diff --git a/DESCRIPTION b/DESCRIPTION index bc5e3973..a9573b74 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a 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("dsBase")'. -Version: 6.3.5.9000 +Version: 6.4.0.9000 Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), @@ -71,10 +71,16 @@ Imports: gamlss, gamlss.dist, mice, - childsds + childsds, + purrr, + tibble, + tidyselect, + stats, + lubridate Suggests: spelling, - testthat -RoxygenNote: 7.3.3 + testthat, + tidytable +RoxygenNote: 8.0.0 Encoding: UTF-8 Language: en-GB diff --git a/NAMESPACE b/NAMESPACE index e52e5d10..0474b2b1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,6 +3,7 @@ export(BooleDS) export(absDS) export(asCharacterDS) +export(asDataFrameDS) export(asDataMatrixDS) export(asFactorDS1) export(asFactorDS2) @@ -35,13 +36,19 @@ export(dataFrameFillDS) export(dataFrameSortDS) export(dataFrameSubsetDS1) export(dataFrameSubsetDS2) +export(dateDS) export(densityGridDS) export(dimDS) export(dmtC2SDS) export(elsplineDS) export(extractQuantilesDS1) export(extractQuantilesDS2) +export(fixClassDS) +export(fixColsDS) +export(fixLevelsDS) export(gamlssDS) +export(getAllLevelsDS) +export(getClassAllColsDS) export(getWGSRDS) export(glmDS1) export(glmDS2) @@ -93,6 +100,7 @@ export(minMaxRandDS) export(namesDS) export(nsDS) export(numNaDS) +export(predictDS) export(qlsplineDS) export(quantileMeanDS) export(rBinomDS) @@ -112,8 +120,10 @@ export(recodeValuesDS) export(repDS) export(replaceNaDS) export(rmDS) +export(roundDS) export(rowColCalcDS) export(sampleDS) +export(scaleDS) export(scatterPlotDS) export(seqDS) export(setSeedDS) @@ -139,5 +149,14 @@ import(dplyr) import(gamlss) import(gamlss.dist) import(mice) +importFrom(dplyr,"%>%") +importFrom(dplyr,across) +importFrom(dplyr,mutate) +importFrom(dplyr,select) importFrom(gamlss.dist,pST3) importFrom(gamlss.dist,qST3) +importFrom(purrr,map) +importFrom(purrr,set_names) +importFrom(tibble,as_tibble) +importFrom(tidyselect,all_of) +importFrom(tidyselect,peek_vars) diff --git a/R/BooleDS.R b/R/BooleDS.R index 0f54dfca..3a905953 100644 --- a/R/BooleDS.R +++ b/R/BooleDS.R @@ -30,127 +30,77 @@ BooleDS <- function(V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL, na.assi # Check Permissive Privacy Control Level. dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) -######################################################################### -# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS # -thr <- dsBase::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) # -#nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) # -#nfilter.kNN<-as.numeric(thr$nfilter.kNN) # -#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) # -######################################################################### - - -#V1: numeric, factor or logical vector or scalar in .GlobalEnv -#V2: numeric, factor or logical vector or scalar in .GlobalEnv or client specified scalar with which to compare V1 - -#EVAL V1 and V2 - -##########CHECK NOT LONG SPECIFIED VECTOR############## - -V1<-eval(parse(text=V1.name), envir = parent.frame()) -V2<-eval(parse(text=V2.name), envir = parent.frame()) - - -if(is.character(V1)){ - studysideMessage<-"FAILED: V_i is character, please convert to numeric, factor or logical before running Boole" - stop(studysideMessage, call. = FALSE) - } - -if(is.character(V2)){ - studysideMessage<-"FAILED: V_ii is character, please convert to numeric, factor or logical before running Boole" - stop(studysideMessage, call. = FALSE) - } - -V1.length<-length(V1) -V2.length<-length(V2) - -if(!((V1.length == V2.length) | (V2.length==1))){ - studysideMessage<-"FAILED: V_ii must either be of length one or of length equal to V_i" - stop(studysideMessage, call. = FALSE) -} - -if(!is.numeric(Boolean.operator.n) | Boolean.operator.n==0){ - studysideMessage<-"FAILED: Boolean.operator specified incorrectly. Must be: '==', '!=', '<', '<=', '>' or '>='" - stop(studysideMessage, call. = FALSE) -} - -Boolean.operator<-" " -if(Boolean.operator.n==1) Boolean.operator<-"==" -if(Boolean.operator.n==2) Boolean.operator<-"!=" -if(Boolean.operator.n==3) Boolean.operator<-"<" -if(Boolean.operator.n==4) Boolean.operator<-"<=" -if(Boolean.operator.n==5) Boolean.operator<-">" -if(Boolean.operator.n==6) Boolean.operator<-">=" - - -#APPLY BOOLEAN OPERATOR SPECIFIED - -Boolean.indicator<-integer(length=V1.length) - -#EVALUATE DIFFERENTLY IF V2 IS SAME LENGTH AS V1 OR OF LENGTH 1 -if(V2.length==V1.length){ -for(j in 1:V1.length){ -command.text<-paste0(V1.name,"[",j,"] ",Boolean.operator," ",V2.name,"[",j,"]") -Boolean.indicator[j]<-eval(parse(text=command.text), envir = parent.frame())*1 -} -} - -if(V2.length==1){ -for(j in 1:V1.length){ -command.text<-paste0(V1.name,"[",j,"] ",Boolean.operator," ",V2.name) -Boolean.indicator[j]<-eval(parse(text=command.text), envir = parent.frame())*1 -} -} - - -#BY DEFAULT NAs REMAIN AS NAs BUT IF YOU WANT TO YOU CAN FORCE THEM TO 1 OR 0 USING ARGUMENT - -if(na.assign.text=="1"){ -Boolean.indicator[is.na(Boolean.indicator)==1]<-1 -} - -if(na.assign.text=="0"){ -Boolean.indicator[is.na(Boolean.indicator)==1]<-0 -} - - -outobj.b<-as.logical(Boolean.indicator) -outobj<-Boolean.indicator - - - -#COMMENT OUT THIS CODE BLOCK BECAUSE TESTS OF MINIMUM CELL SIZE SHOULD ALL BE -#ENACTED IN AGGREGATE FUNCTIONS. NO VECTOR IS DISCLOSIVE UNTIL IT RETURNS -#SOMETHING TO THE CLIENTSIDE. I AM LEAVING THIS COMMENTED BUT UNDELETED -#IN CASE WE LATER DECIDE TO CHANGE THIS STRATEGY -#CHECK OUTPUT VECTOR VALIDITY -# outobj.invalid<-0 -# -# unique.values.outobj<-unique(outobj) -# unique.values.noNA.outobj<-unique.values.outobj[complete.cases(unique.values.outobj)] -# -# #Boolean and can therefore only be binary so check this: -# if(length(unique.values.noNA.outobj)>2) outobj.invalid<-1 -# -# tabvar<-table(outobj,useNA="no")[table(outobj,useNA="no")>=1] -# min.category<-min(tabvar) -# if(min.category' or '>='" + stop(studysideMessage, call. = FALSE) + } + + Boolean.operator <- " " + if(Boolean.operator.n==1) Boolean.operator <- "==" + if(Boolean.operator.n==2) Boolean.operator <- "!=" + if(Boolean.operator.n==3) Boolean.operator <- "<" + if(Boolean.operator.n==4) Boolean.operator <- "<=" + if(Boolean.operator.n==5) Boolean.operator <- ">" + if(Boolean.operator.n==6) Boolean.operator <- ">=" + + # APPLY BOOLEAN OPERATOR SPECIFIED + Boolean.indicator <- integer(length=V1.length) + + # EVALUATE DIFFERENTLY IF V2 IS SAME LENGTH AS V1 OR OF LENGTH 1 + if(V2.length==V1.length){ + for(j in 1:V1.length){ + command.text <- paste0(V1.name,"[",j,"] ",Boolean.operator," ",V2.name,"[",j,"]") + Boolean.indicator[j]<-eval(parse(text=command.text), envir = parent.frame())*1 + } + } + + if(V2.length==1){ + for(j in 1:V1.length){ + command.text<-paste0(V1.name,"[",j,"] ",Boolean.operator," ",V2.name) + Boolean.indicator[j]<-eval(parse(text=command.text), envir = parent.frame())*1 + } + } + + # BY DEFAULT NAs REMAIN AS NAs BUT IF YOU WANT TO YOU CAN FORCE THEM TO 1 OR 0 USING ARGUMENT + if(na.assign.text=="1"){ + Boolean.indicator[is.na(Boolean.indicator)==1]<-1 + } + + if(na.assign.text=="0"){ + Boolean.indicator[is.na(Boolean.indicator)==1]<-0 + } + + outobj.b <- as.logical(Boolean.indicator) + outobj <- Boolean.indicator + + if(numeric.output==TRUE){ + Boole.obj <- outobj + }else{ + Boole.obj <- outobj.b + } + + return(Boole.obj) } -#ASSIGN FUNCTION +# ASSIGN FUNCTION # BooleDS diff --git a/R/asDataFrameDS.R b/R/asDataFrameDS.R new file mode 100644 index 00000000..0e31cdd2 --- /dev/null +++ b/R/asDataFrameDS.R @@ -0,0 +1,29 @@ +#' @title asDataFrameDS a serverside assign function called by ds.asDataFrame +#' @description Coerces an R object into a matrix maintaining original +#' class for all columns in data.frames. +#' @details This assign function is based on the native R function \code{data.frame} +#' @param x.name the name of the input object to be coerced to class +#' data.frame. Must be specified in inverted commas. But this argument is +#' usually specified directly by argument of the clientside function +#' \code{ds.asDataFrame} +#' @return the object specified by the argument (or its default name +#' "asdataframe.newobj") which is written to the serverside. For further +#' details see help on the clientside function \code{ds.asDataMatrix} +#' @author Tim Cadman +#' @export +asDataFrameDS <- function (x.name){ + + if(is.character(x.name)){ + x<-eval(parse(text=x.name), envir = parent.frame()) + + }else{ + studysideMessage<-"ERROR: x.name must be specified as a character string" + stop(studysideMessage, call. = FALSE) + } + + output <- data.frame(x) + + return(output) +} +# ASSIGN FUNCTION +# asDataFrameDS diff --git a/R/asDataMatrixDS.R b/R/asDataMatrixDS.R index 3fff528b..2980965d 100644 --- a/R/asDataMatrixDS.R +++ b/R/asDataMatrixDS.R @@ -1,4 +1,4 @@ -#' @title asDataMatrixDS a serverside assign function called by ds.asDataMatrix +#' @title asDataFrameDS a serverside assign function called by ds.asDataFrame #' @description Coerces an R object into a matrix maintaining original #' class for all columns in data.frames. #' @details This assign function is based on the native R function \code{data.matrix} @@ -8,13 +8,13 @@ #' the data.frame to a matrix but maintains all data columns in their #' original class #' @param x.name the name of the input object to be coerced to class -#' data.matrix. Must be specified in inverted commas. But this argument is +#' data.frame. Must be specified in inverted commas. But this argument is #' usually specified directly by argument of the clientside function -#' \code{ds.asDataMatrix} +#' \code{ds.asDataFrame} #' @return the object specified by the argument (or its default name -#' "asdatamatrix.newobj") which is written to the serverside. For further +#' "asdataframe.newobj") which is written to the serverside. For further #' details see help on the clientside function \code{ds.asDataMatrix} -#' @author Paul Burton for DataSHIELD Development Team +#' @author Tim Cadman #' @export asDataMatrixDS <- function(x.name) { if (is.character(x.name)) { @@ -24,9 +24,9 @@ asDataMatrixDS <- function(x.name) { stop(studysideMessage, call. = FALSE) } - output <- data.matrix(x) + output <- data.frame(x) return(output) } # ASSIGN FUNCTION -# asDataMatrixDS +# asDataFrameDS diff --git a/R/asFactorDS1.R b/R/asFactorDS1.R index 6d4f0507..7a3a4e1a 100644 --- a/R/asFactorDS1.R +++ b/R/asFactorDS1.R @@ -10,6 +10,7 @@ #' @export #' asFactorDS1 <- function(input.var.name=NULL){ + ################################################################## #MODULE 1: CAPTURE THE nfilter SETTINGS # thr<-dsBase::listDisclosureSettingsDS() # @@ -26,27 +27,29 @@ asFactorDS1 <- function(input.var.name=NULL){ input.var <- eval(parse(text=input.var.name), envir = parent.frame()) factor.levels.present.in.source <- levels(factor(input.var)) - num.levels<-length(factor.levels.present.in.source) + num.levels <- length(factor.levels.present.in.source) max.levels.by.density<-nfilter.levels.density*length(input.var) - if(num.levels>nfilter.levels.max) - { - error.message<- - paste0("FAILED: this variable has too many levels and may be disclosive. It exceeds the max number of levels allowed by nfilter.levels.max: that is ",nfilter.levels.max,". In this study this variable has ",num.levels," factor levels") + if(num.levels > nfilter.levels.max){ + error.message <- paste0("FAILED: this variable has too many levels and may be disclosive. + It exceeds the max number of levels allowed by nfilter.levels.max: + that is ", nfilter.levels.max, ". In this study this variable has ", + num.levels," factor levels") stop(error.message, call. = FALSE) } - if(num.levels>(length(input.var)*nfilter.levels.density)) - { - error.message<- - paste0("FAILED: this variable has too many levels and may be disclosive. The number of factor levels must not exceed ", (nfilter.levels.density*100), "% of the length of the variable being converted to a factor. The max number of levels in this study is therefore ",max.levels.by.density," but this variable has ",num.levels," factor levels") + if(num.levels > (length(input.var)*nfilter.levels.density)){ + error.message <- paste0("FAILED: this variable has too many levels and may be disclosive. + The number of factor levels must not exceed ", (nfilter.levels.density*100), + "% of the length of the variable being converted to a factor. The max number + of levels in this study is therefore ",max.levels.by.density," but this + variable has ", num.levels, " factor levels") stop(error.message, call. = FALSE) } return(factor.levels.present.in.source) } -#AGGREGATE FUNCTION +# AGGREGATE FUNCTION # asFactorDS1 - diff --git a/R/asFactorDS2.R b/R/asFactorDS2.R index 74af1d67..6fecabfe 100644 --- a/R/asFactorDS2.R +++ b/R/asFactorDS2.R @@ -4,7 +4,7 @@ #' a factor type that presented as a vector or as a matrix with dummy variables. #' @details The functions converts the input variable into a factor which is presented as a vector #' if the \code{fixed.dummy.vars} is set to FALSE or as a matrix with dummy variables if the -#' \code{fixed.dummy.vars} is set to TRUE (see the help file of ds.asFactor.b for more details). +#' \code{fixed.dummy.vars} is set to TRUE (see the help file of ds.asFactor for more details). #' @param input.var.name the name of the variable that is to be converted to a factor. #' @param all.unique.levels.transmit the levels that the variable will be transmitted to. #' @param fixed.dummy.vars a boolean that determines whether the new object will be represented as diff --git a/R/asListDS.R b/R/asListDS.R index 31da5f0b..0029526b 100644 --- a/R/asListDS.R +++ b/R/asListDS.R @@ -1,3 +1,4 @@ +#' #' @title asListDS a serverside aggregate function called by ds.asList #' @description Coerces an R object into a list #' @details Unlike most other class coercing functions this is @@ -21,25 +22,26 @@ #' the class of the output object should usually be 'list' #' @author Amadou Gaye, Paul Burton for DataSHIELD Development Team #' @export +#' asListDS <- function (x.name, newobj){ newobj.class <- NULL if(is.character(x.name)){ - active.text<-paste0(newobj,"<-as.list(",x.name,")") + active.text <- paste0(newobj,"<-as.list(",x.name,")") eval(parse(text=active.text), envir = parent.frame()) - active.text2<-paste0("class(",newobj,")") + active.text2 <- paste0("class(",newobj,")") assign("newobj.class", eval(parse(text=active.text2), envir = parent.frame())) }else{ - studysideMessage<-"ERROR: x.name must be specified as a character string" + studysideMessage <- "ERROR: x.name must be specified as a character string" stop(studysideMessage, call. = FALSE) } - return.message<-paste0("New object <",newobj,"> created") - object.class.text<-paste0("Class of <",newobj,"> is '",newobj.class,"'") + return.message <- paste0("New object <", newobj, "> created") + object.class.text <- paste0("Class of <", newobj, "> is '", newobj.class, "'") - return(list(return.message=return.message,class.of.newobj=object.class.text)) + return(list(return.message=return.message, class.of.newobj=object.class.text)) } # AGGEGATE FUNCTION # asListDS diff --git a/R/asLogicalDS.R b/R/asLogicalDS.R index 4a1725f5..26199153 100644 --- a/R/asLogicalDS.R +++ b/R/asLogicalDS.R @@ -1,3 +1,4 @@ +#' #' @title Coerces an R object into class numeric #' @description this function is based on the native R function \code{as.numeric} #' @details See help for function \code{as.logical} in native R @@ -10,24 +11,25 @@ #' details see help on the clientside function \code{ds.asLogical} #' @author Amadou Gaye, Paul Burton for DataSHIELD Development Team #' @export +#' asLogicalDS <- function (x.name){ -if(is.character(x.name)){ - x<-eval(parse(text=x.name), envir = parent.frame()) + if(is.character(x.name)){ + x <- eval(parse(text=x.name), envir = parent.frame()) }else{ - studysideMessage<-"ERROR: x.name must be specified as a character string" + studysideMessage <- "ERROR: x.name must be specified as a character string" stop(studysideMessage, call. = FALSE) - } + } - if(!is.numeric(x)&&!is.integer(x)&&!is.character(x)&&!is.matrix(x)){ - studysideMessage<-"ERROR: for ds.asLogical function, x.name must specify an input object of class numeric, integer, character or matrix" - stop(studysideMessage, call. = FALSE) + if(!is.numeric(x) && !is.integer(x) && !is.character(x) && !is.matrix(x)){ + studysideMessage <- "ERROR: for ds.asLogical function, x.name must specify an input object of class numeric, integer, character or matrix" + stop(studysideMessage, call. = FALSE) } output <- as.logical(x) return(output) } -#ASSIGN FUNCTION +# ASSIGN FUNCTION # asLogicalDS diff --git a/R/aucDS.R b/R/aucDS.R index 6afda830..02d7f638 100644 --- a/R/aucDS.R +++ b/R/aucDS.R @@ -31,6 +31,6 @@ aucDS <- function(pred=pred, y=y){ q2 <- 2*AUC^2/(1+AUC)-AUC^2 se <- sqrt((q0+(n0-1)*q1+(n1-1)*q2)/(n0*n1)) - return(list(AUC=AUC,se=se)) + return(list(AUC=AUC, se=se)) } \ No newline at end of file diff --git a/R/dateDS.R b/R/dateDS.R new file mode 100644 index 00000000..f6b442cd --- /dev/null +++ b/R/dateDS.R @@ -0,0 +1,186 @@ +#' +#' @title dateDS +#' @description Takes an object that is either a data-frame column or a vector, and can do extraction of +#' components of full date (\code{extractdate}), can combine date components to a full date (\code{makedate}), +#' or can calculate the time between two dates (\code{timebetween}). +#' +#' @details +#' If the input is a data-frame column, it must be provided in the \code{x} argument as data-frame$column. +#' Inputs for \code{extractdate} and \code{timebetween} must be date objects. +#' For \code{makedate}, three numeric vectors (year, month, day) must be provided in the correct order. +#' The \code{add.column} argument determines whether the result is added as a new column in the existing +#' data-frame (\code{TRUE}), or created as a new server-side object (\code{FALSE}). +#' Note: \code{add.column = TRUE} is only valid for data-frame inputs. +#' +#' +#' @param x Character vector specifying the server-side object(s). For data-frame columns, use the format \code{df$column}. +#' @param type Character string specifying the operation: \code{"extractdate"}, \code{"makedate"}, or \code{"timebetween"}. +#' @param newobj Character string for the name of the object that will be created on the server. Default is \code{"date.result"}. +#' @param unit Character string specifying the unit for \code{extractdate} or \code{timebetween}: \code{"days"}, \code{"months"}, or \code{"years"}. +#' @param add.column Logical. If \code{FALSE}, the result is created as a new server-side object; +#' if \code{TRUE}, the result is added as a new column in the existing data-frame. Default is \code{FALSE}. +#' +#' +#' @author Zulal Bekerecioglu +#' @return the created numeric vector or date object, or the updated dataframe with the added column +#' @export +#' +#' +dateDS <- function(x=NULL, type=NULL, + newobj=NULL, unit=NULL, add.column=NULL) { + + add.column <- as.logical(add.column) + + # If argument not in c("extractdate", "makedate", "timebetween") throw an error + if (!