In qPharmetra/PMDatR: Pharmacometric Data Management in R

library(PMDatR)
library(knitr)
opts_chunk$set(error=TRUE)

PMDatR: Process Settings

This script processes a settings file to create R code that can be run in the PMDatR data management template. The settings are checked for syntactical errors during the generation of the code. Errors are reported in this script.

Create DataManagement Object

Peek into structure of the created DataManagement object

DMobj=list()
if(params$settings_file!=""){
  DMobj = DataManagement(params$settings_file)
  code_text = WriteCode.DataManagement(DMobj)
}
str(DMobj$Settings)

# dynamic generations of error report
print_error_qry = function(qry){
  if(!qry$valid){
    cat(sprintf("### Errors in Query %s\n", qry$mappings$Name))
    cat(sapply(qry$errors,toString),sep="\n\n")
    cat("\n")
    }
}

print_error_dom = function(dom){
  if(!dom$valid){
    cat(sprintf("### Errors in Domain Settings: %s\n", dom$name))
    cat(sapply(dom$errors,toString),sep="\n\n")
    cat("\n")
    }
}

print_error_DM = function(dmo){
  if(length(dmo$errors)){
    cat(sprintf("### Errors in Data Management Object\n"))
    cat(sapply(dmo$errors,toString),sep="\n\n")
    cat("\n")
  }
}


if(!DMobj$valid){
  cat("## Errors in Settings\n")
  #cycle through the elements to print errors
  print_error_DM(DMobj)
  for(dom in DMobj$Domains) print_error_dom(dom)
  for(qry in DMobj$DVs) print_error_qry(qry)
  for(qry in DMobj$IndDoses) print_error_qry(qry)
  for(qry in DMobj$Covs) print_error_qry(qry)
  for(qry in DMobj$CovTs) print_error_qry(qry)

}

Write dynamic functions file

fname = paste0(tools::file_path_sans_ext(basename(params$settings_file)), "_funcs.r")
if(DMobj$valid){
  cat(code_text$text.tidy, file=fname, sep="\n",append=F)
  cat(sprintf("Functions written to file: %s\n\nMD5 = %s", fname, tools::md5sum(fname)))
} else{ 
  cat("Functions not written due to errors in settings file.  Please correct errors and try again.")
}