nmtests

Benchmark tests against nonmem. These aren't tests of speed or performance, but rather tests comparing different behaviors. The primary interests are things like dosing events (infusions and bolus), steady state, lag times, bioavailability, handling time-varying covariates etc..

The most-complete test document is in dosing/dosing-vignette.md. This is usually what users are primarily interested in checking.

There is another vignette testing time-varying covariates. The output is located in time-varying/time-varying-vignette.md.

Results

Dosing vignette

• dosing/dosing-vignette.md - the completed vignette
• dosing/results/1001.csv - mrgsolve / nonmem comparison
• dosing/results/1001-sims.csv - mrgsolve simulated data
• dosing/results/1001-nm.csv - nonmem simulated data
• dosing/results/1001.json - latest run meta data
• dosing/results/img - png files of comparison plots

Time-varying covariate vignette

• time-varying/time-varying-vignette.md - the completed vignette
• time-varying/results/2001.csv - mrgsolve / nonmem comparison
• time-varying/results/2001-sims.csv - mrgsolve simulated data
• time-varying/results/2001-nm.csv - nonmem simulated data
• time-varying/results/2001.json - latest run meta data
• time-varying/results/img - png files of comparison plots

Requirements

• R; check the pkgr.yml file for the required version
• pkgr
  • Required R packages can be found in the pkgr.yml file
• PsN, installed and able to run nonmem
• nonmem, installed and configured to run using PsN
• mrgsolve, installed and able to compile and run models
  • on Windows systems, this will require installation of Rtools
  • on macos systems, this will require installation of a mac-specific toolchain

There is a make file located in the root directory that can be used to run tests and checks; this utility is typically available on unix-alike systems. Note that running the make commands below will not work unless make is installed.

Package installation

• Install pkgr
• Install packages
  • bash$ pkgr install
• The pkgr.yml file places an R version requirement on the installation; this can be modified
• Packages are installed in the renv directory in a R version-specific location so that package availability is always consistent with the R version
• Any issues installing or using pkgr should be resolved with the pkgr maintainers here

Run

All R vignette scripts run from the directory where the reside. The vignette simulates using both mrgsolve and nonmem and requires nonmem and PsN install; it is up to the user to install both and troubleshoot any issues with those tools. There is also a check script that simulates with mrgsolve and compares against previously simulated nonmem output.

• Run dosing/dosing-vignette.R

  • On the command line: bash$ make dosing
  • To check: bash$ make check-dosing
  • Via R studio: knit or run dosing/dosing-vignette.R

• Run time-varying/time-varying-vignette.R

  • On the command line: bash$ make tv
  • To check: bash$ make check-tv
  • Via R studio: knit or run time-varying/time-varying-vignette.R