Package: NMsim 0.2.7.901

Philip Delff

NMsim: Seamless 'Nonmem' Simulation Platform

A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.

Authors:Philip Delff [aut, cre], Brian Reilly [ctb], Sanaya Shroff [ctb], Boris Grinshpun [ctb]

NMsim_0.2.7.901.tar.gz
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NMsim_0.2.7.901.tgz(r-4.6-any)NMsim_0.2.7.901.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
NMsim/json (API)
NEWS

# Install 'NMsim' in R:
install.packages('NMsim', repos = c('https://nmautoverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nmautoverse/nmsim/issues

Pkgdown/docs site:https://nmautoverse.github.io

On CRAN:

Conda:

6.17 score 10 stars 55 scripts 565 downloads 38 exports 10 dependencies

Last updated from:c55fd25917. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE181
source / vignettesOK235
linux-release-x86_64NOTE174
macos-release-arm64NOTE189
macos-oldrel-arm64NOTE136
windows-develNOTE177
windows-releaseNOTE132
windows-oldrelNOTE121
wasm-releaseOK125

Exports:addaddEVID2addResVardeleteTmpDirsexpandCovsforestDefineCovsforestSummarizegenPhiFileinputArchiveDefaultis.NMsimModTabis.NMsimResmodTabNMaddSamplesNMcreateDosesNMexecNMreadSimNMsimNMsim_asisNMsim_defaultNMsim_EBENMsim_knownNMsim_NWPRINMsim_typicalNMsim_VarCovNMsimTestConfNMwriteFiltersNMwriteInitsNMwriteSizesoverwriteprioritizePathsreadParsWidesampleCovssampleParssampleParsSimparsimPopEtassummarizeCovsunNMsimModTabunNMsimRes

Dependencies:data.tablefstfstcoreMASSNMdataR.methodsS3R.ooR.utilsRcppxfun

Readme and manuals

Help Manual

Help pageTopics
Create function that adds text elements to vectoradd
Add simulation records to dosing recordsaddEVID2
Add residual variability based on parameter estimatesaddResVar
clean up temporary directories left by PSN and NMsim.deleteTmpDirs
Create data set where each covariate is univariately varied (see `forestDefineCovs()`)expandCovs
Create data set where each covariate is univariately variedforestDefineCovs
Summarize simulated exposures relative to reference subjectforestSummarize
Generate a .phi file for further simulation with NonmemgenPhiFile
Default location of input archive fileinputArchiveDefault
Get NMsim model metadatamodTab
Add simulation (sample) records to dosing recordsNMaddSamples
Easily and flexibly generate dosing recordsNMcreateDoses
Execute Nonmem and archive input data with model filesNMexec
Read simulation results based on NMsim's track of model runsNMreadSim
Simulate from a Nonmem modelNMsim
Simulation method that uses the provided control stream as isNMsim_asis
Transform an estimated Nonmem model into a simulation control streamNMsim_default
Use emperical Bayes estimates to simulate re-using ETAsNMsim_EBE
Simulate with parameter variability using the NONMEM NWPRI subroutineNMsim_NWPRI
Typical subject simiulation methodNMsim_typical
Simulate with parameter values sampled from a covariance stepNMsim_VarCov
Summarize and test NMsim configurationNMsimTestConf
Writes a parameter values to a control streamNMwriteInits
Create or update $SIZES in a control streamNMwriteSizes
Create function that modifies text elements in a vector Namely used to feed functions to modify control streams using `NMsim()` arguments such as `modify`. Those functions are often onveniently passed a function. `add` and `overwrite` are simple shortcuts to creating such functions. Make sure to see examples.overwrite
print method for NMsimRes summariesprint.summary_NMsimRes
first path that worksprioritizePaths
Parameter data from csvreadParsWide
Sample subject-level covariates from an existing data setsampleCovs
Sample model parameters using `mvrnorm` or the `simpar` packagesamplePars
Sample model parameters using the `simpar` packagesampleParsSimpar
Generate a population based on a Nonmem modelsimPopEtas
Summarize simulated exposures relative to reference subject (see `forestSummarize()`)summarizeCovs
summary method for NMsim results (NMsimRes objects)summary.NMsimRes
Remove NMsimModTab class and discard NMsimModTab meta datacbind.NMsimModTab dimnames.NMsimModTab is.NMsimModTab merge.NMsimModTab NMsimModTabOperations rbind.NMsimModTab t.NMsimModTab unNMsimModTab
Remove NMsimRes class and discard NMsimRes meta datacbind.NMsimRes dimnames.NMsimRes is.NMsimRes merge.NMsimRes NMsimResOperations rbind.NMsimRes t.NMsimRes unNMsimRes