In certara/pmxpartabc: Parameter Tables for PMx Analyses

Example with all information in the yaml file (except from parameter name) and pre-filtered bootstrap results passed by user.

knitr::opts_chunk$set(echo = TRUE)

Setup environment

# ----- Load package -----
library(pmxpartabc)

# ----- Define directory and file names -----
run_dir    <- file.path(system.file(package = "pmxpartabc"), "examples")
run_prefix <- "run"
runno     <-  "6"
boot.object <-  read.csv(file.path(run_dir, "bootstrap_dir2", "raw_results_run5boot.csv"), header = TRUE, check.names = FALSE)
yaml.file.name <- file.path(system.file(package = "pmxpartabc"), "meta.yaml")

Parameter table 1 - using yaml file

output <- parframe2setup(run_dir, 
                         run_prefix, 
                         runno, 
                         bootstrap = TRUE, 
                         conf.level = 0.95, 
                         min_suc = TRUE, 
                         read.boot = TRUE, 
                         boot.obj = boot.object, 
                         yaml.file = TRUE, 
                         yaml.file.name = yaml.file.name)

tab <- parframe(out=output[[1]], meta=output[[2]], bootstrap=TRUE)  

tab1 <- pmxpartab(tab, output[[2]], columns=c(value="Estimate", rse="RSE%", ci95="95%CI", shrinkage="Shrinkage"))

print(tab1)