In MikeKSmith/rspeaksnonmem: Read, Modify and run NONMEM from within R

  library(knitr)
  opts_chunk$set(fig.width=6, fig.height=6)

rspeaksnonmem is designed to allow the user to craft workflows based on a given NONMEM model.

rspeaksnonmem allows the user to run NONMEM models from R either directly running the nmfe.bat or by calling Perl speaks NONMEM (PsN) functions like "execute". Other PsN functions can be run from R - VPC (Visual Predictive Check), bootstrap, SSE (Stochastic Simulation and Estimation).

This allows the user to define sequences of pharmacometrics workflow tasks via R within a single R script. This increases traceability and reproducibility of workflow.

devtools::load_all(pkg=".")
devtools::load_all(pkg = "C:\\Users\\smith_mk\\Documents\\Working documents\\RNMImport")

getwd()

file.copy(from = file.path(system.file("inst/exdata/", package="rspeaksnonmem"),
                           "warfarin_conc_pca.csv"),
          to = getwd(), overwrite = T )
file.copy(from = file.path(system.file("inst/exdata", package="rspeaksnonmem"),
                           "warfarin.ctl"),
          to = getwd(), overwrite = T )

Running NONMEM

estimate_NM runs NONMEM for a given model file. Note that in the command argument to the function we specify the complete path to the NONMEM executable .bat file. This allows you to be very precise about which version of NONMEM you use. If the clean argument is non-zero it cleans up the working directory deleting all of the temporary NONMEM files, leaving only the output.

estimate_NM(modelFile = "warfarin.ctl", 
            command = "c:/nm72/run/nmfe72.bat", 
            clean = 1)

Running PsN

We can now use PsN command sumo to summarise the output. Note that here we are not using the command argument, but instead we specify the installation directory for Perl / PsN and which PsN version we are using. rspeaksnonmem will then create a command based on the directory, sumo and version information.

  sumo_PsN(installPath = "c:/strawberry/perl",
           version = "4.6.0",
           lstFile = "warfarin.lst")

Different ways of specifying the command to be run

The defineExecutable function used by estimate_NM and PsN calling functions can search for user-specified command to find valid executables at the system prompt. If you supply the command with no file path with searchCommand=T then the function uses Sys.which or Sys.which2 (depending on OS) to search the system PATH or shortcut definitions for executables.

defineExecutable(command = "R", searchCommand = T)

If you specify the tool and the installPath, then defineExecutables looks within the installPath directory for executables that match the tool name.

defineExecutable(tool = "nonmem", installPath = "c:/nm72", searchCommand = T)

Note that for PsN there could are a few ways of invoking the routine.

defineExecutable(tool = "vpc", 
                 installPath = "c:/strawberry/perl", 
                 searchCommand = T)

In the rspeaksnonmem calls to PsN routines we explicitly tie the Perl script to the "parent" Perl executable. We use the version number Perl script so that it's clear to anyone looking at the command which version of the Perl script has been used and the Perl executable associated with it.

defineExecutable(tool = "vpc", 
                 installPath = "c:/strawberry/perl", 
                 version = "4.7.0")

Validating PsN option lists

rspeaksnonmem has functionality to check that the name-value pairs specified in the psnOpts arguments of the PsN calling functions are appropriately named and have valid argument types for use with PsN. We do this by checking against the routines' -h help files.

  psnOpts <- list(picky = "yes",  ## retries option should be numeric
                  auto_bin = 4,     ## auto_bin is not a valid option for execute
                  dir = getwd())

  validate_PsN_options(tool = "execute",
                       installPath = "c:/strawberry/perl",
                       version = "4.6.0",
                       psnOpts = psnOpts)

Calling PsN

rspeaksnonmem has PsN call functions for the following routines:

• execute
• sumo
• vpc
• bootstrap
• sse
• runrecord

Other PsN functionality

Although functions have been provided as wrappers to the PsN functions, it is easy to extend these to any other PsN function using the function callPsN.

 linearize-4.7.0 warfarin.ctl -dir=linearize

  callPsN(tool = "linearize", 
          installPath = "c:/strawberry/perl",
          version = "4.7.0",
          file = "warfarin.ctl")

MikeKSmith/rspeaksnonmem documentation built on March 12, 2023, 3:25 p.m.