Function reference • rxode2

Creating/Deleting/Loading rxode2 compiled objects

rxode2() RxODE() rxode(): Create an ODE-based model specification

rxClean(): Cleanup anonymous DLLs by unloading them

rxCompile(): Compile a model if needed

rxCreateCache(): This will create the cache directory for rxode2 to save between sessions

rxDelete(): Delete the DLL for the model

rxUnloadAll(): Unloads all rxode2 compiled DLLs

Creating rxode2 event tables/data frames

reexports scale_type ggplot aes geom_line facet_wrap ylab xlab waiver lotri label_value label_both label_context label_wrap_gen scale_x_discrete scale_y_discrete scale_x_continuous scale_y_continuous scale_x_date scale_y_date expand_limits %>% rxWithPreserveSeed rxSetSeed rxWithSeed rxGetSeed cvPost invWR1d phi rLKJ1 rinvchisq rxRmvn rxSeedEng .vecDf .cbindOme et .s3register add.dosing add.sampling as.et as.rxEvid as.rxRateDur etExpand etRbind etRep etSeq eventTable rxEtDispatchSolve rxEvid rxRateDur rxReq .collectWarnings .clearPipe rxCbindStudyIndividual rxStack rxDerived forderForceBase rxSetIni0 .getLastIdLvl .expandPars: Objects exported from other packages

Solving, Simulating and Solving options

rxSolve rxSolve.function rxSolve.rxUi rxSolve.nlmixr2FitData rxSolve.nlmixr2FitCore rxSolve.default update.rxSolve predict.rxode2 predict.rxSolve predict.rxEt predict.rxParams simulate.rxode2 simulate.rxSolve simulate.rxParams solve.rxSolve solve.rxUi solve.rxode2 solve.rxParams solve.rxEt rxControl: Solving & Simulation of a ODE/solved system (a options) equation

reexports scale_type ggplot aes geom_line facet_wrap ylab xlab waiver lotri label_value label_both label_context label_wrap_gen scale_x_discrete scale_y_discrete scale_x_continuous scale_y_continuous scale_x_date scale_y_date expand_limits %>% rxWithPreserveSeed rxSetSeed rxWithSeed rxGetSeed cvPost invWR1d phi rLKJ1 rinvchisq rxRmvn rxSeedEng .vecDf .cbindOme et .s3register add.dosing add.sampling as.et as.rxEvid as.rxRateDur etExpand etRbind etRep etSeq eventTable rxEtDispatchSolve rxEvid rxRateDur rxReq .collectWarnings .clearPipe rxCbindStudyIndividual rxStack rxDerived forderForceBase rxSetIni0 .getLastIdLvl .expandPars: Objects exported from other packages

Functions for working with nlmixr2/rxode2 functions

model.function model.rxUi model.rxode2 model.rxModelVars model model.default: Model block for rxode2/nlmixr models

ini(): Ini block for rxode2/nlmixr models

zeroRe(): Set random effects and residual error to zero

assertRxUi() assertRxUiPrediction() assertRxUiSingleEndpoint() assertRxUiTransformNormal() assertRxUiNormal() assertRxUiMuRefOnly() assertRxUiEstimatedResiduals() assertRxUiPopulationOnly() assertRxUiMixedOnly() assertRxUiRandomOnIdOnly(): Assert properties of the rxUi models

rxAppendModel(): Append two rxui models together

rxRename .rxRename rename.rxUi rename.function rxRename.rxUi rxRename.function rxRename.default: Rename items inside of a rxode2 ui model

update(<rxUi>): Update for rxUi

as.rxUi as.rxUi.rxode2 as.rxUi.rxModelVars as.rxUi.function as.rxUi.rxUi as.rxUi.default: As rxode2 ui

`ini<-`(): Assign the ini block in the rxode2 related object

`model<-`(): Assign the model block in the rxode2 related object

rxode2 rxode2 rxode2 rxode RxODE: Set the function body of an rxUi object while retaining other object information (like data)

rxSetCovariateNamesForPiping(): Assign covariates for piping

rxUiDecompress() rxUiCompress(): Compress/Decompress rxode2 ui

as.ini(): Turn into an ini block for initialization

as.model(): Turn into a model expression

ggplot2/plot support functions

stat_cens() geom_cens(): Censoring geom/stat

stat_amt() geom_amt(): Dosing/Amt geom/stat

plot(<rxSolve>) plot(<rxSolveConfint1>) plot(<rxSolveConfint2>): Plot rxode2 objects