(type %in% c("extractdate", "makedate", "timebetween"))) { + stop("Invalid argument. Must be one of: ", paste(c("extractdate", "makedate", "timebetween"), collapse=", ")) + } + + # Check if input(s) are valid. + error_message <- "Input object couldn't be found. Please provide the correct format. + For vectors, supply an existing object name; for columns, use the format dataframe$column, + where 'dataframe' is the name of the data frame and 'column' is the column name, + and ensure that both exist." + + + # If x is NULL, throw and error. + if (is.null(x)) { + stop(error_message, call. = FALSE) + } + + # Each argument takes a unique number of elements, check if they match. + if (length(x) != 1 && type=="extractdate") { + stop(paste0("Invalid input length for argument '", type, "'. Expected ", 1, + " elements, but received ", length(x), ". Please provide exactly ", 1, + " object name(s) or column(s)."), call. = FALSE) + } + + if (length(x) != 3 && type=="makedate") { + stop(paste0("Invalid input length for argument '", type, "'. Expected ", 3, + " elements, but received ", length(x), ". Please provide exactly ", 3, + " object name(s) or column(s)."), call. = FALSE) + } + + if (length(x) != 2 && type=="timebetween") { + stop(paste0("Invalid input length for argument '", type, "'. Expected ", 2, + " elements, but received ", length(x), ". Please provide exactly ", 2, + " object name(s) or column(s)."), call. = FALSE) + } + + inputs <- vector("list", length(x)) + + # When add.column = TRUE, the client function ensures that at least one input is a column, + # and if multiple columns are provided, they all come from the same data-frame. + # Therefore, it is safe to use any of these data-frames as common_df on the server. + common_df <- NULL + + for (i in seq_along(x)) { + element <- x[i] + + # Each element must be a single string + if (!is.character(element) || length(element) != 1) stop(error_message, call. = FALSE) + + # Check if it is a df$col reference + if (grepl("\\$", element, perl = TRUE)) { + parts <- strsplit(element, "\\$", perl = TRUE)[[1]] + + # Validate both parts + if (length(parts) != 2 || !nzchar(parts[1]) || !nzchar(parts[2])) stop(error_message, call. = FALSE) + + # Try to get the dataframe + df <- tryCatch(get(parts[1]), error = function(e) NULL) + if (is.null(df)) stop(error_message, call. = FALSE) + + # Check that column exists + if (!(parts[2] %in% names(df))) stop(error_message, call. = FALSE) + + # Save the column values in the list + inputs[[i]] <- df[[parts[2]]] + common_df <- parts[1] + + } else { + # It's a plain object, just get it + obj <- tryCatch(get(element), error = function(e) NULL) + if (is.null(obj)) stop(error_message, call. = FALSE) + + inputs[[i]] <- obj + } + } + + + # extractdate + # x should be a column name or object with a date format, type should be provided, + # a new column or object with outputcolname will be created + if (type == "extractdate") { + + # Only one input is expected + date_input <- inputs[[1]] + + # Extract the requested component + result <- switch(unit, + days = lubridate::day(date_input), + months = lubridate::month(date_input), + years = lubridate::year(date_input), + stop("Invalid unit. Must be one of: days, months, years")) + } + + + # makedate + # inputcolname should be list of 3 strings: year-month-day + if (type == "makedate") { + + # inputs[[1]] = year, inputs[[2]] = month, inputs[[3]] = day + year_vec <- as.numeric(inputs[[1]]) + month_vec <- as.numeric(inputs[[2]]) + day_vec <- as.numeric(inputs[[3]]) + + # Basic plausibility checks + if (length(unique(sapply(list(year_vec, month_vec, day_vec), length))) != 1) { + stop("Inputs for 'makedate' must be of equal length.", call. = FALSE) + } + + if (any(year_vec < 1000 | year_vec > 3000, na.rm = TRUE)) { + stop("The 'year' input in 'makedate' must contain plausible 4-digit years (1000-3000). + Check that year, month, and day are given in the correct order (year, month, day).", call. = FALSE) + } + if (any(month_vec < 1 | month_vec > 12, na.rm = TRUE)) { + stop("The 'month' input in 'makedate' must contain values between 1 and 12. + Check that year, month, and day are given in the correct order (year, month, day).", call. = FALSE) + } + if (any(day_vec < 1 | day_vec > 31, na.rm = TRUE)) { + stop("The 'day' input in 'makedate' must contain values between 1 and 31. + Check that year, month, and day are given in the correct order (year, month, day).", call. = FALSE) + } + + + result <- lubridate::make_date(year = year_vec, + month = month_vec, + day = day_vec) + } + + + # timebetween + # inputcolname should be a list of 2 strings: start and end date + if (type == "timebetween") { + + # inputs[[1]] = start date, inputs[[2]] = end date + units <- list( + years = lubridate::period(years = 1), + months = lubridate::period(months = 1), + days = lubridate::period(days = 1) + ) + + result <- lubridate::interval(inputs[[1]], inputs[[2]]) %/% units[[unit]] + } + + # Save result based on add.column + if (!add.column) { + return(result) + } else { + # Assign to common_df as a new column + df <- get(common_df) + df[[newobj]] <- result + return(df) + } + +} diff --git a/R/glmSLMADS.assign.R b/R/glmSLMADS.assign.R index 275e1f47..f7b5fff4 100644 --- a/R/glmSLMADS.assign.R +++ b/R/glmSLMADS.assign.R @@ -18,40 +18,25 @@ #' @export glmSLMADS.assign <- function(formula, family, offsetName, weightsName, dataName){ -############################################################# -#MODULE 1: CAPTURE THE nfilter SETTINGS # -thr <- dsBase::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) # -############################################################# - -######################################## -############ -#Convert transmitable text for special link variance combinations back to full representation -if(family=="quasigamma.link_log") -{family<-"quasi(link=log,variance=mu^2)"} - -if(family=="Gamma.link_log") -{family<-"Gamma(link=log)"} -############# - -#Activate family object (this may not be necessary as character string may already be OK -#but just checking -final.family.object<-eval(parse(text=family)) - - -#Correctly name offset, weights and data objects in function call -#(to allow glmPredict to work correctly later) -calltext<-paste0("mg<-glm(formula,family=",family,",offset=", - offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)") - -eval(parse(text=calltext)) - -return(mg) + # Convert transmitable text for special link variance combinations back to full representation + if(family=="quasigamma.link_log") + {family<-"quasi(link=log,variance=mu^2)"} + + if(family=="Gamma.link_log") + {family<-"Gamma(link=log)"} + + # Correctly name offset, weights and data objects in function call + # (to allow glmPredict to work correctly later) + calltext <- paste0("mg<-glm(formula,family=",family,",offset=", + offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)") + + eval(parse(text=calltext)) + + # update the call object to include the actual formula + mg$call$formula <- formula + + return(mg) } - # ASSIGN FUNCTION # glmSLMADS.assign diff --git a/R/global.R b/R/global.R index a3c9454e..f4402723 100644 --- a/R/global.R +++ b/R/global.R @@ -2,4 +2,5 @@ utils::globalVariables(c('offset.to.use', 'weights.to.use', 'out.table.real', 'out.table.dim', 'out.table.dimnames', 'list.obj', 'mg', 'blackbox.output.df', 'blackbox.ranks.df', 'global.bounds.df', 'global.ranks.quantiles.df', 'sR4.df', - 'min.max.df','sR5.df','input.mean.sd.df','input.ranks.sd.df','RS','CG','mixed','x','y','.old_seed','.Random.seed')) + 'min.max.df','sR5.df','input.mean.sd.df','input.ranks.sd.df','RS','CG','mixed','x','y','.old_seed','.Random.seed', + 'subsetByClassHelper1', 'subsetByClassHelper2', 'subsetByClassHelper3')) diff --git a/R/minMaxRandDS.R b/R/minMaxRandDS.R index 64caf7ae..8846147f 100644 --- a/R/minMaxRandDS.R +++ b/R/minMaxRandDS.R @@ -1,3 +1,4 @@ +#' #' @title Secure ranking of "V2BR" (vector to be ranked) across all sources #' @description Creates a minimum value that is more negative, and less positive #' than any real value in V2BR and a maximum value that is more positive and @@ -68,9 +69,5 @@ rand.min.max<-c(rand.min,rand.max) return(rand.min.max) } -#AGGREGATE +# AGGREGATE # minMaxRandDS - - - - diff --git a/R/predictDS.R b/R/predictDS.R new file mode 100644 index 00000000..e3311f91 --- /dev/null +++ b/R/predictDS.R @@ -0,0 +1,137 @@ +#' +#' @title predictDS +#' @description Generates server-side predictions using the client-side output from \code{ds.glm}. +#' +#' @details +#' This function uses the components supplied by the client-side function (coefficients, family, formula, +#' and any categorical variables) to generate predictions on the server. To use the base R \code{predict()} function, +#' a "dummy" glm object is created using the same model formula, family, and link function as the original model. +#' The dummy model's coefficients are then replaced with the client-side coefficient estimates. +#' +#' To avoid mismatches between the factors used in the original glm and those in the dummy glm, the categorical +#' variables saved by the client-side function are applied to the newdata. +#' +#' For intercept-only models, the function simply returns a vector of predicted values equal to the model intercept, with the appropriate length +#' based on the row length of \code{newdataname}. +#' +#' +#' @param newdataname A character string specifying the name of the new dataset to be used for predictions. +#' @param traindataname A character string specifying the name of the dataset used for model training. +#' @param type A character string specifying the type of prediction. Options are \code{"response"} or \code{"link"}. +#' @param na.action A character string to specify the action to take if missing values are present. Default is \code{"na.pass"}. +#' +#' +#' @author Zulal Bekerecioglu +#' @return a numeric vector containing the predicted values +#' @export +#' +#' +predictDS <- function(newdataname, traindataname, type = c("response", "link"), + na.action = "na.pass") { + + # Get the objects saved by the client function ds.predict + coefficients<-get("predictDS_coefficients") + model_formula <-get("predictDS_formula") + family <- get("predictDS_family") + categorical_variables <- get("predictDS_categorical_variables") + + + + if(!is.null(traindataname)) + { + traindata<-get(traindataname) + + }else{ + stop("'traindataname' couldn't be found, please provide a valid object name.", call.=FALSE) + } + + + if(!is.null(newdataname)) + { + newdf<-get(newdataname) + + }else{ + stop("'newdataname' couldn't be found, please provide a valid object name.", call.=FALSE) + } + + if (!is.character(type) || !(type %in% c("link","response"))) { + stop("Invalid argument. Must be one of: 'link','response'.", call. = FALSE) + } + + # Convert the family object to it's corresponding function, i.e. poisson.link.log -> poisson(link= "log") + family_dist <- strsplit(family, "\\.")[[1]] + + family_name <- family_dist[1] # "binomial" + link_name <- family_dist[3] # "logit" + + family_func <- get(family_name) # gets the function binomial() + family_obj <- family_func(link = link_name) + + + + # SPECIAL CASE HANDLING: y ~ 1, intercept only ###################### + # A numeric vector will be created wit the mean, with the same length as the row number in newdataname + special_case <- length(attr(stats::terms(stats::formula(model_formula)), "term.labels")) == 0 + + if(special_case){ + intercept <- coefficients + + # If the input is just a numeric vector, get the length + if(all(c("numeric") %in% class(newdf))){ + predictions.f <- rep(intercept, length(newdf)) + } else if(all(c("data.frame") %in% class(newdf))){ + predictions.f <- rep(intercept, nrow(newdf)) # Otherwise use the number of rows + } else { + stop("Invalid input: The object called 'newdataname' must be either a numeric vector or a data.frame.",, call. = FALSE) + } + + if (type == "link") { + predictions.f <- predictions.f + } else if (family_name == "gaussian") { # if type is 'response' + # identity + predictions.f <- predictions.f + } else if (family_name == "poisson") { + # log + predictions.f <- exp(predictions.f) + } else if (family_name == "binomial") { + # logit + predictions.f <- stats::plogis(predictions.f) + } else { + stop("Unsupported family for intercept-only prediction: Family must be either Gaussian, Poisson, or Binomial.", call. = FALSE) + } + + return(predictions.f) + } + # END OF SPECIAL CASE ###################### + + + + # Fix factor levels if any exists + for (var in categorical_variables) { + + # First get all the factor levels from the train data + traindata[[var]] <- factor(traindata[[var]]) + + # Ensure new data variable is a factor with the SAME levels (this is needed if the newdf is missing some categories) + newdf[[var]] <- factor(newdf[[var]], + levels = levels(traindata[[var]])) + } + + # Get the na.action argument + na.action.fun <- match.fun(na.action) + + # Use a dummy glm object with the correct formula and family + dummy_fit <- stats::glm(model_formula, + data = traindata, + family = family_obj, + control = stats::glm.control(maxit = 1)) + + # Change its coefficients with the correct ones + names(coefficients) <- names(dummy_fit$coefficients) + dummy_fit$coefficients <- coefficients + + # New predictions + prediction <- stats::predict(dummy_fit, newdata = newdf, type = type, na.action = na.action.fun) + + return(prediction) +} diff --git a/R/roundDS.R b/R/roundDS.R new file mode 100644 index 00000000..6e0d0c10 --- /dev/null +++ b/R/roundDS.R @@ -0,0 +1,77 @@ +#' +#' @title roundDS +#' @description Generates objects from a server-side object, which can be either a vector or +#' a data-frame column. Supports five operations: +#' 1. (\code{round}) +#' 2. (\code{ceiling}) +#' 3. (\code{floor}) +#' 4. (\code{trunc}) +#' 5. (\code{signif}) +#' where each function in baseR is applied on the server side to the specified object. +#' +#' @details +#' Note: \code{add.column = TRUE} is only valid for data-frame inputs. +#' +#' +#' @param x Character vector specifying the server-side object(s). For data-frame columns, use the format \code{df$column}. +#' @param type Character string specifying the operation: \code{"round"}, \code{"ceiling"}, \code{"floor"}, +#' \code{trunc}, or \code{"signif"}. +#' @param digits Number of digits to be used in arguments \code{"round"} and \code{"signif"}. +#' @param add.column Logical. If \code{FALSE}, the result is created as a new server-side object; +#' if \code{TRUE}, the result is added as a new column in the existing data-frame. Default is \code{FALSE}. +#' @param newobj Character string for the name of the object that will be created on the server. Default is \code{"rounding.result"}. +#' +#' +#' @author Zulal Bekerecioglu +#' @return the created numeric vector or the updated dataframe with the added column +#' @export +#' +#' +roundDS <- function(x, type, digits, add.column, newobj) { + + # If x is NULL, throw and error. + if (is.null(x)) { + stop("Input object couldn't be found, please provide an object for rounding in the correct format. + For vectors, supply an existing object name; for columns, use the format dataframe$column, + where 'dataframe' is the name of the data frame and 'column' is the column name, + and ensure that both exist.", call. = FALSE) + } + + add.column <- as.logical(add.column) + + # Check if object is a column (contains $), if it is then save the dataframe name for later use if necessary + if(grepl("\\$", x)) { + is_column <- TRUE + dataframe_name <- strsplit(x, "\\$")[[1]][1] + column_name <- strsplit(x, "\\$")[[1]][2] + } else { + is_column <- FALSE + } + + + if(!is.null(x)&&!(is_column)) + { + object <- get(x) + + } else if(!is.null(x)&&is_column){ + df <- get(dataframe_name) + object <- df[[column_name]] + } + + result <- switch(type, + round = round(object, digits = digits), + ceiling = ceiling(object), + floor = floor(object), + trunc = trunc(object), + signif = signif(object, digits = digits)) + + if(!