Import model outputs

Benjamin Guiastrennec

02 June, 2024

Source: vignettes/import_model_outputs.Rmd

The xpose_data function

The function xpose_data() collects all model output files and table and organizes them into an R object commonly called xpdb for xpose data base.

xpdb <- xpose_data(runno = '001')

Imported files

NONMEM runs

To make full use of the functionality offered by xpose the following NONMEM output files should be available:

  • .lst/.out/.res: used to collect information on the run (template_titles) as well as the output table names. Alternatively a model file (.mod/.ctl) can be used but some of the information in template_titles may not be available.
  • .ext: used to collect final parameter estimates and residual standard error (RSE)
  • .phi: used for the random effects and iOFV
  • .cov: used for the covariance matrix
  • .cor: used for the correlation matrix
  • .grd: used for the estimation gradients
  • .shk: used to compute random effect shrinkage template_titles
  • output and simulation tables: for the actual data

When importing the files, xpose will return messages to the console and inform of any issue encountered during the import.

xpdb <- xpose_data(runno = '001')

Looking for nonmem output tables
Reading: sdtab001, catab001, cotab001, patab001 [$prob no.1]

Looking for nonmem output files
Reading: run001.cor, run001.cov, run001.ext, run001.grd, run001.phi

These messages can be silenced with the option quiet = TRUE.

FIRSTONLY tables

xpose is compatible with the $TABLE FIRSTONLY option of NONMEM. The option FIRSTONLY only output the first record for each ID and hence can be used to decrease the size of output tables having no time-varying columns. During tables import xpose will merge FIRSTONLY tables with regular tables allowing seamless use of columns from FIRSTONLY in plots.

Compressed tables

xpose makes use of the readr which offers the advantages of 1) rapidly import big tables and 2) automatically import compressed table (e.g. sdtab001.zip) to increase storage capacity.

Others NLME tools

Coming with future releases…

Structure of the xpdb object

A typical xpdb object contains 8 levels namely:

  • code: the parsed model code
  • summary: contains key information regarding the model. All the information contained in the summary can be used as part of the template_titles.
  • data: contains all output and simulation tables as well as the column indexing
  • files: contains all output files
  • special: contains post-processed datasets used by functions like vpc()
  • gg_theme: an attached ggplot2 theme
  • xp_theme: an attached xpose theme
  • options: attached global options