Convenience function for ingesting a bbr model into xpose and xpose.xtras

bbr is a Metrum Research Group package for managing NONMEM modeling workflows via bbi. It is not distributed on CRAN (see Additional_repositories in this package's DESCRIPTION for where to obtain it).

Reading a bbr-managed model into xpose/xpose.xtras normally requires manually reconstructing the output file path from the model object, e.g.

xtras_data(
  file = file.path(bbr::get_output_dir(mod), paste0(bbr::get_model_id(mod), ".lst"))
)

xp_from_bbr() wraps that pipeline.

Usage

xp_from_bbr(.mod, ..., .use_bbr_descr = TRUE)

Arguments

.mod

<bbi_nonmem_model> A bbr NONMEM model object, e.g. as returned by bbr::read_model().

...

Passed to xtras_data() (and, in turn, xpose::xpose_data()).

.use_bbr_descr

<logical> If TRUE (default) and .mod carries a bbr description, use it to set the descr property of the result (see set_prop()), taking precedence over any description parsed from the NONMEM output itself.

Value

An <xp_xtras> object

See also

bbr::read_model(), xtras_data()

Examples

if (requireNamespace("bbr", quietly = TRUE)) {
  # Build a bbr-style model directory from the bundled pheno_saemimp example
  src_dir <- system.file("pheno_saemimp", package = "xpose.xtras")
  mod_dir <- tempfile("xp_from_bbr_ex")
  dir.create(mod_dir)
  file.copy(file.path(src_dir, "run18.mod"), file.path(mod_dir, "18.mod"))
  out_dir <- file.path(mod_dir, "18")
  dir.create(out_dir)
  out_files <- setdiff(list.files(src_dir, pattern = "^run18\\."), "run18.mod")
  for (f in out_files) {
    file.copy(
      file.path(src_dir, f),
      file.path(out_dir, paste0("18.", sub("^run18\\.", "", f)))
    )
  }
  # bbr considers a run finished once bbi has written this file
  writeLines("{}", file.path(out_dir, "bbi_config.json"))

  mod <- bbr::new_model(file.path(mod_dir, "18"), .description = "Phenobarbital SAEM model")
  print(xp_from_bbr(mod))
  unlink(mod_dir, recursive = TRUE)
}
#> Warning: No table files could be found.
#> 
#> ── ~ xp_xtras object 
#> Model description: Phenobarbital SAEM model
#> 18.lst overview: 
#>  - Software: nonmem 7.5.0 
#>  - Attached files (memory usage 348.5 Kb): 
#>    + obs tabs: <none> 
#>    + sim tabs: <none> 
#>    + output files: 18.cor, 18.cov, 18.ext, 18.phi, 18.shk 
#>    + special: <none> 
#>  - gg_theme: theme_readable 
#>  - xp_theme: xp_xtra_theme new_x$xp_theme 
#>  - Options: dir = /tmp/RtmpnYMwYM/xp_from_bbr_ex1b59222a3d6f/18, quiet = TRUE, manual_import = NULL, cvtype = exact