.quantile.df",datasources = datasources.in.current.function)
 
-  cat("\n\n\n"," FINAL RANKING PROCEDURES COMPLETE:
+  message("\n\n\n"," FINAL RANKING PROCEDURES COMPLETE:
   PRIMARY RANKING OUTPUT IS IN DATA FRAME",extract.summary.output.ranks.df,
 "
   WHICH IS SORTED BY",extract.ranks.sort.by," AND HAS BEEN

R/ds.forestplot.R

@@ -10,6 +10,7 @@
 #' See details from \code{?meta::metagen} for the different options.
 #' @param layout \code{character} (default \code{"JAMA"}) Layout of the plot. 
 #' See details from \code{?meta::metagen} for the different options.
+#' @return Results a foresplot object created with `meta::forest`.
 #'
 #' @export
 #'