read_nm_output {pmxpartab}

Read NONMEM output

Description

Read NONMEM output

Usage

read_nm_output(
  rundir = getwd(),
  runname = basename(normalizePath(rundir)),
  lst.file = file.path(rundir, sprintf("%s.lst", runname)),
  ext.file = file.path(rundir, sprintf("%s.ext", runname)),
  shk.file = file.path(rundir, sprintf("%s.shk", runname)),
  phi.file = file.path(rundir, sprintf("%s.phi", runname)),
  phm.file = file.path(rundir, sprintf("%s.phm", runname)),
  cov.file = file.path(rundir, sprintf("%s.cov", runname)),
  cor.file = file.path(rundir, sprintf("%s.cor", runname)),
  bootstrap.file = file.path(rundir, "bootstrap", sprintf("raw_results_%s.csv",
    runname)),
  meta = read_meta(file.path(rundir, "meta.yaml")),
  th_names = meta$namemap$theta,
  om_names = meta$namemap$omega,
  sg_names = meta$namemap$sigma,
  use.vcov = FALSE,
  ...
)

Arguments

rundir

Name of the directory containing the output files.

runname

Name of the run (i.e., corresponds to the basename of the output files).

lst.file

Name of the .lst file (standard NONMEM output file).

ext.file

Name of the .ext file (standard NONMEM output file).

shk.file

Name of the .shk file (standard NONMEM output file).

phi.file

Name of the .phi file (standard NONMEM output file).

phm.file

Name of the .phm file (standard NONMEM output file).

cov.file

Name of the .cov file (standard NONMEM output file).

cor.file

Name of the .cor file (standard NONMEM output file).

bootstrap.file

Name of the file containing bootstrap results (typically produced by PsN).

meta

Object containing meta information that accompanies the model (e.g., names of the THETA, OMEGA and SIGMA parameters).

th_names

A character vector containing the names associated with the THETA parameters in their respective order (e.g., THETA(1) is given the name th_names[1], and so on).

om_names

A character vector containing the names associated with the the OMEGA matrix diagonal elements, in their respective order (e.g., OMEGA(1,1) is given the name om_names[1], and so on).

sg_names

A character vector containing the names associated with the SIGMA matrix diagonal elements, in their respective order (e.g., SIGMA(1,1) is given the name sg_names[1], and so on).

use.vcov

Should the default OMEGA and SIGMA be on the variance/covariance scale instead of the SD/correlation scale?

...

Additional arguments (ignored).

Details

All arguments are optional. If a particular output file cannot be found, then it is simply skipped (and the resulting object won't contain the components that would normally be read from there).

Value

A named list with components containing the outputs from the NONMEM run. Notably, the components th, om and sg contain the final estimates of the THETA, SD(ETA) and SD(EPS) parameters respectively (SD means standard deviation).