Exploring rxode2 and creating models with Shiny

rxShiny(): Use Shiny to help develop an rxode2 model

genShinyApp.template() write.template.server() write.template.ui(): Generate an example (template) of a dosing regimen shiny app

Using rxode2 in Packages

rxUse(): Use model object in your package

rxPkg(): Creates a package from compiled rxode2 models

Specialized Simulation functions

reexports scale_type ggplot aes geom_line facet_wrap ylab xlab waiver lotri label_value label_both label_context label_wrap_gen scale_x_discrete scale_y_discrete scale_x_continuous scale_y_continuous scale_x_date scale_y_date expand_limits %>% rxWithPreserveSeed rxSetSeed rxWithSeed rxGetSeed cvPost invWR1d phi rLKJ1 rinvchisq rxRmvn rxSeedEng .vecDf .cbindOme et .s3register add.dosing add.sampling as.et as.rxEvid as.rxRateDur etExpand etRbind etRep etSeq eventTable rxEtDispatchSolve rxEvid rxRateDur rxReq .collectWarnings .clearPipe rxCbindStudyIndividual rxStack rxDerived forderForceBase rxSetIni0 .getLastIdLvl .expandPars: Objects exported from other packages

rxPp(): Simulate a from a Poisson process

rxSimThetaOmega(): Simulate Parameters from a Theta/Omega specification

rxbeta(): Simulate beta variable from threefry generator

rxbinom(): Simulate Binomial variable from threefry generator

rxcauchy(): Simulate Cauchy variable from threefry generator

rxchisq(): Simulate chi-squared variable from threefry generator

rxexp(): Simulate exponential variable from threefry generator

rxf(): Simulate F variable from threefry generator

rxgamma(): Simulate gamma variable from threefry generator

rxgeom(): Simulate geometric variable from threefry generator

rxnbinom() rxnbinomMu(): Simulate Binomial variable from threefry generator

rxnormV() rxnorm(): Simulate random normal variable from threefry generator

rxord(): Simulate ordinal value

rxpois(): Simulate random Poisson variable from threefry generator

rxt(): Simulate student t variable from threefry generator

rxunif(): Simulate uniform variable from threefry generator

rxweibull(): Simulate Weibull variable from threefry generator

Optimizing models and/or adding precision

rxOptExpr(): Optimize rxode2 for computer evaluation

rxSumProdModel(): Recast model in terms of sum/prod

rxSetProd(): Defunct setting of product

rxSetSum(): Defunct setting of sum

Adding/Modifying rxode2 C-based functions and derivatives

rxD(): Add to rxode2's derivative tables

Running unit tests in rxode2

rxValidate() rxTest(): Validate rxode2 This allows easy validation/qualification of nlmixr by running the testing suite on your system.

Special Functions for rxode2

gammap(): Gammap: normalized lower incomplete gamma function

gammapDer(): gammapDer: derivative of gammap

gammapInv() gammapInva(): gammapInv and gammapInva: Inverses of normalized gammap function

gammaq(): Gammaq: normalized upper incomplete gamma function

gammaqInv() gammaqInva(): gammaqInv and gammaqInva: Inverses of normalized gammaq function

reexports scale_type ggplot aes geom_line facet_wrap ylab xlab waiver lotri label_value label_both label_context label_wrap_gen scale_x_discrete scale_y_discrete scale_x_continuous scale_y_continuous scale_x_date scale_y_date expand_limits %>% rxWithPreserveSeed rxSetSeed rxWithSeed rxGetSeed cvPost invWR1d phi rLKJ1 rinvchisq rxRmvn rxSeedEng .vecDf .cbindOme et .s3register add.dosing add.sampling as.et as.rxEvid as.rxRateDur etExpand etRbind etRep etSeq eventTable rxEtDispatchSolve rxEvid rxRateDur rxReq .collectWarnings .clearPipe rxCbindStudyIndividual rxStack rxDerived forderForceBase rxSetIni0 .getLastIdLvl .expandPars: Objects exported from other packages

logit() expit() logitNormInfo() probitNormInfo(): logit and inverse logit (expit) functions

