R/readAllData.R

In MSToolkit: The MSToolkit library for clinical trial design

"readAllData" <- function(                            
  dataType = c("ReplicateData", "MicroEvaluation", "MacroEvaluation"),    #@ Type of data, should be "Replicate", "Macro", or "Micro"
  workingPath = getwd(),      #   The working directory
  dirName = dataType,       #@ Directory to use in case one doesn't want to use the default directory
  prefix = switch(dataType, ReplicateData = "replicate", MicroEvaluation = "micro", MacroEvaluation = "macro"), 
  replicates = NULL,
  consolidate = TRUE, 
  replicateCol = getEctdColName("Replicate"),
  method = getEctdDataMethod()   #@ Data Storage Method to use
){  
  ###############################################################################
  # Mango Solutions, Chippenham SN14 0SQ 2006
  # Thurs Jun 21 16:51 BST 2007 @445 /Internet Time/
  # Author: Francisco
  ###############################################################################
  # DESCRIPTION: Returns all data for a particular data type, or a subset of
  # the data if replicates is specified.  Returns either a list of data frames or
  # if consolidate is set to TRUE, consolidates into a single data frame
  # KEYWORDS: IO
  ###############################################################################

  # Check dataType input
  dataType <- match.arg(dataType)
  if (dataType != "ReplicateData") method <- "CSV" 
  
  # Attempt to extract all replicate numbers
  if (!length(replicates)) replicates <- getReplicates(dirName, prefix, method, workingPath = workingPath)

  # Read all replicate data using call to "readData"
  out <- lapply(replicates, readData, dataType=dataType, workingPath = workingPath, method = method)
  names(out) <- sprintf("%04d", replicates)

  # Consolidate datasets if required
  if (consolidate) {
    repColData <- rep(replicates, sapply(out, nrow))
    columnNames <- unique(unlist(lapply(out, names)))
    out <- lapply( out, function(d) {
      missings <- columnNames [ !(columnNames %in% names(d))]
      if (length(missings) > 0 ) d[,missings] <- NA
      d
    })
    out <- do.call( rbind, out )
    out[[replicateCol]] <- repColData
    out <- out[ , c(replicateCol, setdiff(names(out), replicateCol))]
    rownames(out) <- as.character(1:nrow(out))
  }

  out
}