Skip to contents

Read NONMEM output into a list.

Source: R/read_nmext.R
read_nmext.Rd

read_nmext returns a summary of a given NONMEM run, including termination messages, parameter estimates, and precision estimates. Minimally, the NONMEM output and '.ext' files must be available.

Usage

read_nmext(
  fileName,
  fileExt = ".lst",
  directory = NULL,
  quiet = FALSE,
  estNo = NULL,
  ...
)

Arguments

fileName

A NONMEM output file prefix, without extension (e.g. "run315").

fileExt

The file extension for NONMEM output, set to ".lst" by default.

directory

The directory to look for files within. If NULL, uses the current directory.

quiet

Flag for displaying intermediate output.

estNo

The estimation number to report (by default, if only one estimation step is present, that will be reported; if multiple are reported, the last will be reported by default).

...

Passed to each of the read functions (ignored in the functions).

Value

A list of lists, containing 'Termination' (summary of NONMEM's termination output, including shrinkages and ETABAR estimates), 'OFV' (the objective function value), 'Thetas' (a vector of structural parameter estimates, or THETAs), 'Omega', a list of lists containing the OMEGA matrix, 'Sigma', a list of lists containing the SIGMA matrix, 'seThetas', a vector of standard errors for THETAs, 'seOmega', a list of lists containing standard errors for the OMEGA matrix, and 'seSigma', a list of lists containing standard errors for the SIGMA matrix.

See also

NONMEM (https://www.iconplc.com/innovation/nonmem/)

Other NONMEM reading: plot_scm(), read_nm_all(), read_nm_multi_table(), read_nmcov(), read_nmtables(), read_nm(), read_scm()

Author

Justin Wilkins, justin.wilkins@occams.com

Examples

if (FALSE) { # \dontrun{
read_nmext("run315")
read_nmext("run315", ".nmlst")
} # }