# Seamless 'Nonmem' Simulation Platform

## Documentation for package ‘NMsim’ version 0.2.5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

add | Create function that adds text elements to vector
addEVID2 | Add simulation records to dosing records
addResVar | Add residual variability based on parameter estimates
as.NMctl | Convert object to class NMctl
cbind.NMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
cbind.NMsimRes | Remove NMsimRes class and discard NMsimRes meta data
deleteTmpDirs | clean up temporary directories left by PSN and NMsim.
dimnames.NMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
dimnames.NMsimRes | Remove NMsimRes class and discard NMsimRes meta data
expandCovs | Create data set where each covariate is univariately varied (see 'forestDefineCovs()')
forestDefineCovs | Create data set where each covariate is univariately varied
forestSummarize | Summarize simulated exposures relative to reference subject
genPhiFile | Generate a .phi file for further simulation with Nonmem
inputArchiveDefault | Default location of input archive file
is.NMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
is.NMsimRes | Remove NMsimRes class and discard NMsimRes meta data
merge.NMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
merge.NMsimRes | Remove NMsimRes class and discard NMsimRes meta data
modTab | Get NMsim model metadata
NMaddSamples | Add simulation (sample) records to dosing records
NMcreateDoses | Easily and flexibly generate dosing records
NMexec | Execute Nonmem and archive input data with model files
NMreadInits | Tabulate information from parameter sections in control streams
NMreadSim | Read simulation results based on NMsim's track of model runs
NMsim | Simulate from a Nonmem model
NMsimModTabOperations | Remove NMsimModTab class and discard NMsimModTab meta data
NMsimResOperations | Remove NMsimRes class and discard NMsimRes meta data
NMsimTestConf | Summarize and test NMsim configuration
NMsim_asis | Simulation method that uses the provided control stream as is
NMsim_default | Transform an estimated Nonmem model into a simulation control stream
NMsim_EBE | Use emperical Bayes estimates to simulate re-using ETAs
NMsim_NWPRI | Simulate with parameter variability using the NONMEM NWPRI subroutine
NMsim_typical | Typical subject simiulation method
NMsim_VarCov | Simulate with parameter values sampled from a covariance step
NMwriteInits | Writes a parameter values to a control stream
NMwriteSizes | Create or update $SIZES in a control stream
overwrite | 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.
print.summary_NMsimRes | print method for NMsimRes summaries
rbind.NMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
rbind.NMsimRes | Remove NMsimRes class and discard NMsimRes meta data
readCtl | Read as class NMctl
readParsWide | Parameter data from csv
sampleCovs | Sample subject-level covariates from an existing data set
samplePars | Sample model parameters using 'mvrnorm' or the 'simpar' package
sampleParsSimpar | Sample model parameters using the 'simpar' package
simPopEtas | Generate a population based on a Nonmem model
summarizeCovs | Summarize simulated exposures relative to reference subject (see 'forestSummarize()')
summary.NMsimRes | summary method for NMsim results (NMsimRes objects)
t.NMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
t.NMsimRes | Remove NMsimRes class and discard NMsimRes meta data
triagSize | Calculate number of elements for matrix specification
unNMsimModTab | Remove NMsimModTab class and discard NMsimModTab meta data
unNMsimRes | Remove NMsimRes class and discard NMsimRes meta data