(is_column)){ # if the object was a numerical vector, save the result in a new object + return(result) + } else if((is_column)&&!add.column){ # if the object was a column and add.column is FALSE, save the result in a new object + return(result) + } else if((is_column)&&add.column){ # if the object was a column and add.column is TRUE, save the result as a column + df[[newobj]] <- result + return(df) + } + +} diff --git a/R/scaleDS.R b/R/scaleDS.R new file mode 100644 index 00000000..96cbd103 --- /dev/null +++ b/R/scaleDS.R @@ -0,0 +1,61 @@ +#' +#' @title scaleDS +#' @description Generates scaled objects using a server-side object, which can be either a vector or +#' a data-frame column. +#' +#' @details +#' Note: \code{add.column = TRUE} is only valid for data-frame inputs. +#' +#' +#' @param x Character string specifying the server-side vector For data-frame columns, use the format \code{df$column}. +#' @param newobj Character string for the name of the object that will be created on the server. Default is \code{"scaled.data"}. +#' @param add.column Logical. If \code{FALSE}, the result is created as a new server-side object; +#' if \code{TRUE}, the result is added as a new column in the existing data-frame. Default is \code{FALSE}. +#' +#' @author Zulal Bekerecioglu +#' @return the created numeric vector or the updated dataframe with the added column +#' @export +#' +#' +scaleDS <- function(x=NULL, newobj=NULL, add.column=NULL) { + + add.column <- as.logical(add.column) + + error_message <- "Input object couldn't found, please provide the correct format. For vectors, supply an existing object name; + for columns, use df$colname and ensure the dataframe and column exist." + + # If x is NULL, throw and error. + if (is.null(x)) { + stop(error_message, call. = FALSE) + } else { + is_dataframe <- grepl("\\$", x) + + if(is_dataframe) { + # Extract dataframe name + dataframe_name <- strsplit(x, "\\$")[[1]][1] + column_name <- strsplit(x, "\\$")[[1]][2] + + df <-get(dataframe_name) + } else { + + object <-get(x) + } + } + + + if(is_dataframe) { + result <- as.numeric(scale(df[[column_name]])) # scale the column + } else { + result <- as.numeric(scale(object)) # scale the vector + } + + # Return the dataframe with the added column, or the new object. + if(is_dataframe&&add.column) { + df[[newobj]] <- result + return(df) + } else { + return(result) + } + + +} diff --git a/R/standardiseDfDS.R b/R/standardiseDfDS.R new file mode 100644 index 00000000..35e15e6e --- /dev/null +++ b/R/standardiseDfDS.R @@ -0,0 +1,88 @@ +#' Get the Class of All Columns in a Data Frame +#' @param df.name A string representing the name of the data frame. +#' @return A tibble with the class of each column in the data frame. +#' @importFrom dplyr %>% +#' @importFrom tibble as_tibble +#' @importFrom purrr map +#' @export +getClassAllColsDS <- function(df.name){ + df.name <- eval(parse(text = df.name), envir = parent.frame()) + all_classes <- map(df.name, class) %>% as_tibble() + return(all_classes) +} + +#' Change Class of Target Variables in a Data Frame +#' @param df.name A string representing the name of the data frame. +#' @param target_vars A character vector specifying the columns to be modified. +#' @param target_class A character vector specifying the new classes for each column (1 = factor, +#' 2 = integer, 3 = numeric, 4 = character, 5 = logical). +#' @return A modified data frame with the specified columns converted to the target classes. +#' @importFrom dplyr mutate across +#' @importFrom tidyselect all_of +#' @export +fixClassDS <- function(df.name, target_vars, target_class) { + df <- eval(parse(text = df.name), envir = parent.frame()) + df_transformed <- df %>% + mutate( + across(all_of(target_vars), + ~ .convertClass(.x, target_class[which(target_vars == cur_column())]))) + return(df_transformed) +} + +#' Convert a Vector to a Specified Class +#' @param x The vector to be converted. +#' @param class_name A string indicating the target class (1 = factor, 2 = integer, 3 = numeric, +#' 4 = character, 5 = logical). +#' @return The converted vector. +#' @noRd +.convertClass <- function(target_var, target_class_code) { + switch(target_class_code, + "1" = as.factor(target_var), + "2" = as.integer(target_var), + "3" = as.numeric(target_var), + "4" = as.character(target_var), + "5" = as.logical(target_var) + ) +} + +#' Add Missing Columns with NA Values +#' @param .data A string representing the name of the data frame. +#' @param cols A character vector specifying the columns to be added if missing. +#' @return A modified data frame with missing columns added and filled with NA. +#' @importFrom dplyr mutate select +#' @importFrom tidyselect peek_vars +#' @importFrom purrr set_names +#' @export +fixColsDS <- function(.data, cols) { + .data <- eval(parse(text = .data), envir = parent.frame()) + missing <- setdiff(cols, colnames(.data)) + out <- .data %>% + mutate(!!!set_names(rep(list(NA), length(missing)), missing)) %>% + select(sort(peek_vars())) + return(out) +} + +#' Retrieve Factor Levels for Specific Columns +#' @param df.name A string representing the name of the data frame. +#' @param factor_vars A character vector specifying the factor columns. +#' @return A list of factor levels for the specified columns. +#' @importFrom tidyselect all_of +#' @importFrom purrr map +#' @export +getAllLevelsDS <- function(df.name, factor_vars) { + df <- eval(parse(text = df.name), envir = parent.frame()) + return(df %>% dplyr::select(all_of(factor_vars)) %>% map(levels)) +} + + +#' Set Factor Levels for Specific Columns in a Data Frame +#' @param df.name A string representing the name of the data frame to modify. +#' @param vars A character vector specifying the columns to be modified. +#' @param levels A named list where each element contains the levels for the corresponding factor variable. +#' @return A modified data frame with the specified columns converted to factors with the provided levels. +#' @export +fixLevelsDS <- function(df.name, vars, levels) { + df.name <- eval(parse(text = df.name), envir = parent.frame()) + out <- df.name %>% + mutate(across(all_of(vars), ~factor(., levels = levels[[dplyr::cur_column()]]))) +} diff --git a/R/subsetByClassHelper1.R b/R/subsetByClassHelper1.R deleted file mode 100644 index 7c288da3..00000000 --- a/R/subsetByClassHelper1.R +++ /dev/null @@ -1,41 +0,0 @@ -#' -#' @title generates subsets vectors from a factor vector -#' @description This is an internal function called by the function 'subsetByClassDS'. -#' @details The function generates subsets if the input of 'subsetByClassDS' is a factor vector. -#' @param xvect a vector of type factor. -#' @param xname the name of the vector. -#' @param filter the minimum number observation (i.e. rows) that are allowed. -#' @return a list which contains the subsets. -#' @keywords internal -#' @noRd -#' @author Gaye, A. -#' -subsetByClassHelper1 <- function(xvect=NULL, xname=NULL, filter=NULL){ - vectname <- xname - subsets <- list() - names.of.subsets <- c() - categories <- levels(xvect) - for(i in 1:length(categories)){ - indices <- which(xvect == as.numeric(categories[i])) - if(!(length(indices) < filter)){ - subsets[[i]] <- xvect[indices] - name.of.subD <- paste(vectname,".level_", categories[i], sep="") - names.of.subsets <- append(names.of.subsets, name.of.subD) - }else{ - # if any one category has between 0 and 'filter' observation turn subset content into missing values - if(length(indices) == 0){ - subsets[[i]] <- xvect[-c(1:length(xvect))] - name.of.subD <- paste(vectname,".level_", categories[i], "_EMPTY", sep="") - }else{ - temp1 <- xvect[indices] - temp1[1:length(temp1)] <- NA - subsets[[i]] <- temp1 - name.of.subD <- paste(vectname,".level_", categories[i], "_INVALID", sep="") - } - names.of.subsets <- append(names.of.subsets, name.of.subD) - } - names(subsets) <- names.of.subsets - output <- subsets - } - return(output) -} diff --git a/R/subsetByClassHelper2.R b/R/subsetByClassHelper2.R deleted file mode 100644 index f59cc907..00000000 --- a/R/subsetByClassHelper2.R +++ /dev/null @@ -1,64 +0,0 @@ -#' -#' @title generates subset tables from a data frame -#' @description This is an internal function called by the function 'subsetByClassDS' -#' @details The function generates subsets if the input of 'subsetByClassDS' is a data frame -#' and if the number variables(columns) to subset by are greater than 1; i.e. this -#' function is called if the user specified more than one variable or no variable to subset by -#' (if no variables are specified the function 'subsetByClassDS' produces a subset for each category -#' in each variable). -#' @param df a data frame. -#' @param iter the indices of columns to loop trough. -#' @param filter the minimum number of observations (i.e. rows) that are allowed. -#' @return a list which contains the subsets, their names and an integer that indicates how many columns were -#' not factors. -#' @keywords internal -#' @noRd -#' @author Gaye, A. -#' -subsetByClassHelper2 <- function(df=NULL, iter=NULL, filter=NULL){ - # various counters and temporary variables to hold info - subsets <- list() - names.of.subsets <- c() - count <- 0 - nonfactorvars <- 0 - ncols <- length(colnames(df)) - for(i in iter){ - var <- df[,i] - varname <- colnames(df)[i] - if(is.factor(var)){ - # get the levels - categories <- levels(var) - # loop through the levels and generate a dataset for each level - # if the number of observations for that level > 0 and < 'filter' - for(j in 1:length(categories)){ - indices <- which(var == as.numeric(categories[j])) - if(!(length(indices) < filter)){ - count <- count+1 - subD <- df[indices,] - subsets[[count]] <- subD - name.of.subD <- paste(varname,".level_", categories[j], sep="") - names.of.subsets <- append(names.of.subsets, name.of.subD) - }else{ - # if any one category has between 1 and 'filter' number of observation turn subset content into missing values - count <- count+1 - if(length(indices) == 0){ - subsets[[count]] <- df[-c(1:dim(df)[1]),] - name.of.subD <- paste(varname,".level_", categories[j], "_EMPTY",sep="") - }else{ - subD <- df[indices,] - subD[] <- NA - subsets[[count]] <- subD - name.of.subD <- paste(varname,".level_", categories[j], "_INVALID",sep="") - } - colnames(subsets[[count]]) <- colnames(df) - names.of.subsets <- append(names.of.subsets, name.of.subD) - } - } - names(subsets) <- names.of.subsets - }else{ - # if a variable is not a factor increment the below counter - nonfactorvars <- nonfactorvars + 1 - } - } - return(list(subsets, nonfactorvars)) -} \ No newline at end of file diff --git a/R/subsetByClassHelper3.R b/R/subsetByClassHelper3.R deleted file mode 100644 index de401f62..00000000 --- a/R/subsetByClassHelper3.R +++ /dev/null @@ -1,59 +0,0 @@ -#' -#' @title generates subset tables from a data frame -#' @description This is an internal function called by the function 'subsetByClassDS' -#' @details The function generates subsets if the input of 'subsetByClassDS' is a data frame -#' and if the number of variables (columns) to subset by is 1; i.e. this -#' function is called if the user specified one variable to subset by. -#' @param df a data frame. -#' @param indx1 the column index of the variable specified by the user. -#' @param filter the minimum number of observations (i.e. rows) that are allowed. -#' @return a list which contains the subsets, their names and an integer that indicates if -#' the variable specified by user is a factor. -#' @keywords internal -#' @noRd -#' @author Gaye, A. -#' -subsetByClassHelper3 <- function(df=NULL, indx1=NULL, filter=NULL){ - # various counters and temporary variables to hold info - subsets <- list() - names.of.subsets <- c() - count <- 0 - nonfactorvars <- 0 - ncols <- length(colnames(df)) - var <- df[,indx1] - varname <- colnames(df)[indx1] - if(is.factor(var)){ - # get the levels - categories <- levels(var) - # loop through the levels and generate a dataset for each level - # if the number of observations for that level > 0 and < 'filter' - for(j in 1:length(categories)){ - indices <- which(var == as.numeric(categories[j])) - if(!(length(indices) < filter)){ - count <- count+1 - subD <- df[indices,] - subsets[[count]] <- subD - name.of.subD <- paste(varname,".level_", categories[j], sep="") - names.of.subsets <- append(names.of.subsets, name.of.subD) - }else{ - # if any one category has between 1 and 'filter' number of observations turn subset content into missing values - count <- count+1 - if(length(indices) == 0){ - subsets[[count]] <- df[-c(1:dim(df)[1]),] - name.of.subD <- paste(varname,".level_", categories[j], "_EMPTY",sep="") - }else{ - subD <- df[indices,] - subD[] <- NA - subsets[[count]] <- subD - name.of.subD <- paste(varname,".level_", categories[j], "_INVALID",sep="") - } - colnames(subsets[[count]]) <- colnames(df) - names.of.subsets <- append(names.of.subsets, name.of.subD) - } - } - names(subsets) <- names.of.subsets - }else{ - nonfactorvars <- 1 - } - return(list(subsets, nonfactorvars)) -} \ No newline at end of file diff --git a/R/tableDS.R b/R/tableDS.R index c190ffc3..cf636c02 100644 --- a/R/tableDS.R +++ b/R/tableDS.R @@ -1,3 +1,4 @@ +#' #' @title tableDS is the first of two serverside aggregate functions #' called by ds.table #' @description creates 1-dimensional, 2-dimensional and 3-dimensional @@ -34,153 +35,118 @@ #' @return For information see help for \code{ds.table} #' @author Paul Burton for DataSHIELD Development Team, 13/11/2019 #' @export -tableDS<-function(rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, - stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit, force.nfilter.transmit){ - - -######################################################################### -# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS # -thr<-dsBase::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) # -#nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) # -#nfilter.kNN<-as.numeric(thr$nfilter.kNN) # -#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) # -######################################################################### - -#Force higher value of nfilter - - -if(!is.null(force.nfilter.transmit)) -{ -force.nfilter.active<-eval(parse(text=force.nfilter.transmit), envir = parent.frame()) - - if(force.nfilter.active= to nfilter.tab i.e.",nfilter.tab) - stop(return.message, call. = FALSE) - } -} -else -{ -force.nfilter.active<-NULL -} - -if(!is.null(force.nfilter.active)&&!is.na(force.nfilter.active)&&force.nfilter.active>nfilter.tab) -{ -nfilter.tab<-force.nfilter.active -} - +#' +tableDS <- function(rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, + cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, + useNA.transmit, force.nfilter.transmit){ + + # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS + thr <- dsBase::listDisclosureSettingsDS() + nfilter.tab <- as.numeric(thr$nfilter.tab) + + # Force higher value of nfilter + if(!is.null(force.nfilter.transmit)){ + force.nfilter.active <- eval(parse(text=force.nfilter.transmit), envir = parent.frame()) + if(force.nfilter.active < nfilter.tab){ + return.message <- paste0("Failed: if force.nfilter is non-null it must be >= to nfilter.tab i.e.", + nfilter.tab) + stop(return.message, call. = FALSE) + } + }else{ + force.nfilter.active <- NULL + } + if(!is.null(force.nfilter.active) && !is.na(force.nfilter.active) && force.nfilter.active>nfilter.tab){ + nfilter.tab <- force.nfilter.active + } -#Activate via eval when needed -#rvar - rvar<-eval(parse(text=rvar.transmit), envir = parent.frame()) - if(!is.factor(rvar)) - { - rvar.all.unique.levels <- unlist(strsplit(rvar.all.unique.levels.transmit,split=",")) - rvar<-factor(as.factor(rvar), levels=rvar.all.unique.levels) + # Activate via eval when needed + + # rvar + rvar <- eval(parse(text=rvar.transmit), envir = parent.frame()) + if(!is.factor(rvar)){ + rvar.all.unique.levels <- unlist(strsplit(rvar.all.unique.levels.transmit, split=",")) + rvar <- factor(as.factor(rvar), levels=rvar.all.unique.levels) }else{ - rvar.all.unique.levels <- unlist(strsplit(rvar.all.unique.levels.transmit,split=",")) - rvar<-factor(rvar, levels=rvar.all.unique.levels) + rvar.all.unique.levels <- unlist(strsplit(rvar.all.unique.levels.transmit, split=",")) + rvar <- factor(rvar, levels=rvar.all.unique.levels) } -#cvar - if(!is.null(cvar.transmit)) -{ - cvar<-eval(parse(text=cvar.transmit), envir = parent.frame()) - if(!is.factor(cvar)) - { + + # cvar + if(!is.null(cvar.transmit)){ + cvar <- eval(parse(text=cvar.transmit), envir = parent.frame()) + if(!is.factor(cvar)){ cvar.all.unique.levels <- unlist(strsplit(cvar.all.unique.levels.transmit,split=",")) - cvar<-factor(as.factor(cvar), levels=cvar.all.unique.levels) + cvar <- factor(as.factor(cvar), levels=cvar.all.unique.levels) }else{ cvar.all.unique.levels <- unlist(strsplit(cvar.all.unique.levels.transmit,split=",")) - cvar<-factor(cvar, levels=cvar.all.unique.levels) + cvar <- factor(cvar, levels=cvar.all.unique.levels) } - -} -else -{ -cvar<-NULL -} -#stvar -if(!is.null(stvar.transmit)) -{ - stvar<-eval(parse(text=stvar.transmit), envir = parent.frame()) - if(!is.factor(stvar)) - { - stvar.all.unique.levels<- unlist(strsplit(stvar.all.unique.levels.transmit,split=",")) - stvar<-factor(as.factor(stvar), levels=stvar.all.unique.levels) }else{ - stvar.all.unique.levels<- unlist(strsplit(stvar.all.unique.levels.transmit,split=",")) - stvar<-factor(stvar, levels=stvar.all.unique.levels) + cvar <- NULL + } + + # stvar + if(!is.null(stvar.transmit)){ + stvar <- eval(parse(text=stvar.transmit), envir = parent.frame()) + if(!is.factor(stvar)){ + stvar.all.unique.levels <- unlist(strsplit(stvar.all.unique.levels.transmit,split=",")) + stvar <- factor(as.factor(stvar), levels=stvar.all.unique.levels) + }else{ + stvar.all.unique.levels <- unlist(strsplit(stvar.all.unique.levels.transmit,split=",")) + stvar <- factor(stvar, levels=stvar.all.unique.levels) + } + }else{ + stvar <- NULL } -} -else -{ -stvar<-NULL -} - -#exclude -if(!is.null(exclude.transmit)) -{ -exclude.text<-strsplit(exclude.transmit, split=",") -exclude<-eval(parse(text=exclude.text), envir = parent.frame()) -} -else -{ -exclude<-NULL -} - -if(!is.null(rvar)&&!is.null(cvar)&&!is.null(stvar)) -{ -#Check cell counts valid without NAs or NaNs -counts.valid<-TRUE -test.outobj<-table(rvar,cvar,stvar,exclude="NaN",useNA="no") - -numcells<-length(test.outobj) - for (cell in 1:numcells) - { - if(test.outobj[cell]>0&&test.outobj[cell]0 && test.outobj[cell]0&&test.outobj[cell]0 && test.outobj[cell] dsBase - 6.3.5.9000 + 6.4.0.9000 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 5faa2d0e..f1cadf0d 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBase - 6.3.5.9000 + 6.4.0.9000 diff --git a/docs/authors.html b/docs/authors.html index a1aec549..dc54dd5e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev @@ -102,12 +106,20 @@

