| add | Create function that adds text elements to vector |
| addBlocks | Add blocking info to parameter set |
| addClass | Add class if not already present |
| addEVID2 | Add simulation records to dosing records |
| addParameter | add parameter based on par.type and i,j |
| addParType | Fill parameter names indexes in a data set |
| addResVar | Add residual variability based on parameter estimates |
| as.NMctl | Convert object to class NMctl |
| callNonmemDirect | Generate system command to call Nonmem directly |
| checkTimes | Test if file modification times indicate that Nonmem models... |
| cleanStrings | Drop spaces and odd characters. Use to ensure generated file... |
| completeCov | Expand a set of covariate values into a data.set with... |
| count_ij | Assign i and j indexes based on parameter section text |
| dcastSe | A standard-evaluation interface to 'data.table::dcast()' |
| deleteTmpDirs | clean up temporary directories left by PSN and NMsim. |
| expandCovs | Create data set where each covariate is univariately varied... |
| findUpdated | Filter control streams to only those updated since last run |
| fnAppend | paste something before file name extension. |
| 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 |
| initsToExt | Convert inits elements to a parameter data.frame |
| inputArchiveDefault | Default location of input archive file |
| itriag | Row numbers of elements in a triangular representation of a... |
| jtriag | Column numbers of elements in a triangular representation of... |
| message_dt | print a data.table |
| modifyModel | Internal method for handling modify argument to NMsim |
| modTab | Get NMsim model metadata |
| nameMultipleFiles | Create file names for multiple list elements |
| NMaddSamples | Add simulation (sample) records to dosing records |
| NMcreateDoses | Easily and flexibly generate dosing records |
| NMcreateMatLines | Create text lines for OMEGA and SIGMA Nonmem sections |
| NMexec | Execute Nonmem and archive input data with model files |
| NMexecDirectory | Execute Nonmem inside a dedicated directory |
| NMextractText | Versatile text extractor from Nonmem (input or output)... |
| NMgenPNM | Generate PNM file for sge clusters |
| NMreadInits | Tabulate information from parameter sections in control... |
| NMreadSection | Extract sections of Nonmem control streams |
| NMreadSim | Read simulation results based on NMsim's track of model runs |
| NMreadSimModTab | Read simulation results from rds objects and/or NMsimModTab... |
| NMreadSimModTabOne | Read simulation results from an rds or a NMsimModTab object |
| NMreadSimRes | Read simulation results from data.frames or fst files |
| NMreadSimResOne | read one sim element. This will be run in lapply in... |
| NMreadSizes | Read SIZES info from a control stream |
| NMreplaceInits | Replace initial values in Nonmem control stream |
| NMrunLin | Internal function to run Nonmem on linux |
| NMseed | Add seed string to simulation model data.table |
| NMsim | Simulate from a Nonmem model |
| NMsim_asis | Simulation method that uses the provided control stream as is |
| NMsimCheckMod | Check a simulation control streams for things that can cause... |
| NMsim_default | Transform an estimated Nonmem model into a simulation control... |
| NMsim_EBE | Use emperical Bayes estimates to simulate re-using ETAs |
| NMsim_known | NMsim_known is an old name for NMsim_EBE() |
| NMsimModTabOperations | Remove NMsimModTab class and discard NMsimModTab meta data |
| NMsim_NWPRI | Simulate with parameter variability using the NONMEM NWPRI... |
| NMsimResOperations | Remove NMsimRes class and discard NMsimRes meta data |
| NMsimTestConf | Summarize and test NMsim configuration |
| NMsim_typical | Typical subject simiulation method |
| NMsim_VarCov | Simulate with parameter values sampled from a covariance step |
| NMupdateFn | Update file names in control stream to match model name |
| NMupdateInits | Create new Nonmem control stream with updated initial... |
| NMwriteFilters | Write IGNORE/ACCEPT filters to NONMEM model |
| NMwriteInits | Writes a parameter values to a control stream |
| NMwriteSizes | Create or update $SIZES in a control stream |
| NWPRI_df | Add degrees of freedom by OMEGA/SIGMA block |
| overwrite | Create function that modifies text elements in a vector... |
| padZeros | pad zeros on integers |
| pasteFuns | Paste string to start of vector only |
| prettyMatLines | Print OMEGA and SIGMA matrices for NONMEM sections in block... |
| print.summary_NMsimRes | print method for NMsimRes summaries |
| prioritizePaths | first path that works |
| 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'... |
| sampleParsSimpar | Sample model parameters using the 'simpar' package |
| simpleCharArg | Check that a variable is a single character string meeting... |
| simplePath | Simplify file paths by dropping .. and // |
| simPopEtas | Generate a population based on a Nonmem model |
| summarizeCovs | Summarize simulated exposures relative to reference subject... |
| summary.NMsimRes | summary method for NMsim results (NMsimRes objects) |
| triagSize | Calculate number of elements for matrix specification |
| typicalize | Set variability parameters to zero |
| writeTextFile | Conveniently write text lines to file |
