Extract estimates from NONMEM ext file — read

This function retrieves NONMEM estimates for use in the mrgsolve model when $NMEXT is invoked. See nmext().

Usage

read_nmext(
  run = NA_real_,
  project = getwd(),
  file = paste0(run, ".ext"),
  path = NULL,
  read_fun = c("data.table", "read.table"),
  index = "last"
)

Arguments

run: a run number or run identifier.
project: the NONMEM project directory.
file: the ext file name.
path: full path and file name for ext file.
read_fun: function to read the ext file; data.table::fread() will be used if available; otherwise utils::read.table() is used.
index: selects the table number whose results will be returned; use value "last" to select the last table in the .ext file; or pass an integer specifying the table number; in case there is exactly one table in the .ext file, pass the value "single" to bypass parsing the file to look for sub tables (this might be useful when BAYES analysis was performed as the only estimation method and there are 10000s of posterior samples in the file).

Value

A list with param, omega, and sigma in a format ready to be used to update a model object.

Examples

project <- system.file("nonmem", package = "mrgsolve")

est <- read_nmext(1005, project = project)

est$param
#> $THETA1
#> [1] 9.50789
#> 
#> $THETA2
#> [1] 22.791
#> 
#> $THETA3
#> [1] 0.0714337
#> 
#> $THETA4
#> [1] 3.47451
#> 
#> $THETA5
#> [1] 113.277
#> 
#> $THETA6
#> [1] 1.02435
#> 
#> $THETA7
#> [1] 1.19212
#> 

est$omega
#>            [,1]       [,2]       [,3]
#> [1,]  0.2138790  0.1207700 -0.0116278
#> [2,]  0.1207700  0.0945105 -0.0372064
#> [3,] -0.0116278 -0.0372064  0.0465631

est$sigma
#>           [,1]     [,2]
#> [1,] 0.0491707 0.000000
#> [2,] 0.0000000 0.201769

est <- read_nmext(2005, project = project, index = 3)