Citation

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. +<<<<<<< HEAD +R package version 6.4.0.9000. +======= R package version 6.3.5.9000. +>>>>>>> origin/v6.3.5-dev 

@Manual{,
   title = {dsBase: 'DataSHIELD' Server Side Base Functions},
   author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
+<<<<<<< HEAD
+  note = {R package version 6.4.0.9000},
+=======
   note = {R package version 6.3.5.9000},
+>>>>>>> origin/v6.3.5-dev
 }

Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” diff --git a/docs/index.html b/docs/index.html index 1f70741d..41bcede1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c3eb19af..6f09758f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,4 +2,8 @@ pandoc: 3.1.3 pkgdown: 2.2.0 pkgdown_sha: ~ articles: {} +<<<<<<< HEAD +last_built: 2025-11-28T12:54Z +======= last_built: 2025-11-30T16:44Z +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/BooleDS.html b/docs/reference/BooleDS.html index 7cecbed2..d5f322aa 100644 --- a/docs/reference/BooleDS.html +++ b/docs/reference/BooleDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/absDS.html b/docs/reference/absDS.html index ca83bf9d..fc172e34 100644 --- a/docs/reference/absDS.html +++ b/docs/reference/absDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/asCharacterDS.html b/docs/reference/asCharacterDS.html index 8f461038..40f94a04 100644 --- a/docs/reference/asCharacterDS.html +++ b/docs/reference/asCharacterDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/asDataFrameDS.html b/docs/reference/asDataFrameDS.html new file mode 100644 index 00000000..21529f3b --- /dev/null +++ b/docs/reference/asDataFrameDS.html @@ -0,0 +1,101 @@ + +asDataFrameDS a serverside assign function called by ds.asDataFrame — asDataFrameDS • dsBase + + +

+
+ + + +
+
+
+

asDataFrameDS a serverside assign function called by ds.asDataFrame

+ + +
+ +
+

Coerces an R object into a matrix maintaining original +class for all columns in data.frames.

+
+ +
+ 
asDataFrameDS(x.name)
+
+ +
+

Arguments

+ + +
x.name
+

the name of the input object to be coerced to class +data.frame. Must be specified in inverted commas. But this argument is +usually specified directly by <x.name> argument of the clientside function +ds.asDataFrame

+ +
+
+

Value

+

the object specified by the <newobj> argument (or its default name +"asdataframe.newobj") which is written to the serverside. For further +details see help on the clientside function ds.asDataMatrix

+
+
+

Details

+

This assign function is based on the native R function data.frame

+
+
+

Author

+

Tim Cadman

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.0.

+
+ +
+ + + + + + + + diff --git a/docs/reference/asDataMatrixDS.html b/docs/reference/asDataMatrixDS.html index 2b8fb1d3..a3a54d0c 100644 --- a/docs/reference/asDataMatrixDS.html +++ b/docs/reference/asDataMatrixDS.html @@ -1,5 +1,9 @@ +<<<<<<< HEAD +asDataFrameDS a serverside assign function called by ds.asDataFrame — asDataMatrixDS • dsBaseasDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS • dsBasecheckPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel • dsBasecheckPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel • dsBase @@ -17,7 +21,15 @@ dsBase +<<<<<<< HEAD +<<<<<<< HEAD + 6.4.0-9000 +======= + 6.3.4 +>>>>>>> origin/v6.3.5-dev +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/classDS.html b/docs/reference/classDS.html index 47976968..5a0fab58 100644 --- a/docs/reference/classDS.html +++ b/docs/reference/classDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/colnamesDS.html b/docs/reference/colnamesDS.html index 4282c514..d1e770d4 100644 --- a/docs/reference/colnamesDS.html +++ b/docs/reference/colnamesDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/completeCasesDS.html b/docs/reference/completeCasesDS.html index d84a6ede..af9b8d44 100644 --- a/docs/reference/completeCasesDS.html +++ b/docs/reference/completeCasesDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/corDS.html b/docs/reference/corDS.html index a1972b2c..b4fb7229 100644 --- a/docs/reference/corDS.html +++ b/docs/reference/corDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/corTestDS.html b/docs/reference/corTestDS.html index 40678688..2ead0203 100644 --- a/docs/reference/corTestDS.html +++ b/docs/reference/corTestDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/covDS.html b/docs/reference/covDS.html index b92bbd44..bfc552fb 100644 --- a/docs/reference/covDS.html +++ b/docs/reference/covDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dataFrameDS.html b/docs/reference/dataFrameDS.html index 8791fbbe..50ae4fac 100644 --- a/docs/reference/dataFrameDS.html +++ b/docs/reference/dataFrameDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dataFrameFillDS.html b/docs/reference/dataFrameFillDS.html index 6114470e..3e6098c1 100644 --- a/docs/reference/dataFrameFillDS.html +++ b/docs/reference/dataFrameFillDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dataFrameSortDS.html b/docs/reference/dataFrameSortDS.html index d8e8cd13..d4395261 100644 --- a/docs/reference/dataFrameSortDS.html +++ b/docs/reference/dataFrameSortDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dataFrameSubsetDS1.html b/docs/reference/dataFrameSubsetDS1.html index 98c1bb41..1210c05c 100644 --- a/docs/reference/dataFrameSubsetDS1.html +++ b/docs/reference/dataFrameSubsetDS1.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dataFrameSubsetDS2.html b/docs/reference/dataFrameSubsetDS2.html index 91a1413e..5e41ee7e 100644 --- a/docs/reference/dataFrameSubsetDS2.html +++ b/docs/reference/dataFrameSubsetDS2.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/densityGridDS.html b/docs/reference/densityGridDS.html index b84830f0..823b1bc2 100644 --- a/docs/reference/densityGridDS.html +++ b/docs/reference/densityGridDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dimDS.html b/docs/reference/dimDS.html index 36ae7dbf..92e4c87f 100644 --- a/docs/reference/dimDS.html +++ b/docs/reference/dimDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dmtC2SDS.html b/docs/reference/dmtC2SDS.html index e5bce26b..0a8f128d 100644 --- a/docs/reference/dmtC2SDS.html +++ b/docs/reference/dmtC2SDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/dsBase-package.html b/docs/reference/dsBase-package.html index 36aa5804..7270ec16 100644 --- a/docs/reference/dsBase-package.html +++ b/docs/reference/dsBase-package.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/elsplineDS.html b/docs/reference/elsplineDS.html index 699ad119..4b5e028f 100644 --- a/docs/reference/elsplineDS.html +++ b/docs/reference/elsplineDS.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/extract.html b/docs/reference/extract.html index 2626fec8..4d91f651 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.3 +>>>>>>> origin/v6.3.3-dev diff --git a/docs/reference/extractQuantilesDS1.html b/docs/reference/extractQuantilesDS1.html index 8db3348b..96214bba 100644 --- a/docs/reference/extractQuantilesDS1.html +++ b/docs/reference/extractQuantilesDS1.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/extractQuantilesDS2.html b/docs/reference/extractQuantilesDS2.html index ab0bab81..3dc4bcbe 100644 --- a/docs/reference/extractQuantilesDS2.html +++ b/docs/reference/extractQuantilesDS2.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/subsetByClassHelper3.html b/docs/reference/fixClassDS.html similarity index 61% rename from docs/reference/subsetByClassHelper3.html rename to docs/reference/fixClassDS.html index 46aea1ab..82687799 100644 --- a/docs/reference/subsetByClassHelper3.html +++ b/docs/reference/fixClassDS.html @@ -1,5 +1,5 @@ -generates subset tables from a data frame — subsetByClassHelper3 • dsBaseChange Class of Target Variables in a Data Frame — fixClassDS • dsBase @@ -17,7 +17,7 @@ dsBase - 6.3.3 + 6.4.0.9000 @@ -34,49 +34,39 @@
-

generates subset tables from a data frame

+

Change Class of Target Variables in a Data Frame

- +
-

This is an internal function called by the function 'subsetByClassDS'

+

Change Class of Target Variables in a Data Frame

- 
subsetByClassHelper3(df = NULL, indx1 = NULL, filter = NULL)
+ 
fixClassDS(df.name, target_vars, target_class)

Arguments

-
df
-

a data frame.

+
df.name
+

A string representing the name of the data frame.

-
indx1
-

the column index of the variable specified by the user.

+
target_vars
+

A character vector specifying the columns to be modified.

-
filter
-

the minimum number of observations (i.e. rows) that are allowed.

+
target_class
+

A character vector specifying the new classes for each column (1 = factor, +2 = integer, 3 = numeric, 4 = character, 5 = logical).

Value

-

a list which contains the subsets, their names and an integer that indicates if -the variable specified by user is a factor.

-
-
-

Details

-

The function generates subsets if the input of 'subsetByClassDS' is a data frame -and if the number of variables (columns) to subset by is 1; i.e. this -function is called if the user specified one variable to subset by.

-
-
-

Author

-

Gaye, A.

+

A modified data frame with the specified columns converted to the target classes.

@@ -87,11 +77,11 @@

Author

-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/fixColsDS.html b/docs/reference/fixColsDS.html new file mode 100644 index 00000000..7a294694 --- /dev/null +++ b/docs/reference/fixColsDS.html @@ -0,0 +1,90 @@ + +Add Missing Columns with NA Values — fixColsDS • dsBase + + +
+
+ + + +
+
+
+

Add Missing Columns with NA Values

+ + +
+ +
+

Add Missing Columns with NA Values

+
+ +
+ 
fixColsDS(.data, cols)
+
+ +
+

Arguments

+ + +
.data
+

A string representing the name of the data frame.

+ + +
cols
+

A character vector specifying the columns to be added if missing.

+ +
+
+

Value

+

A modified data frame with missing columns added and filled with NA.

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.0.

+
+ +
+ + + + + + + + diff --git a/docs/reference/fixLevelsDS.html b/docs/reference/fixLevelsDS.html new file mode 100644 index 00000000..30820d2f --- /dev/null +++ b/docs/reference/fixLevelsDS.html @@ -0,0 +1,94 @@ + +Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS • dsBase + + +
+
+ + + +
+
+
+

Set Factor Levels for Specific Columns in a Data Frame

+ + +
+ +
+

Set Factor Levels for Specific Columns in a Data Frame

+
+ +
+ 
fixLevelsDS(df.name, vars, levels)
+
+ +
+

Arguments

+ + +
df.name
+

A string representing the name of the data frame to modify.

