parframe2setup: Import NONMEM output for parameter tables

In certara/pmxpartabc: Parameter Tables for PMx Analyses

Import NONMEM output for parameter tables

Description

Reads all relevant inputs (ie, parameter estimates, bootstrap, shrinkage, etc.) using directly model run or with the help of a YAML file. The parameter name must be provided in the model file. Other fields are optional and can be provided either in (1) the model file or a (2) YAML file. Few fields needs to be inputted directly from user to complete the table:

• name (compulsory): name of parameter (eg, CL, Vd, nCL, nVd, etc.)

• label: description of parameter (eg, "Volume of distribution", "Apparent Clearance", etc.)

• units: parameter unit (eg, L/h, 1/hr, etc)

• trans: parameter transformation (ie, %, exp, ilogit, sqrt, CV%)

• type: Typical Values, Between Subject Variability, Inter Occasion Variability, Residual Error or Covariates (ie respectively, Structural, IIV, IOV, RUV or CovariateEffect)

Usage

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

Arguments

run_dir	NONMEM model directory
run_prefix	NONMEM run number prefix
runno	NONMEM run number
bootstrap	flag for availability of bootstrap results
run_dir.boot	bootstrap results directory
runno.boot	bootstrap NONMEM run number, if changes from runno
conf.level	bootstrap results confidence interval. By default set to 95%
min_suc	filter bootstrap results on minimization successful. By default set to TRUE
read.boot	flag for reading directly the customized filtering bootstrap raw_results.csv
boot.obj	customized filtered bootstrap raw_results.csv data frame passed by user
yaml.file	flag for using the yaml.file option; all the non-compulsory fields e.g., label, trans, units, type will be read from yaml file
yaml.file.name	name of the yaml file

certara/pmxpartabc documentation built on March 16, 2024, 4:38 p.m.