inst/extdata/CodeLibrary/R/gof_ggplot.R

In tsahota/NMproject: Script Based 'NONMEM' Model Development

#' Create pdf diagnostic report with ggplot
#' 
#' @param m An nm object.
#' 
#' @export

gof_ggplot <- function(m){

  NMproject::wait_finish(m)  ## ensures m is finished
  d <- NMproject::output_table_first(m)  ## reads in all table files

  library(ggplot2)

  pl <- list()
  p <- ggplot(d,aes_string(x="PRED",y="DV")) + theme_bw() +
    geom_abline(slope=1)+
    geom_point()
  pl[[length(pl)+1]] <- p
  pl[[length(pl)+1]] <- p + scale_x_log10() + scale_y_log10()

  p <- ggplot(d,aes_string(x="IPRED",y="DV")) + theme_bw() +
    geom_abline(slope=1)+
    geom_point()
  pl[[length(pl)+1]] <- p
  pl[[length(pl)+1]] <- p + scale_x_log10() + scale_y_log10()

  maxCWRES <- max(abs(d$CWRES),na.rm=TRUE)
  p <- ggplot(d,aes_string(x="PRED",y="CWRES")) + theme_bw() +
    geom_hline(yintercept=0)+
    geom_point() + scale_y_continuous(limits=c(-1.05*maxCWRES,1.05*maxCWRES))
  pl[[length(pl)+1]] <- p

  p <- ggplot(d,aes_string(x="TIME",y="CWRES")) + theme_bw() +
    geom_hline(yintercept=0)+
    geom_point() + scale_y_continuous(limits=c(-1.05*maxCWRES,1.05*maxCWRES))
  pl[[length(pl)+1]] <- p

  maxNPDE <- max(abs(d$NPDE),na.rm=TRUE)
  p <- ggplot(d,aes_string(x="PRED",y="NPDE")) + theme_bw() +
    geom_hline(yintercept=0)+
    geom_point() + scale_y_continuous(limits=c(-1.05*maxNPDE,1.05*maxNPDE))
  pl[[length(pl)+1]] <- p

  p <- ggplot(d,aes_string(x="TIME",y="NPDE")) + theme_bw() +
    geom_hline(yintercept=0)+
    geom_point() + scale_y_continuous(limits=c(-1.05*maxNPDE,1.05*maxNPDE))
  pl[[length(pl)+1]] <- p



  pdf(file.path(NMproject::results_dir(m), 
                paste0("gof_ggplot_run_",
                       NMproject::run_id(m),
                       ".pdf")))
  print(pl)
  dev.off()

}