+ + +
vars
+

A character vector specifying the columns to be modified.

+ + +
levels
+

A named list where each element contains the levels for the corresponding factor variable.

+ +
+
+

Value

+

A modified data frame with the specified columns converted to factors with the provided levels.

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.0.

+
+ +
+ + + + + + + + diff --git a/docs/reference/gamlssDS.html b/docs/reference/gamlssDS.html index fc7898fe..87c1c2ec 100644 --- a/docs/reference/gamlssDS.html +++ b/docs/reference/gamlssDS.html @@ -23,7 +23,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/getAllLevelsDS.html b/docs/reference/getAllLevelsDS.html new file mode 100644 index 00000000..b02c140d --- /dev/null +++ b/docs/reference/getAllLevelsDS.html @@ -0,0 +1,90 @@ + +Retrieve Factor Levels for Specific Columns — getAllLevelsDS • dsBase + + +
+
+ + + +
+
+
+

Retrieve Factor Levels for Specific Columns

+ + +
+ +
+

Retrieve Factor Levels for Specific Columns

+
+ +
+ 
getAllLevelsDS(df.name, factor_vars)
+
+ +
+

Arguments

+ + +
df.name
+

A string representing the name of the data frame.

+ + +
factor_vars
+

A character vector specifying the factor columns.

+ +
+
+

Value

+

A list of factor levels for the specified columns.

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.0.

+
+ +
+ + + + + + + + diff --git a/docs/reference/getClassAllColsDS.html b/docs/reference/getClassAllColsDS.html new file mode 100644 index 00000000..0f95926f --- /dev/null +++ b/docs/reference/getClassAllColsDS.html @@ -0,0 +1,86 @@ + +Get the Class of All Columns in a Data Frame — getClassAllColsDS • dsBase + + +
+
+ + + +
+
+
+

Get the Class of All Columns in a Data Frame

+ + +
+ +
+

Get the Class of All Columns in a Data Frame

+
+ +
+ 
getClassAllColsDS(df.name)
+
+ +
+

Arguments

+ + +
df.name
+

A string representing the name of the data frame.

+ +
+
+

Value

+

A tibble with the class of each column in the data frame.

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.0.

+
+ +
+ + + + + + + + diff --git a/docs/reference/getWGSRDS.html b/docs/reference/getWGSRDS.html index 7ed44dbb..bc8addbf 100644 --- a/docs/reference/getWGSRDS.html +++ b/docs/reference/getWGSRDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmDS1.html b/docs/reference/glmDS1.html index ecd2010f..b679c6e0 100644 --- a/docs/reference/glmDS1.html +++ b/docs/reference/glmDS1.html @@ -1,5 +1,9 @@ +<<<<<<< HEAD +glmDS1 called by ds.glm — glmDS1 • dsBaseglmDS1 called by ds.glm — glmDS1 • dsBase @@ -17,7 +21,15 @@ dsBase +<<<<<<< HEAD +<<<<<<< HEAD + 6.4.0-9000 +======= + 6.3.4 +>>>>>>> origin/v6.3.5-dev +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmDS2.html b/docs/reference/glmDS2.html index 03731c72..6ebc1453 100644 --- a/docs/reference/glmDS2.html +++ b/docs/reference/glmDS2.html @@ -1,5 +1,9 @@ +<<<<<<< HEAD +glmDS2 called by ds.glm — glmDS2 • dsBaseglmDS2 called by ds.glm — glmDS2 • dsBase @@ -17,7 +21,15 @@ dsBase +<<<<<<< HEAD +<<<<<<< HEAD + 6.4.0-9000 +======= + 6.3.4 +>>>>>>> origin/v6.3.5-dev +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmPredictDS.ag.html b/docs/reference/glmPredictDS.ag.html index 8d31da48..a3fa4124 100644 --- a/docs/reference/glmPredictDS.ag.html +++ b/docs/reference/glmPredictDS.ag.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmPredictDS.as.html b/docs/reference/glmPredictDS.as.html index 62461b0b..2ba9f101 100644 --- a/docs/reference/glmPredictDS.as.html +++ b/docs/reference/glmPredictDS.as.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmSLMADS.assign.html b/docs/reference/glmSLMADS.assign.html index 7a63760d..6eb9263c 100644 --- a/docs/reference/glmSLMADS.assign.html +++ b/docs/reference/glmSLMADS.assign.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmSLMADS1.html b/docs/reference/glmSLMADS1.html index a4d8badd..5f31583e 100644 --- a/docs/reference/glmSLMADS1.html +++ b/docs/reference/glmSLMADS1.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmSLMADS2.html b/docs/reference/glmSLMADS2.html index b50e51c9..517c0e88 100644 --- a/docs/reference/glmSLMADS2.html +++ b/docs/reference/glmSLMADS2.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmSummaryDS.ag.html b/docs/reference/glmSummaryDS.ag.html index e0f2239e..23900009 100644 --- a/docs/reference/glmSummaryDS.ag.html +++ b/docs/reference/glmSummaryDS.ag.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmSummaryDS.as.html b/docs/reference/glmSummaryDS.as.html index ca99af8e..560f1c9e 100644 --- a/docs/reference/glmSummaryDS.as.html +++ b/docs/reference/glmSummaryDS.as.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmerSLMADS.assign.html b/docs/reference/glmerSLMADS.assign.html index 983b845e..1bc06981 100644 --- a/docs/reference/glmerSLMADS.assign.html +++ b/docs/reference/glmerSLMADS.assign.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/glmerSLMADS2.html b/docs/reference/glmerSLMADS2.html index d1c2c9c2..29b69c56 100644 --- a/docs/reference/glmerSLMADS2.html +++ b/docs/reference/glmerSLMADS2.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/heatmapPlotDS.html b/docs/reference/heatmapPlotDS.html index 7c0acfa9..6d0d668b 100644 --- a/docs/reference/heatmapPlotDS.html +++ b/docs/reference/heatmapPlotDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/hetcorDS.html b/docs/reference/hetcorDS.html index f080e55c..4eaa70ca 100644 --- a/docs/reference/hetcorDS.html +++ b/docs/reference/hetcorDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/histogramDS1.html b/docs/reference/histogramDS1.html index 3d90be9e..e4a874f9 100644 --- a/docs/reference/histogramDS1.html +++ b/docs/reference/histogramDS1.html @@ -23,7 +23,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/histogramDS2.html b/docs/reference/histogramDS2.html index 21f77287..3aa9fc39 100644 --- a/docs/reference/histogramDS2.html +++ b/docs/reference/histogramDS2.html @@ -21,7 +21,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/igb_standardsDS.html b/docs/reference/igb_standardsDS.html index 56a62b4a..25725319 100644 --- a/docs/reference/igb_standardsDS.html +++ b/docs/reference/igb_standardsDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/index.html b/docs/reference/index.html index ce6e0a97..b1f06f78 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev @@ -53,10 +57,14 @@

All functions asCharacterDS()

Coerces an R object into class character

+ +

asDataFrameDS()

+ +

asDataFrameDS a serverside assign function called by ds.asDataFrame

asDataMatrixDS()

-

asDataMatrixDS a serverside assign function called by ds.asDataMatrix

+

asDataFrameDS a serverside assign function called by ds.asDataFrame

asFactorDS1()

@@ -205,10 +213,30 @@

All functions extractQuantilesDS2()

Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies

+ +

fixClassDS()

+ +

Change Class of Target Variables in a Data Frame

+ +

fixColsDS()

+ +

Add Missing Columns with NA Values

+ +

fixLevelsDS()

+ +

Set Factor Levels for Specific Columns in a Data Frame

gamlssDS()

gamlssDS an aggregate function called by ds.gamlss

+ +

getAllLevelsDS()

+ +

Retrieve Factor Levels for Specific Columns

+ +

getClassAllColsDS()

+ +

Get the Class of All Columns in a Data Frame

getWGSRDS()

