Execute diagnostic plots
In NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

#START OF AUTO-GENERATED PREAMBLE, WILL BE OVERWRITTEN WHEN THIS FILE IS USED AS A TEMPLATE
#Created 2022-10-30 at 09:58

xpose.runno <- '014.mod'
toolname <- 'execute'
pdf.filename <- paste0('PsN_',toolname,'_plots.pdf')
working.directory<-'/data/home/philipde/wdirs/NMdata/tests/testthat/testData/nonmem/xgxr014.dir2/'
results.directory <- '..'
subset.variable<-NULL
tab.suffix <- '' 
rscripts.directory <- '/usr/local/share/perl/5.26.1/PsN_5_2_6/R-scripts' # This is not used
raw.results.file <- 'raw_results_xgxr014.csv'
theta.labels <- c('POPKA','POPCL','POPV2')
theta.fixed <- c(FALSE,FALSE,FALSE)
omega.labels <- c('OMEGA(1,1)','OMEGA(2,2)','OMEGA(3,3)')
omega.fixed <- c(FALSE,FALSE,FALSE)
sigma.labels <- c('SIGMA(1,1)','SIGMA(2,2)')
sigma.fixed <- c(FALSE,FALSE)
n.eta <- 3
n.eps <- 2

res.table <- ''

setwd(working.directory)

############################################################################
#END OF AUTO-GENERATED PREAMBLE
#WHEN THIS FILE IS USED AS A TEMPLATE THIS LINE MUST LOOK EXACTLY LIKE THIS

# get libPaths
library(PsNR)
library(magrittr)
library(methods)
library(xpose4)

#add R_info to the meta file
R_info(directory=working.directory)
meta <- PsNR::metadata(working.directory)
model_path <- PsNR::model_path(meta)
xpose_runno <- xpose.runno

model_suffix <- paste0('.', tools::file_ext(model_path))
xpdb <- xpose4::xpose.data(xpose_runno, directory=results.directory, tab.suffix=tab.suffix, mod.prefix=PsNR::model_prefix(meta), mod.suffix=model_suffix)

#uncomment below to change the idv from TIME to something else such as TAD.
#Other xpose preferences could also be changed
#xpdb@Prefs@Xvardef$idv="TAD"
xpose4::runsum(xpdb, dir=results.directory,
         modfile=PsNR::model_path(meta),
         listfile=file.path(results.directory, sub(model_suffix, ".lst", basename(PsNR::model_path(meta)))))

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::basic.gof(xpdb))
}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::basic.gof(xpdb,by=subset.variable,max.plots.per.page=1))
}

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::ranpar.hist(xpdb))
}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::ranpar.hist(xpdb,by=subset.variable,scales="free",max.plots.per.page=1))
}

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::ranpar.qq(xpdb))
}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::ranpar.qq(xpdb,by=subset.variable,max.plots.per.page=1))
}

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::dv.preds.vs.idv(xpdb))
}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::dv.preds.vs.idv(xpdb,by=subset.variable))
}

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::dv.vs.idv(xpdb))
}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::dv.vs.idv(xpdb,by=subset.variable))
}

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::ipred.vs.idv(xpdb))
}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::ipred.vs.idv(xpdb,by=subset.variable))
}

\pagebreak

if (is.null(subset.variable)){
    print(xpose4::pred.vs.idv(xpdb))

}else{
    # change the subset variable from categorical to continuous or vice versa.
    # change.cat.cont(xpdb) <- c(subset.variable)
    print(xpose4::pred.vs.idv(xpdb,by=subset.variable))
}

\pagebreak

rplots.gr.1 <- FALSE
if (PsNR::rplots_level(meta) > 1){
  rplots.gr.1 <- TRUE
  #individual plots of ten random IDs
  #find idcolumn
  idvar <- xpose4::xvardef("id",xpdb)
  ten.random.ids <- sort(sample(unique(xpdb@Data[,idvar]),10,replace=FALSE))
  subset.string <- paste0(idvar,'==',paste(ten.random.ids,collapse=paste0(' | ',idvar,'==')))

  if (is.null(subset.variable)){
    print(xpose4::ind.plots(xpdb,subset=subset.string))
  }else{
    for (flag in unique(xpdb@Data[,subset.variable])){
      print(xpose4::ind.plots(xpdb,layout=c(1,1),subset=paste0(subset.variable,'==',flag,' & (',subset.string,')')))
    }
  }
}

```{asis Add_pagebreak_on_condition, echo=rplots.gr.1} \pagebreak

```r
if (PsNR::rplots_level(meta) > 1){
  #check if files exist
  if (res.table != '') {
      model_prefix <- PsNR::model_prefix(meta)
    file_1_exists <- file_existence_in_directory(directory=results.directory, file_name=paste0(model_prefix, xpose_runno, ".phi"))
    file_2_exists <- file_existence_in_directory(directory=results.directory, file_name=res.table)

    if ((file_1_exists) && (file_2_exists)) {
      # calculate data
      list_out <- data.obj.obsi(obj.data.dir=file.path(results.directory, paste0(model_prefix, xpose_runno, ".phi")),
                                obsi.data.dir=file.path(results.directory, res.table))
      have_needed_columns <- list_out$have_needed_columns
      if(have_needed_columns) {
        OBJ_data <- list_out$OBJ_data
        OBSi_vector <- list_out$OBSi_vector
        OBJ_vector <- list_out$OBJ_vecto

        # plot data
        PsNR::plot_obj_obsi(OBJ_data,OBSi_vector,OBJ_vector)
      }
    }
  }
}