diff --git a/docs/reference/isNaDS.html b/docs/reference/isNaDS.html index 60110a6c..1a66df1a 100644 --- a/docs/reference/isNaDS.html +++ b/docs/reference/isNaDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/isValidDS.html b/docs/reference/isValidDS.html index 453aa84d..c02ede88 100644 --- a/docs/reference/isValidDS.html +++ b/docs/reference/isValidDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/kurtosisDS1.html b/docs/reference/kurtosisDS1.html index 6c942ba4..04665d0e 100644 --- a/docs/reference/kurtosisDS1.html +++ b/docs/reference/kurtosisDS1.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/kurtosisDS2.html b/docs/reference/kurtosisDS2.html index a3be6590..69e52f40 100644 --- a/docs/reference/kurtosisDS2.html +++ b/docs/reference/kurtosisDS2.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lengthDS.html b/docs/reference/lengthDS.html index 550e337b..6f5e9d66 100644 --- a/docs/reference/lengthDS.html +++ b/docs/reference/lengthDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/levelsDS.html b/docs/reference/levelsDS.html index 93bec9bb..bdc7da95 100644 --- a/docs/reference/levelsDS.html +++ b/docs/reference/levelsDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lexisDS1.html b/docs/reference/lexisDS1.html index d59e1378..8fec6e1c 100644 --- a/docs/reference/lexisDS1.html +++ b/docs/reference/lexisDS1.html @@ -1,5 +1,9 @@ +<<<<<<< HEAD +lexisDS1 — lexisDS1 • dsBaselexisDS1 — lexisDS1 • dsBase @@ -17,7 +21,15 @@ dsBase +<<<<<<< HEAD +<<<<<<< HEAD + 6.4.0-9000 +======= + 6.3.4 +>>>>>>> origin/v6.3.5-dev +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lexisDS2.html b/docs/reference/lexisDS2.html index 9e1e61a3..8b4802d9 100644 --- a/docs/reference/lexisDS2.html +++ b/docs/reference/lexisDS2.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lexisDS3.html b/docs/reference/lexisDS3.html index 97182f3d..e90963c5 100644 --- a/docs/reference/lexisDS3.html +++ b/docs/reference/lexisDS3.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/listDS.html b/docs/reference/listDS.html index 8e1f3729..aab15eb1 100644 --- a/docs/reference/listDS.html +++ b/docs/reference/listDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/listDisclosureSettingsDS.html b/docs/reference/listDisclosureSettingsDS.html index 37e561ee..6f051378 100644 --- a/docs/reference/listDisclosureSettingsDS.html +++ b/docs/reference/listDisclosureSettingsDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lmerSLMADS.assign.html b/docs/reference/lmerSLMADS.assign.html index 160ae781..a8c903db 100644 --- a/docs/reference/lmerSLMADS.assign.html +++ b/docs/reference/lmerSLMADS.assign.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lmerSLMADS2.html b/docs/reference/lmerSLMADS2.html index e34c8da9..f2201bd4 100644 --- a/docs/reference/lmerSLMADS2.html +++ b/docs/reference/lmerSLMADS2.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lsDS.html b/docs/reference/lsDS.html index 886204b6..0747857d 100644 --- a/docs/reference/lsDS.html +++ b/docs/reference/lsDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/lsplineDS.html b/docs/reference/lsplineDS.html index bced6894..03a511ea 100644 --- a/docs/reference/lsplineDS.html +++ b/docs/reference/lsplineDS.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixDS.html b/docs/reference/matrixDS.html index c095cf58..39e1cea8 100644 --- a/docs/reference/matrixDS.html +++ b/docs/reference/matrixDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixDetDS1.html b/docs/reference/matrixDetDS1.html index 1f6f482a..e1c28b77 100644 --- a/docs/reference/matrixDetDS1.html +++ b/docs/reference/matrixDetDS1.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixDetDS2.html b/docs/reference/matrixDetDS2.html index 85e2457e..8c0be8db 100644 --- a/docs/reference/matrixDetDS2.html +++ b/docs/reference/matrixDetDS2.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixDiagDS.html b/docs/reference/matrixDiagDS.html index 8939f343..ffe9cfa1 100644 --- a/docs/reference/matrixDiagDS.html +++ b/docs/reference/matrixDiagDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixDimnamesDS.html b/docs/reference/matrixDimnamesDS.html index bb2d6cfb..49ade78e 100644 --- a/docs/reference/matrixDimnamesDS.html +++ b/docs/reference/matrixDimnamesDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixInvertDS.html b/docs/reference/matrixInvertDS.html index 31bf8aee..f555d483 100644 --- a/docs/reference/matrixInvertDS.html +++ b/docs/reference/matrixInvertDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixMultDS.html b/docs/reference/matrixMultDS.html index 4a473555..2dc680b3 100644 --- a/docs/reference/matrixMultDS.html +++ b/docs/reference/matrixMultDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/matrixTransposeDS.html b/docs/reference/matrixTransposeDS.html index 2dc8d9a7..7f1abc24 100644 --- a/docs/reference/matrixTransposeDS.html +++ b/docs/reference/matrixTransposeDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/mdPatternDS.html b/docs/reference/mdPatternDS.html index 6ed7c777..d5469e97 100644 --- a/docs/reference/mdPatternDS.html +++ b/docs/reference/mdPatternDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/meanDS.html b/docs/reference/meanDS.html index 7806e4e4..c0123dc2 100644 --- a/docs/reference/meanDS.html +++ b/docs/reference/meanDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/meanSdGpDS.html b/docs/reference/meanSdGpDS.html index da49bc49..076528d1 100644 --- a/docs/reference/meanSdGpDS.html +++ b/docs/reference/meanSdGpDS.html @@ -1,5 +1,9 @@ +<<<<<<< HEAD +MeanSdGpDS — meanSdGpDS • dsBaseMeanSdGpDS — meanSdGpDS • dsBase @@ -17,7 +21,15 @@ dsBase +<<<<<<< HEAD +<<<<<<< HEAD + 6.4.0-9000 +======= + 6.3.4 +>>>>>>> origin/v6.3.5-dev +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/mergeDS.html b/docs/reference/mergeDS.html index 3687174e..55b7aa45 100644 --- a/docs/reference/mergeDS.html +++ b/docs/reference/mergeDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/messageDS.html b/docs/reference/messageDS.html index ec5f3f82..26e2dc2d 100644 --- a/docs/reference/messageDS.html +++ b/docs/reference/messageDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/metadataDS.html b/docs/reference/metadataDS.html index 83b97211..ac629de7 100644 --- a/docs/reference/metadataDS.html +++ b/docs/reference/metadataDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/miceDS.html b/docs/reference/miceDS.html index e8d36df9..e0244b84 100644 --- a/docs/reference/miceDS.html +++ b/docs/reference/miceDS.html @@ -23,7 +23,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/minMaxRandDS.html b/docs/reference/minMaxRandDS.html index 573110da..ca3d03d1 100644 --- a/docs/reference/minMaxRandDS.html +++ b/docs/reference/minMaxRandDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/namesDS.html b/docs/reference/namesDS.html index c7de77a6..6441b400 100644 --- a/docs/reference/namesDS.html +++ b/docs/reference/namesDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/nsDS.html b/docs/reference/nsDS.html index 7d74fa0b..39bfe0c6 100644 --- a/docs/reference/nsDS.html +++ b/docs/reference/nsDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/numNaDS.html b/docs/reference/numNaDS.html index 7599a247..ad021f9a 100644 --- a/docs/reference/numNaDS.html +++ b/docs/reference/numNaDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/qlsplineDS.html b/docs/reference/qlsplineDS.html index 5db49162..56969fb1 100644 --- a/docs/reference/qlsplineDS.html +++ b/docs/reference/qlsplineDS.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/quantileMeanDS.html b/docs/reference/quantileMeanDS.html index 741edf5f..0cdd525a 100644 --- a/docs/reference/quantileMeanDS.html +++ b/docs/reference/quantileMeanDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rBinomDS.html b/docs/reference/rBinomDS.html index fe27c36a..e29f7be7 100644 --- a/docs/reference/rBinomDS.html +++ b/docs/reference/rBinomDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rNormDS.html b/docs/reference/rNormDS.html index 8f07ac7f..b757e36e 100644 --- a/docs/reference/rNormDS.html +++ b/docs/reference/rNormDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rPoisDS.html b/docs/reference/rPoisDS.html index 5eae496f..d8ecfbcb 100644 --- a/docs/reference/rPoisDS.html +++ b/docs/reference/rPoisDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rUnifDS.html b/docs/reference/rUnifDS.html index 5fdd2c11..1811a44c 100644 --- a/docs/reference/rUnifDS.html +++ b/docs/reference/rUnifDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rangeDS.html b/docs/reference/rangeDS.html index e05a1a91..4231406b 100644 --- a/docs/reference/rangeDS.html +++ b/docs/reference/rangeDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/ranksSecureDS1.html b/docs/reference/ranksSecureDS1.html index 6ed0128f..9f04e270 100644 --- a/docs/reference/ranksSecureDS1.html +++ b/docs/reference/ranksSecureDS1.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/ranksSecureDS2.html b/docs/reference/ranksSecureDS2.html index 904eee81..96e92343 100644 --- a/docs/reference/ranksSecureDS2.html +++ b/docs/reference/ranksSecureDS2.html @@ -24,7 +24,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/ranksSecureDS3.html b/docs/reference/ranksSecureDS3.html index 3d5df277..f1d08714 100644 --- a/docs/reference/ranksSecureDS3.html +++ b/docs/reference/ranksSecureDS3.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/ranksSecureDS4.html b/docs/reference/ranksSecureDS4.html index ae6ef70a..eddcaf6f 100644 --- a/docs/reference/ranksSecureDS4.html +++ b/docs/reference/ranksSecureDS4.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/ranksSecureDS5.html b/docs/reference/ranksSecureDS5.html index 1b6788c3..f51096cb 100644 --- a/docs/reference/ranksSecureDS5.html +++ b/docs/reference/ranksSecureDS5.html @@ -20,7 +20,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rbindDS.html b/docs/reference/rbindDS.html index 43b5148a..fc36b471 100644 --- a/docs/reference/rbindDS.html +++ b/docs/reference/rbindDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/reShapeDS.html b/docs/reference/reShapeDS.html index 3efbac3d..2e5315ee 100644 --- a/docs/reference/reShapeDS.html +++ b/docs/reference/reShapeDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/recodeLevelsDS.html b/docs/reference/recodeLevelsDS.html index a2d5b275..7f0e5c81 100644 --- a/docs/reference/recodeLevelsDS.html +++ b/docs/reference/recodeLevelsDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/recodeValuesDS.html b/docs/reference/recodeValuesDS.html index da0679e3..e744d6bf 100644 --- a/docs/reference/recodeValuesDS.html +++ b/docs/reference/recodeValuesDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/repDS.html b/docs/reference/repDS.html index d7a1fb03..9cc5876d 100644 --- a/docs/reference/repDS.html +++ b/docs/reference/repDS.html @@ -21,7 +21,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/replaceNaDS.html b/docs/reference/replaceNaDS.html index 60d2bb00..2029f0a4 100644 --- a/docs/reference/replaceNaDS.html +++ b/docs/reference/replaceNaDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rmDS.html b/docs/reference/rmDS.html index 0e722d5b..f55083b3 100644 --- a/docs/reference/rmDS.html +++ b/docs/reference/rmDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/rowColCalcDS.html b/docs/reference/rowColCalcDS.html index d5acc41a..cdde7901 100644 --- a/docs/reference/rowColCalcDS.html +++ b/docs/reference/rowColCalcDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/sampleDS.html b/docs/reference/sampleDS.html index 9e63a62b..39f03b28 100644 --- a/docs/reference/sampleDS.html +++ b/docs/reference/sampleDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/scatterPlotDS.html b/docs/reference/scatterPlotDS.html index e7391a39..2bd086c0 100644 --- a/docs/reference/scatterPlotDS.html +++ b/docs/reference/scatterPlotDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/seqDS.html b/docs/reference/seqDS.html index 5436c17f..89f85c1b 100644 --- a/docs/reference/seqDS.html +++ b/docs/reference/seqDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/setFilterDS.html b/docs/reference/setFilterDS.html index dc702f6d..252a4d6f 100644 --- a/docs/reference/setFilterDS.html +++ b/docs/reference/setFilterDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.3 +>>>>>>> origin/v6.3.3-dev diff --git a/docs/reference/setSeedDS.html b/docs/reference/setSeedDS.html index 3f93d5d5..846a68dc 100644 --- a/docs/reference/setSeedDS.html +++ b/docs/reference/setSeedDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/skewnessDS1.html b/docs/reference/skewnessDS1.html index 7fcff17c..95722055 100644 --- a/docs/reference/skewnessDS1.html +++ b/docs/reference/skewnessDS1.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/skewnessDS2.html b/docs/reference/skewnessDS2.html index 96ca37f2..5f555c1c 100644 --- a/docs/reference/skewnessDS2.html +++ b/docs/reference/skewnessDS2.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/sqrtDS.html b/docs/reference/sqrtDS.html index 7b232fd0..36f7eae9 100644 --- a/docs/reference/sqrtDS.html +++ b/docs/reference/sqrtDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/subsetByClassDS.html b/docs/reference/subsetByClassDS.html index fc546a46..290fa538 100644 --- a/docs/reference/subsetByClassDS.html +++ b/docs/reference/subsetByClassDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/subsetDS.html b/docs/reference/subsetDS.html index 82f92ba4..151c0ab1 100644 --- a/docs/reference/subsetDS.html +++ b/docs/reference/subsetDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/table1DDS.html b/docs/reference/table1DDS.html index 574f90e4..48e865ec 100644 --- a/docs/reference/table1DDS.html +++ b/docs/reference/table1DDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/table2DDS.html b/docs/reference/table2DDS.html index b120d9ab..1c375976 100644 --- a/docs/reference/table2DDS.html +++ b/docs/reference/table2DDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/tableDS.assign.html b/docs/reference/tableDS.assign.html index 5c5ea7d7..d17715a4 100644 --- a/docs/reference/tableDS.assign.html +++ b/docs/reference/tableDS.assign.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/tableDS.html b/docs/reference/tableDS.html index 96b9b031..3d0ed49f 100644 --- a/docs/reference/tableDS.html +++ b/docs/reference/tableDS.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/tableDS2.html b/docs/reference/tableDS2.html index 360bd692..6b5e0ef7 100644 --- a/docs/reference/tableDS2.html +++ b/docs/reference/tableDS2.html @@ -18,7 +18,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/tapplyDS.assign.html b/docs/reference/tapplyDS.assign.html index 325a9d7c..6050a06a 100644 --- a/docs/reference/tapplyDS.assign.html +++ b/docs/reference/tapplyDS.assign.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/tapplyDS.html b/docs/reference/tapplyDS.html index ba1dec6d..2097b7b2 100644 --- a/docs/reference/tapplyDS.html +++ b/docs/reference/tapplyDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/testObjExistsDS.html b/docs/reference/testObjExistsDS.html index d8baf8bd..7bed49f9 100644 --- a/docs/reference/testObjExistsDS.html +++ b/docs/reference/testObjExistsDS.html @@ -1,5 +1,9 @@ +<<<<<<< HEAD +testObjExistsDS — testObjExistsDS • dsBasetestObjExistsDS — testObjExistsDS • dsBase @@ -17,7 +21,15 @@ dsBase +<<<<<<< HEAD +<<<<<<< HEAD + 6.4.0-9000 +======= + 6.3.4 +>>>>>>> origin/v6.3.5-dev +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/unListDS.html b/docs/reference/unListDS.html index c59d955e..330d2969 100644 --- a/docs/reference/unListDS.html +++ b/docs/reference/unListDS.html @@ -19,7 +19,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/uniqueDS.html b/docs/reference/uniqueDS.html index c65fdb87..090658a6 100644 --- a/docs/reference/uniqueDS.html +++ b/docs/reference/uniqueDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/varDS.html b/docs/reference/varDS.html index f4a05a39..ab4deeb4 100644 --- a/docs/reference/varDS.html +++ b/docs/reference/varDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/reference/vectorDS.html b/docs/reference/vectorDS.html index 36faaa54..49ca4a00 100644 --- a/docs/reference/vectorDS.html +++ b/docs/reference/vectorDS.html @@ -17,7 +17,11 @@ dsBase +<<<<<<< HEAD + 6.4.0.9000 +======= 6.3.5.9000 +>>>>>>> origin/v6.3.5-dev diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 0d5e1008..a38f2f20 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -6,6 +6,7 @@ /reference/BooleDS.html /reference/absDS.html /reference/asCharacterDS.html +/reference/asDataFrameDS.html /reference/asDataMatrixDS.html /reference/asFactorDS1.html /reference/asFactorDS2.html @@ -46,7 +47,12 @@ /reference/extract.html /reference/extractQuantilesDS1.html /reference/extractQuantilesDS2.html +/reference/fixClassDS.html +/reference/fixColsDS.html +/reference/fixLevelsDS.html /reference/gamlssDS.html +/reference/getAllLevelsDS.html +/reference/getClassAllColsDS.html /reference/getWGSRDS.html /reference/glmDS1.html /reference/glmDS2.html @@ -131,7 +137,6 @@ /reference/subsetByClassDS.html /reference/subsetByClassHelper1.html /reference/subsetByClassHelper2.html -/reference/subsetByClassHelper3.html /reference/subsetDS.html /reference/table1DDS.html /reference/table2DDS.html diff --git a/man/asDataFrameDS.Rd b/man/asDataFrameDS.Rd new file mode 100644 index 00000000..8e1b1029 --- /dev/null +++ b/man/asDataFrameDS.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/asDataFrameDS.R +\name{asDataFrameDS} +\alias{asDataFrameDS} +\title{asDataFrameDS a serverside assign function called by ds.asDataFrame} +\usage{ +asDataFrameDS(x.name) +} +\arguments{ +\item{x.name}{the name of the input object to be coerced to class +data.frame. Must be specified in inverted commas. But this argument is +usually specified directly by argument of the clientside function +\code{ds.asDataFrame}} +} +\value{ +the object specified by the argument (or its default name +"asdataframe.newobj") which is written to the serverside. For further +details see help on the clientside function \code{ds.asDataMatrix} +} +\description{ +Coerces an R object into a matrix maintaining original +class for all columns in data.frames. +} +\details{ +This assign function is based on the native R function \code{data.frame} +} +\author{ +Tim Cadman +} diff --git a/man/asDataMatrixDS.Rd b/man/asDataMatrixDS.Rd index 3170e9af..82bebec3 100644 --- a/man/asDataMatrixDS.Rd +++ b/man/asDataMatrixDS.Rd @@ -2,19 +2,19 @@ % Please edit documentation in R/asDataMatrixDS.R \name{asDataMatrixDS} \alias{asDataMatrixDS} -\title{asDataMatrixDS a serverside assign function called by ds.asDataMatrix} +\title{asDataFrameDS a serverside assign function called by ds.asDataFrame} \usage{ asDataMatrixDS(x.name) } \arguments{ \item{x.name}{the name of the input object to be coerced to class -data.matrix. Must be specified in inverted commas. But this argument is +data.frame. Must be specified in inverted commas. But this argument is usually specified directly by argument of the clientside function -\code{ds.asDataMatrix}} +\code{ds.asDataFrame}} } \value{ the object specified by the argument (or its default name -"asdatamatrix.newobj") which is written to the serverside. For further +"asdataframe.newobj") which is written to the serverside. For further details see help on the clientside function \code{ds.asDataMatrix} } \description{ @@ -30,5 +30,5 @@ the data.frame to a matrix but maintains all data columns in their original class } \author{ -Paul Burton for DataSHIELD Development Team +Tim Cadman } diff --git a/man/asFactorDS2.Rd b/man/asFactorDS2.Rd index 16b4a50f..fff7b73b 100644 --- a/man/asFactorDS2.Rd +++ b/man/asFactorDS2.Rd @@ -35,5 +35,5 @@ a factor type that presented as a vector or as a matrix with dummy variables. \details{ The functions converts the input variable into a factor which is presented as a vector if the \code{fixed.dummy.vars} is set to FALSE or as a matrix with dummy variables if the -\code{fixed.dummy.vars} is set to TRUE (see the help file of ds.asFactor.b for more details). +\code{fixed.dummy.vars} is set to TRUE (see the help file of ds.asFactor for more details). } diff --git a/man/dateDS.Rd b/man/dateDS.Rd new file mode 100644 index 00000000..91546ab7 --- /dev/null +++ b/man/dateDS.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dateDS.R +\name{dateDS} +\alias{dateDS} +\title{dateDS} +\usage{ +dateDS(x = NULL, type = NULL, newobj = NULL, unit = NULL, add.column = NULL) +} +\arguments{ +\item{x}{Character vector specifying the server-side object(s). For data-frame columns, use the format \code{df$column}.} + +\item{type}{Character string specifying the operation: \code{"extractdate"}, \code{"makedate"}, or \code{"timebetween"}.} + +\item{newobj}{Character string for the name of the object that will be created on the server. Default is \code{"date.result"}.} + +\item{unit}{Character string specifying the unit for \code{extractdate} or \code{timebetween}: \code{"days"}, \code{"months"}, or \code{"years"}.} + +\item{add.column}{Logical. If \code{FALSE}, the result is created as a new server-side object; +if \code{TRUE}, the result is added as a new column in the existing data-frame. Default is \code{FALSE}.} +} +\value{ +the created numeric vector or date object, or the updated dataframe with the added column +} +\description{ +Takes an object that is either a data-frame column or a vector, and can do extraction of +components of full date (\code{extractdate}), can combine date components to a full date (\code{makedate}), +or can calculate the time between two dates (\code{timebetween}). +} +\details{ +If the input is a data-frame column, it must be provided in the \code{x} argument as data-frame$column. +Inputs for \code{extractdate} and \code{timebetween} must be date objects. +For \code{makedate}, three numeric vectors (year, month, day) must be provided in the correct order. +The \code{add.column} argument determines whether the result is added as a new column in the existing +data-frame (\code{TRUE}), or created as a new server-side object (\code{FALSE}). +Note: \code{add.column = TRUE} is only valid for data-frame inputs. +} +\author{ +Zulal Bekerecioglu +} diff --git a/man/fixClassDS.Rd b/man/fixClassDS.Rd new file mode 100644 index 00000000..d7b6bf17 --- /dev/null +++ b/man/fixClassDS.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{fixClassDS} +\alias{fixClassDS} +\title{Change Class of Target Variables in a Data Frame} +\usage{ +fixClassDS(df.name, target_vars, target_class) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame.} + +\item{target_vars}{A character vector specifying the columns to be modified.} + +\item{target_class}{A character vector specifying the new classes for each column (1 = factor, +2 = integer, 3 = numeric, 4 = character, 5 = logical).} +} +\value{ +A modified data frame with the specified columns converted to the target classes. +} +\description{ +Change Class of Target Variables in a Data Frame +} diff --git a/man/fixColsDS.Rd b/man/fixColsDS.Rd new file mode 100644 index 00000000..709d9472 --- /dev/null +++ b/man/fixColsDS.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{fixColsDS} +\alias{fixColsDS} +\title{Add Missing Columns with NA Values} +\usage{ +fixColsDS(.data, cols) +} +\arguments{ +\item{.data}{A string representing the name of the data frame.} + +\item{cols}{A character vector specifying the columns to be added if missing.} +} +\value{ +A modified data frame with missing columns added and filled with NA. +} +\description{ +Add Missing Columns with NA Values +} diff --git a/man/fixLevelsDS.Rd b/man/fixLevelsDS.Rd new file mode 100644 index 00000000..096757a9 --- /dev/null +++ b/man/fixLevelsDS.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{fixLevelsDS} +\alias{fixLevelsDS} +\title{Set Factor Levels for Specific Columns in a Data Frame} +\usage{ +fixLevelsDS(df.name, vars, levels) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame to modify.} + +\item{vars}{A character vector specifying the columns to be modified.} + +\item{levels}{A named list where each element contains the levels for the corresponding factor variable.} +} +\value{ +A modified data frame with the specified columns converted to factors with the provided levels. +} +\description{ +Set Factor Levels for Specific Columns in a Data Frame +} diff --git a/man/getAllLevelsDS.Rd b/man/getAllLevelsDS.Rd new file mode 100644 index 00000000..e5030725 --- /dev/null +++ b/man/getAllLevelsDS.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{getAllLevelsDS} +\alias{getAllLevelsDS} +\title{Retrieve Factor Levels for Specific Columns} +\usage{ +getAllLevelsDS(df.name, factor_vars) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame.} + +\item{factor_vars}{A character vector specifying the factor columns.} +} +\value{ +A list of factor levels for the specified columns. +} +\description{ +Retrieve Factor Levels for Specific Columns +} diff --git a/man/getClassAllColsDS.Rd b/man/getClassAllColsDS.Rd new file mode 100644 index 00000000..cb2de0e7 --- /dev/null +++ b/man/getClassAllColsDS.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/standardiseDfDS.R +\name{getClassAllColsDS} +\alias{getClassAllColsDS} +\title{Get the Class of All Columns in a Data Frame} +\usage{ +getClassAllColsDS(df.name) +} +\arguments{ +\item{df.name}{A string representing the name of the data frame.} +} +\value{ +A tibble with the class of each column in the data frame. +} +\description{ +Get the Class of All Columns in a Data Frame +} diff --git a/man/predictDS.Rd b/man/predictDS.Rd new file mode 100644 index 00000000..d795b422 --- /dev/null +++ b/man/predictDS.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/predictDS.R +\name{predictDS} +\alias{predictDS} +\title{predictDS} +\usage{ +predictDS( + newdataname, + traindataname, + type = c("response", "link"), + na.action = "na.pass" +) +} +\arguments{ +\item{newdataname}{A character string specifying the name of the new dataset to be used for predictions.} + +\item{traindataname}{A character string specifying the name of the dataset used for model training.} + +\item{type}{A character string specifying the type of prediction. Options are \code{"response"} or \code{"link"}.} + +\item{na.action}{A character string to specify the action to take if missing values are present. Default is \code{"na.pass"}.} +} +\value{ +a numeric vector containing the predicted values +} +\description{ +Generates server-side predictions using the client-side output from \code{ds.glm}. +} +\details{ +This function uses the components supplied by the client-side function (coefficients, family, formula, +and any categorical variables) to generate predictions on the server. To use the base R \code{predict()} function, +a "dummy" glm object is created using the same model formula, family, and link function as the original model. +The dummy model's coefficients are then replaced with the client-side coefficient estimates. + +To avoid mismatches between the factors used in the original glm and those in the dummy glm, the categorical +variables saved by the client-side function are applied to the newdata. + +For intercept-only models, the function simply returns a vector of predicted values equal to the model intercept, with the appropriate length +based on the row length of \code{newdataname}. +} +\author{ +Zulal Bekerecioglu +} diff --git a/man/roundDS.Rd b/man/roundDS.Rd new file mode 100644 index 00000000..00d0e106 --- /dev/null +++ b/man/roundDS.Rd @@ -0,0 +1,40 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/roundDS.R +\name{roundDS} +\alias{roundDS} +\title{roundDS} +\usage{ +roundDS(x, type, digits, add.column, newobj) +} +\arguments{ +\item{x}{Character vector specifying the server-side object(s). For data-frame columns, use the format \code{df$column}.} + +\item{type}{Character string specifying the operation: \code{"round"}, \code{"ceiling"}, \code{"floor"}, +\code{trunc}, or \code{"signif"}.} + +\item{digits}{Number of digits to be used in arguments \code{"round"} and \code{"signif"}.} + +\item{add.column}{Logical. If \code{FALSE}, the result is created as a new server-side object; +if \code{TRUE}, the result is added as a new column in the existing data-frame. Default is \code{FALSE}.} + +\item{newobj}{Character string for the name of the object that will be created on the server. Default is \code{"rounding.result"}.} +} +\value{ +the created numeric vector or the updated dataframe with the added column +} +\description{ +Generates objects from a server-side object, which can be either a vector or +a data-frame column. Supports five operations: +1. (\code{round}) +2. (\code{ceiling}) +3. (\code{floor}) +4. (\code{trunc}) +5. (\code{signif}) +where each function in baseR is applied on the server side to the specified object. +} +\details{ +Note: \code{add.column = TRUE} is only valid for data-frame inputs. +} +\author{ +Zulal Bekerecioglu +} diff --git a/man/scaleDS.Rd b/man/scaleDS.Rd new file mode 100644 index 00000000..a7ab4e25 --- /dev/null +++ b/man/scaleDS.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/scaleDS.R +\name{scaleDS} +\alias{scaleDS} +\title{scaleDS} +\usage{ +scaleDS(x = NULL, newobj = NULL, add.column = NULL) +} +\arguments{ +\item{x}{Character string specifying the server-side vector For data-frame columns, use the format \code{df$column}.} + +\item{newobj}{Character string for the name of the object that will be created on the server. Default is \code{"scaled.data"}.} + +\item{add.column}{Logical. If \code{FALSE}, the result is created as a new server-side object; +if \code{TRUE}, the result is added as a new column in the existing data-frame. Default is \code{FALSE}.} +} +\value{ +the created numeric vector or the updated dataframe with the added column +} +\description{ +Generates scaled objects using a server-side object, which can be either a vector or +a data-frame column. +} +\details{ +Note: \code{add.column = TRUE} is only valid for data-frame inputs. +} +\author{ +Zulal Bekerecioglu +} diff --git a/tests/testthat/disclosure/set_disclosure_settings.R b/tests/testthat/disclosure/set_disclosure_settings.R index 4642cc53..4ee70213 100644 --- a/tests/testthat/disclosure/set_disclosure_settings.R +++ b/tests/testthat/disclosure/set_disclosure_settings.R @@ -24,3 +24,27 @@ set.standard.disclosure.settings <- function() { options(default.nfilter.levels.density = "0.33") options(default.nfilter.levels.max = "40") } + +set.specific.disclosure.settings <- function(datashield.privacyControlLevel='permissive', + nfilter.tab='3', + nfilter.subset='3', + nfilter.glm='0.33', + nfilter.string='80', + nfilter.stringShort='20', + nfilter.kNN='3', + nfilter.levels.density='0.33', + nfilter.levels.max='40', + nfilter.noise='0.25', + nfilter.privacy.old='5') { + options(datashield.privacyLevel = nfilter.privacy.old) + options(default.datashield.privacyControlLevel = datashield.privacyControlLevel) + options(default.nfilter.glm = nfilter.glm) + options(default.nfilter.kNN = nfilter.kNN) + options(default.nfilter.string = nfilter.string) + options(default.nfilter.subset = nfilter.subset) + options(default.nfilter.stringShort = nfilter.stringShort) + options(default.nfilter.tab = nfilter.tab) + options(default.nfilter.noise = nfilter.noise) + options(default.nfilter.levels.density = nfilter.levels.density) + options(default.nfilter.levels.max = nfilter.levels.max) +} diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R new file mode 100644 index 00000000..403fdfb9 --- /dev/null +++ b/tests/testthat/helper.R @@ -0,0 +1,162 @@ +#' Create a mixed dataframe with factor and other types of columns +#' +#' This function generates a dataframe with a specified number of rows, +#' factor columns, and other columns (integer, numeric, and string). +#' +#' @param n_rows Number of rows in the dataframe. Default is 10,000. +#' @param n_factor_cols Number of factor columns in the dataframe. Default is 15. +#' @param n_other_cols Number of other columns (integer, numeric, and string) in the dataframe. Default is 15. +#' +#' @return A dataframe with the specified number of rows and columns, containing mixed data types. +#' @importFrom dplyr bind_cols +#' @importFrom purrr map_dfc +#' @examples +#' df <- create_mixed_dataframe(n_rows = 100, n_factor_cols = 10, n_other_cols = 5) +create_mixed_dataframe <- function(n_rows = 10000, n_factor_cols = 15, n_other_cols = 15) { + + create_factor_column <- function(levels, n = n_rows) { + set.seed(123) # Set seed before sample + factor(sample(levels, n, replace = TRUE)) + } + + factor_levels <- list( + c("Low", "Medium", "High"), + c("Red", "Green", "Blue"), + c("Yes", "No"), + c("A", "B", "C"), + c("One", "Two", "Three"), + c("Cat", "Dog", "Bird"), + c("Small", "Medium", "Large"), + c("Alpha", "Beta", "Gamma"), + c("True", "False"), + c("Left", "Right"), + c("North", "South", "East", "West"), + c("Day", "Night"), + c("Up", "Down"), + c("Male", "Female"), + c("Summer", "Winter", "Spring", "Fall") + ) + + factor_columns <- purrr::map_dfc(factor_levels[1:n_factor_cols], create_factor_column) + colnames(factor_columns) <- paste0("fac_col", 1:n_factor_cols) + + create_other_column <- function(type, n = n_rows) { + set.seed(123) # Set seed before sample + switch(type, + "int" = sample(1:100, n, replace = TRUE), + "num" = runif(n, 0, 100), + "str" = sample(letters, n, replace = TRUE) + ) + } + + column_types <- c( + "int", "int", "num", "num", "str", + "str", "int", "num", "str", "int", + "num", "str", "int", "num", "str" + ) + + other_columns <- purrr::map_dfc(column_types[1:n_other_cols], create_other_column) + colnames(other_columns) <- paste0("col", (n_factor_cols + 1):(n_factor_cols + n_other_cols)) + df <- bind_cols(factor_columns, other_columns) + + return(df) +} + + +#' Modify factor levels for partial overlap +#' +#' This function takes two sets of factor levels, computes the common and unique levels, +#' and returns a new set of levels with partial overlap. +#' +#' @param levels1 First set of factor levels. +#' @param levels2 Second set of factor levels. +#' +#' @return A character vector of new factor levels with partial overlap. +#' @examples +#' new_levels <- partial_overlap_levels(c("A", "B", "C"), c("B", "C", "D")) +partial_overlap_levels <- function(levels1, levels2) { + common <- intersect(levels1, levels2) + unique1 <- setdiff(levels1, common) + unique2 <- setdiff(levels2, common) + + # Set seed before each sample call + set.seed(123) + sampled_unique1 <- sample(unique1, length(unique1) * 0.5) + + set.seed(123) + sampled_unique2 <- sample(unique2, length(unique2) * 0.5) + + new_levels <- c(common, sampled_unique1, sampled_unique2) + return(new_levels) +} + + +#' Create additional dataframes with specific conditions +#' +#' This function generates additional dataframes based on an input dataframe, modifying column classes and levels, +#' and adding new columns with unique names. Different seeds are used for each iteration of the loop, +#' ensuring reproducibility of the generated dataframes. +#' +#' @param base_df The base dataframe used to create the additional dataframes. +#' @param n_rows Number of rows in the additional dataframes. Default is 10,000. +#' @param df_names Names of the additional dataframes to be created. Default is c("df1", "df2", "df3"). +#' +#' @return A list of dataframes with the specified modifications. +#' @importFrom dplyr bind_cols +#' @examples +#' base_df <- create_mixed_dataframe(n_rows = 100, n_factor_cols = 10, n_other_cols = 5) +#' additional_dfs <- create_additional_dataframes(base_df, n_rows = 1000, df_names = c("df1", "df2")) +create_additional_dataframes <- function(base_df, n_rows = 10000, df_names = c("df1", "df2", "df3")) { + + # Define a fixed sequence of seeds, one for each dataframe to be created + seeds <- c(123, 456, 789, 101112) + + df_list <- list() + + for (i in seq_along(df_names)) { + # Set the seed for this iteration based on the pre-defined seeds + set.seed(seeds[i]) + + # Proceed with the dataframe generation process + overlap_cols <- sample(colnames(base_df), size = round(0.8 * ncol(base_df))) + df <- base_df + cols_to_modify_class <- sample(overlap_cols, size = round(0.2 * length(overlap_cols))) + + # Modify columns to have different data types + for (col in cols_to_modify_class) { + current_class <- class(df[[col]]) + new_class <- switch(current_class, + "factor" = as.character(df[[col]]), + "character" = as.factor(df[[col]]), + "numeric" = as.integer(df[[col]]), + "integer" = as.numeric(df[[col]]), + df[[col]]) + df[[col]] <- new_class + } + + # Modify factor levels for partial overlap + factor_cols <- colnames(base_df)[sapply(base_df, is.factor)] + overlap_factor_cols <- intersect(overlap_cols, factor_cols) + cols_to_modify_levels <- sample(overlap_factor_cols, size = round(0.5 * length(overlap_factor_cols))) + + for (col in cols_to_modify_levels) { + original_levels <- levels(base_df[[col]]) + new_levels <- partial_overlap_levels(original_levels, original_levels) + df[[col]] <- factor(df[[col]], levels = new_levels) + } + + # Create new random columns for each dataframe (these will vary by seed) + set.seed(seeds[i]) # Set the seed again for generating new columns + n_new_cols <- round(0.2 * ncol(base_df)) + new_col_names <- paste0(df_names[i], "_new_col_", 1:n_new_cols) + new_cols <- data.frame(matrix(runif(n_rows * n_new_cols), ncol = n_new_cols)) + colnames(new_cols) <- new_col_names + + # Bind new columns to the dataframe + df <- bind_cols(df, new_cols) + df_list[[df_names[i]]] <- df + } + + return(df_list) +} + diff --git a/tests/testthat/test-smk-BooleDS.R b/tests/testthat/test-smk-BooleDS.R index dd10c782..c7ee5af0 100644 --- a/tests/testthat/test-smk-BooleDS.R +++ b/tests/testthat/test-smk-BooleDS.R @@ -18,6 +18,30 @@ context("BooleDS::smk::setup") # Tests # +context("BooleDS::smk::make errors") +test_that("make errors, character V1", { + input <- data.frame(v1 = c('0.0', '1.0', '2.0', '3.0', '4.0'), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) + expect_error(BooleDS("input$v1", "input$v2", 1, "NA", TRUE), "FAILED: V1 is character, please convert to numeric, factor or logical before running Boole", fixed=TRUE) +}) + +test_that("make errors, character V2", { + input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c('4.0', '3.0', '2.0', '1.0', '0.0')) + expect_error(BooleDS("input$v1", "input$v2", 1, "NA", TRUE), "FAILED: V2 is character, please convert to numeric, factor or logical before running Boole", fixed=TRUE) +}) + +test_that("make errors, V1 and V2 are vectors of different length", { + v1 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0) + v2 = c(4.0, 3.0, 2.0, 1.0, 0.0) + expect_error(BooleDS("v1", "v2", 1, "NA", TRUE), "FAILED: V2 must either be of length one or of length equal to V1", fixed=TRUE) +}) + +test_that("make errors, incorrect Boolean operator", { + v1 = c(0.0, 1.0, 2.0, 3.0, 4.0) + v2 = c(4.0, 3.0, 2.0, 1.0, 0.0) + boolean.op = 10 + expect_error(BooleDS("v1", "v2", boolean.op, "NA", TRUE), "FAILED: Boolean.operator specified incorrectly. Must be: '==', '!=', '<', '<=', '>' or '>='", fixed=TRUE) +}) + context("BooleDS::smk::simple equal") test_that("simple BooleDS, equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) diff --git a/tests/testthat/test-smk-asDataFrameDS.R b/tests/testthat/test-smk-asDataFrameDS.R new file mode 100644 index 00000000..2d967f38 --- /dev/null +++ b/tests/testthat/test-smk-asDataFrameDS.R @@ -0,0 +1,47 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + +# +# Set up +# + +context("asDataFrameDS::smk::setup") + +# +# Tests +# + +context("asDataFrameDS::smk::simple") +test_that("simple asDataFrameDS", { + input <- tibble(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) + + res <- asDataFrameDS("input") + + res.class <- class(res) + expect_length(res.class, 1) + expect_true("data.frame" %in% res.class) + expect_equal( + dim(res), c(5, 2) + ) + + expect_equal(res$v1, 0:4) + expect_equal(res$v2, 4:0) + res.colnames <- colnames(res) + expect_length(res.colnames, 2) + expect_equal(res.colnames[1], "v1") + expect_equal(res.colnames[2], "v2") +}) + +# +# Done +# + +context("asDataMatrixDS::smk::shutdown") +context("asDataMatrixDS::smk::done") diff --git a/tests/testthat/test-smk-asDataMatrixDS.R b/tests/testthat/test-smk-asDataMatrixDS.R index 6c4f567c..cfcd5f2f 100644 --- a/tests/testthat/test-smk-asDataMatrixDS.R +++ b/tests/testthat/test-smk-asDataMatrixDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2026 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -29,25 +30,53 @@ test_that("simple asDataMatrixDS", { { expect_length(res.class, 1) expect_true("matrix" %in% res.class) + + expect_length(res, 10) + expect_equal(res[1], 0) + expect_equal(res[2], 1) + expect_equal(res[3], 2) + expect_equal(res[4], 3) + expect_equal(res[5], 4) + expect_equal(res[6], 4) + expect_equal(res[7], 3) + expect_equal(res[8], 2) + expect_equal(res[9], 1) + expect_equal(res[10], 0) } - else + else if (base::getRversion() < '4.0.1') { expect_length(res.class, 2) - expect_true("matrix" %in% res.class) - expect_true("array" %in% res.class) + expect_true(all(c("matrix", "array") %in% res.class)) + + expect_length(res, 10) + expect_equal(res[1], 0) + expect_equal(res[2], 1) + expect_equal(res[3], 2) + expect_equal(res[4], 3) + expect_equal(res[5], 4) + expect_equal(res[6], 4) + expect_equal(res[7], 3) + expect_equal(res[8], 2) + expect_equal(res[9], 1) + expect_equal(res[10], 0) } + else + { + expect_length(res.class, 1) + expect_true(all("data.frame" %in% res.class)) - expect_length(res, 10) - expect_equal(res[1], 0) - expect_equal(res[2], 1) - expect_equal(res[3], 2) - expect_equal(res[4], 3) - expect_equal(res[5], 4) - expect_equal(res[6], 4) - expect_equal(res[7], 3) - expect_equal(res[8], 2) - expect_equal(res[9], 1) - expect_equal(res[10], 0) + expect_length(res, 2) + expect_equal(res[1, 1], 0) + expect_equal(res[2, 1], 1) + expect_equal(res[3, 1], 2) + expect_equal(res[4, 1], 3) + expect_equal(res[5, 1], 4) + expect_equal(res[1, 2], 4) + expect_equal(res[2, 2], 3) + expect_equal(res[3, 2], 2) + expect_equal(res[4, 2], 1) + expect_equal(res[5, 2], 0) + } res.colnames <- colnames(res) expect_length(res.colnames, 2) diff --git a/tests/testthat/test-smk-asFactorDS1.R b/tests/testthat/test-smk-asFactorDS1.R index fd59cefc..78d44bf7 100644 --- a/tests/testthat/test-smk-asFactorDS1.R +++ b/tests/testthat/test-smk-asFactorDS1.R @@ -33,6 +33,49 @@ test_that("simple asFactorDS1", { expect_equal(res[3], "3") }) +context("asFactorDS1::smk::make errors") +test_that("make errors, vector with more unique values than nfilter.levels.max", { + input <- c(1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0) + + factor.levels.present.in.source <- levels(factor(input)) + num.levels <- length(factor.levels.present.in.source) + + thr <- dsBase::listDisclosureSettingsDS() + nfilter.levels.density <- as.numeric(thr$nfilter.levels.density) + nfilter.levels.max <- as.numeric(thr$nfilter.levels.max) + max.levels.by.density <- nfilter.levels.density*length(input) + + error.message <- paste0("FAILED: this variable has too many levels and may be disclosive. + The number of factor levels must not exceed ", (nfilter.levels.density*100), + "% of the length of the variable being converted to a factor. The max number + of levels in this study is therefore ",max.levels.by.density," but this + variable has ", num.levels, " factor levels") + + expect_error(asFactorDS1("input"), error.message, fixed=TRUE) +}) + +test_that("make errors, vector with more levels than nfilter.levels.max", { + input <- c(2.0, 1.0, 3.0, 3.0, 3.0, 1.0, 2.0, 2.0, 1.0, 2.0) + + factor.levels.present.in.source <- levels(factor(input)) + num.levels <- length(factor.levels.present.in.source) + + set.specific.disclosure.settings(nfilter.levels.max='2') + + thr <- dsBase::listDisclosureSettingsDS() + nfilter.levels.density <- as.numeric(thr$nfilter.levels.density) + nfilter.levels.max <- as.numeric(thr$nfilter.levels.max) + max.levels.by.density <- nfilter.levels.density*length(input) + + error.message <- paste0("FAILED: this variable has too many levels and may be disclosive. + It exceeds the max number of levels allowed by nfilter.levels.max: + that is ", nfilter.levels.max, ". In this study this variable has ", + num.levels," factor levels") + + expect_error(asFactorDS1("input"), error.message, fixed=TRUE) +}) + + # # Done # diff --git a/tests/testthat/test-smk-standardiseDfDS.R b/tests/testthat/test-smk-standardiseDfDS.R new file mode 100644 index 00000000..1bfd6720 --- /dev/null +++ b/tests/testthat/test-smk-standardiseDfDS.R @@ -0,0 +1,163 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2025 University Medical Center Groningen (UCMG), Netherlands. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + +# +# Set up +# + +context("standardiseDfDS::smk::setup") + +df <- create_mixed_dataframe() +df_list <- create_additional_dataframes(df) + +df_1 <- df +df_2 <- df_list[[1]] +df_3 <- df_list[[2]] +df_4 <- df_list[[3]] + +context("standardiseDfDS::smk") +test_that("getClassAllColsDS returns correct classes", { + expect_equal( + getClassAllColsDS("df_1"), + tibble( + fac_col1 = "factor", fac_col2 = "factor", fac_col3 = "factor", fac_col4 = "factor", fac_col5 = "factor", + fac_col6 = "factor", fac_col7 = "factor", fac_col8 = "factor", fac_col9 = "factor", fac_col10 = "factor", + fac_col11 = "factor", fac_col12 = "factor", fac_col13 = "factor", fac_col14 = "factor", fac_col15 = "factor", + col16 = "integer", col17 = "integer", col18 = "numeric", col19 = "numeric", col20 = "character", + col21 = "character", col22 = "integer", col23 = "numeric", col24 = "character", col25 = "integer", + col26 = "numeric", col27 = "character", col28 = "integer", col29 = "numeric", col30 = "character" + ) + ) +}) + +test_that("fixClassDS sets classes correctly", { + + cols_to_set <- c("fac_col13", "fac_col5", "col22", "col19", "col25", "col20", "col28", + "fac_col14", "fac_col3", "fac_col8") + + classes_to_set <- c("4", "1", "3", "5", "3", "2", "5", "5", "3", "2") + + expect_warning( + classes_changed_df <- fixClassDS("df_1", cols_to_set, classes_to_set) + ) + + expect_equal( + classes_changed_df %>% tidytable::map_chr(class) %>% unname(), + c("factor", "factor", "numeric", "factor", "factor", "factor", "factor", "integer", "factor", + "factor", "factor", "factor", "character", "logical", "factor", "integer", "integer", + "numeric", "logical", "integer", "character", "numeric", "numeric", "character", "numeric", + "numeric", "character", "logical", "numeric", "character") + ) +}) + +test_that("convert_class calls the correct function", { + + result <- .convertClass(c(1, 2, 3), "1") + expect_true(is.factor(result)) + + result <- .convertClass(c(1.5, 2.5, 3.7), "2") + expect_true(is.integer(result)) + + result <- .convertClass(c("1", "2", "3"), "3") + expect_true(is.numeric(result)) + + result <- .convertClass(c(1, 2, 3), "4") + expect_true(is.character(result)) + + result <- .convertClass(c(0, 1, 0), "5") + expect_true(is.logical(result)) + +}) + +test_that("fixColsDS correctly adds missing columns", { + + all_cols <- unique(c(colnames(df_1), colnames(df_2), colnames(df_3), colnames(df_4))) + out <- fixColsDS("df_3", all_cols) + + expect_equal( + colnames(out), + sort(all_cols)) + +}) + +test_that("getAllLevelsDS correctly retrieves the levels of specified factor columns", { + + factor_vars <- c("fac_col1", "fac_col2", "fac_col3", "fac_col4", "fac_col5", "fac_col6", "fac_col7", + "fac_col8", "fac_col9", "fac_col10", "fac_col11", "fac_col12", "fac_col14", + "fac_col15", "col27") + + observed <- getAllLevelsDS("df_3", factor_vars) + + expected <- list( + fac_col1 = c("High", "Low", "Medium"), + fac_col2 = c("Blue", "Green", "Red"), + fac_col3 = c("No", "Yes"), + fac_col4 = c("A", "B", "C"), + fac_col5 = c("One", "Three", "Two"), + fac_col6 = c("Bird", "Cat", "Dog"), + fac_col7 = c("Large", "Medium", "Small"), + fac_col8 = c("Alpha", "Beta", "Gamma"), + fac_col9 = c("False", "True"), + fac_col10 = c("Left", "Right"), + fac_col11 = c("East", "North", "South", "West"), + fac_col12 = c("Day", "Night"), + fac_col14 = c("Female", "Male"), + fac_col15 = c("Fall", "Spring", "Summer", "Winter"), + col27 = letters + ) + + expect_equal(expected, observed) + +}) + +example_df <- data.frame( + col1 = c("A", "B", "A", "C"), + col2 = c("X", "Y", "X", "Z"), + col3 = c("Yes", "No", "Yes", "No"), + stringsAsFactors = FALSE +) + +test_that("fixLevelsDS sets factor levels correctly", { + + levels <- list( + col1 = c("A", "B", "C"), + col2 = c("X", "Y", "Z"), + col3 = c("Yes", "No") + ) + + modified_df <- fixLevelsDS("example_df", c("col1", "col2", "col3"), levels) + + expect_s3_class(modified_df$col1, "factor") + expect_s3_class(modified_df$col2, "factor") + expect_s3_class(modified_df$col3, "factor") + + expect_equal(levels(modified_df$col1), levels$col1) + expect_equal(levels(modified_df$col2), levels$col2) + expect_equal(levels(modified_df$col3), levels$col3) + +}) + +test_that("fixLevelsDS throws an error for invalid input", { + + levels <- list( + col1 = c("A", "B", "C"), + col2 = c("X", "Y", "Z") + ) + + expect_error(fixLevelsDS("example_df", c("col1", "non_existent_col"), levels)) +}) + +# +# Done +# + +context("standardiseDfDS::smk::shutdown") + +context("standardiseDfDS::smk::done") diff --git a/tests/testthat/test-smk-subsetByClassDS.R b/tests/testthat/test-smk-subsetByClassDS.R deleted file mode 100644 index 8de5114b..00000000 --- a/tests/testthat/test-smk-subsetByClassDS.R +++ /dev/null @@ -1,87 +0,0 @@ -#------------------------------------------------------------------------------- -# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# -# This program and the accompanying materials -# are made available under the terms of the GNU Public License v3.0. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . -#------------------------------------------------------------------------------- - -# -# Set up -# - -context("subsetByClassDS::smk::setup") - -set.standard.disclosure.settings() - -# -# Tests -# - -context("subsetByClassDS::smk") -test_that("simple subsetByClassDS, data.frame, unspecified variables", { - data <- data.frame(v1 = factor(c(0, 0, 0, 1, 1, 1, 2, 1, 2, 2)), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, 3.0, 0.0, 4.0), v3 = c(1:10), v4 = c(1:10)) - variables <- NULL - - res <- subsetByClassDS("data", variables) - - expect_equal(class(res), "list") - expect_length(res, 3) - - expect_equal(class(res$v1.level_0), "data.frame") - expect_length(res$v1.level_0, 4) - - expect_equal(class(res$v1.level_1), "data.frame") - expect_length(res$v1.level_1, 4) - - expect_equal(class(res$v1.level_2), "data.frame") - expect_length(res$v1.level_2, 4) -}) - -test_that("simple subsetByClassDS, data.frame, specified variables", { - data <- data.frame(v1 = factor(c(0, 0, 0, 1, 1, 1, 2, 1, 2, 2)), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, 3.0, 0.0, 4.0), v3 = c(1:10), v4 = c(1:10)) - variables <- c("v1") - - res <- subsetByClassDS("data", variables) - - expect_equal(class(res), "list") - expect_length(res, 3) - - expect_equal(class(res$v1.level_0), "data.frame") - expect_length(res$v1.level_0, 4) - - expect_equal(class(res$v1.level_1), "data.frame") - expect_length(res$v1.level_1, 4) - - expect_equal(class(res$v1.level_2), "data.frame") - expect_length(res$v1.level_2, 4) -}) - -test_that("simple subsetByClassDS, factor vector, specified variables", { - data <- factor(c(0, 0, 0, 1, 1, 1, 2, 1, 2, 2)) - variables <- NULL - - res <- subsetByClassDS("data", variables) - - expect_equal(class(res), "list") - expect_length(res, 3) - - expect_equal(class(res$data.level_0), "factor") - expect_length(res$data.level_0, 3) - - expect_equal(class(res$data.level_1), "factor") - expect_length(res$data.level_1, 4) - - expect_equal(class(res$data.level_2), "factor") - expect_length(res$data.level_2, 3) -}) - -# -# Done -# - -context("subsetByClassDS::smk::shutdown") - -context("subsetByClassDS::smk::done") diff --git a/tests/testthat/test-smk-subsetDS.R b/tests/testthat/test-smk-subsetDS.R deleted file mode 100644 index f34119c4..00000000 --- a/tests/testthat/test-smk-subsetDS.R +++ /dev/null @@ -1,125 +0,0 @@ -#------------------------------------------------------------------------------- -# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# -# This program and the accompanying materials -# are made available under the terms of the GNU Public License v3.0. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . -#------------------------------------------------------------------------------- - -# -# Set up -# - -context("subsetDS::smk::setup") - -set.standard.disclosure.settings() - -# -# Tests -# - -context("subsetDS::smk") -test_that("simple subsetDS, no NAs", { - data <- data.frame(v1 = c(0, 0, 1, 1, 2, 2, 3, 3, 4, 4), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, 3.0, 0.0, 4.0)) - complt <- FALSE - rs <- NULL - cs <- NULL - lg <- 2 - th <- 2 - varname <- "v1" - - res <- subsetDS("data", complt, rs, cs, lg, th, varname) - - expect_equal(class(res), "data.frame") - expect_length(res, 2) - - expect_equal(class(res$v1), "numeric") - expect_length(res$v1, 6) - expect_equal(res$v1[1], 2) - expect_equal(res$v1[2], 2) - expect_equal(res$v1[3], 3) - expect_equal(res$v1[4], 3) - expect_equal(res$v1[5], 4) - expect_equal(res$v1[6], 4) - - expect_equal(class(res$v2), "numeric") - expect_length(res$v2, 6) - expect_equal(res$v2[1], 2.0) - expect_equal(res$v2[2], 2.0) - expect_equal(res$v2[3], 1.0) - expect_equal(res$v2[4], 3.0) - expect_equal(res$v2[5], 0.0) - expect_equal(res$v2[6], 4.0) -}) - -test_that("simple subsetDS, NAs, complete.case FALSE", { - data <- data.frame(v1 = c(0, 0, 1, 1, 2, 2, 3, 3, 4, 4), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, NA, NA, 4.0)) - complt <- FALSE - rs <- NULL - cs <- NULL - lg <- 2 - th <- 2 - varname <- "v1" - - res <- subsetDS("data", complt, rs, cs, lg, th, varname) - - expect_equal(class(res), "data.frame") - expect_length(res, 2) - - expect_equal(class(res$v1), "numeric") - expect_length(res$v1, 6) - expect_equal(res$v1[1], 2) - expect_equal(res$v1[2], 2) - expect_equal(res$v1[3], 3) - expect_equal(res$v1[4], 3) - expect_equal(res$v1[5], 4) - expect_equal(res$v1[6], 4) - - expect_equal(class(res$v2), "numeric") - expect_length(res$v2, 6) - expect_equal(res$v2[1], 2.0) - expect_equal(res$v2[2], 2.0) - expect_equal(res$v2[3], 1.0) - expect_true(is.na(res$v2[4])) - expect_true(is.na(res$v2[5])) - expect_equal(res$v2[6], 4.0) -}) - -test_that("simple subsetDS, NAs, complete.case TRUE", { - data <- data.frame(v1 = c(0, 0, 1, 1, 2, 2, 3, 3, 4, 4), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, NA, NA, 4.0)) - complt <- TRUE - rs <- NULL - cs <- NULL - lg <- 2 - th <- 2 - varname <- "v1" - - res <- subsetDS("data", complt, rs, cs, lg, th, varname) - - expect_equal(class(res), "data.frame") - expect_length(res, 2) - - expect_equal(class(res$v1), "numeric") - expect_length(res$v1, 4) - expect_equal(res$v1[1], 2) - expect_equal(res$v1[2], 2) - expect_equal(res$v1[3], 3) - expect_equal(res$v1[4], 4) - - expect_equal(class(res$v2), "numeric") - expect_length(res$v2, 4) - expect_equal(res$v2[1], 2.0) - expect_equal(res$v2[2], 2.0) - expect_equal(res$v2[3], 1.0) - expect_equal(res$v2[4], 4.0) -}) - -# -# Done -# - -context("subsetDS::smk::shutdown") - -context("subsetDS::smk::done")