lowergamma(): lowergamma: upper incomplete gamma function

probit() probitInv(): probit and inverse probit functions

erf(): Error function

log likelihood functions supporting generalized likelihoods for focei methods

llikBeta(): Calculate the log likelihood of the binomial function (and its derivatives)

llikBinom(): Calculate the log likelihood of the binomial function (and its derivatives)

llikCauchy(): log likelihood of Cauchy distribution and it's derivatives (from stan)

llikChisq(): log likelihood and derivatives for chi-squared distribution

llikExp(): log likelihood and derivatives for exponential distribution

llikF(): log likelihood and derivatives for F distribution

llikGamma(): log likelihood and derivatives for Gamma distribution

llikGeom(): log likelihood and derivatives for Geom distribution

llikNbinom(): Calculate the log likelihood of the negative binomial function (and its derivatives)

llikNbinomMu(): Calculate the log likelihood of the negative binomial function (and its derivatives)

llikNorm(): Log likelihood for normal distribution

llikPois(): log-likelihood for the Poisson distribution

llikT(): Log likelihood of T and it's derivatives (from stan)

llikUnif(): log likelihood and derivatives for Unif distribution

llikWeibull(): log likelihood and derivatives for Weibull distribution

Parallel processing support commands

getRxThreads() setRxThreads() rxCores(): Get/Set the number of threads that rxode2 uses

rxode2 utility functions

reexports scale_type ggplot aes geom_line facet_wrap ylab xlab waiver lotri label_value label_both label_context label_wrap_gen scale_x_discrete scale_y_discrete scale_x_continuous scale_y_continuous scale_x_date scale_y_date expand_limits %>% rxWithPreserveSeed rxSetSeed rxWithSeed rxGetSeed cvPost invWR1d phi rLKJ1 rinvchisq rxRmvn rxSeedEng .vecDf .cbindOme et .s3register add.dosing add.sampling as.et as.rxEvid as.rxRateDur etExpand etRbind etRep etSeq eventTable rxEtDispatchSolve rxEvid rxRateDur rxReq .collectWarnings .clearPipe rxCbindStudyIndividual rxStack rxDerived forderForceBase rxSetIni0 .getLastIdLvl .expandPars: Objects exported from other packages

rxInv(): Invert matrix using RcppArmadillo.

rxIsCurrent(): Checks if the rxode2 object was built with the current build

rxLhs(): Left handed Variables

rxLock() rxUnlock(): Lock/unlocking of rxode2 dll file

rxNorm(): Get the normalized model

rxParams() rxParam(): Parameters specified by the model

rxProgress() rxTick() rxProgressStop() rxProgressAbort(): rxode2 progress bar functions

rxState(): State variables

rxSymInvChol(): Get Omega^-1 and derivatives

uppergamma(): uppergamma: upper incomplete gamma function

Internal Functions

.copyUi(): This copies the rxode2 UI object so it can be modified

.handleSingleErrTypeNormOrTFoceiBase(): Handle the single error for normal or t distributions

.modelHandleModelLines(): Handle model lines

.quoteCallInfoLines(): Returns quoted call information

.rxLinCmtGen(): Internal function to generate the model variables for a linCmt() model

.rxWithOptions(): Temporarily set options then restore them while running code

.rxWithWd(): Temporarily set options then restore them while running code

reexports scale_type ggplot aes geom_line facet_wrap ylab xlab waiver lotri label_value label_both label_context label_wrap_gen scale_x_discrete scale_y_discrete scale_x_continuous scale_y_continuous scale_x_date scale_y_date expand_limits %>% rxWithPreserveSeed rxSetSeed rxWithSeed rxGetSeed cvPost invWR1d phi rLKJ1 rinvchisq rxRmvn rxSeedEng .vecDf .cbindOme et .s3register add.dosing add.sampling as.et as.rxEvid as.rxRateDur etExpand etRbind etRep etSeq eventTable rxEtDispatchSolve rxEvid rxRateDur rxReq .collectWarnings .clearPipe rxCbindStudyIndividual rxStack rxDerived forderForceBase rxSetIni0 .getLastIdLvl .expandPars: Objects exported from other packages

odeMethodToInt(): Conversion between character and integer ODE integration methods for rxode2

rxAllowUnload(): Allow unloading of dlls

rxAssignControlValue(): Assign Control Variable

rxAssignPtr(): Assign pointer based on model variables

rxChain() `+`(<solveRxDll>): rxChain Chain or add item to solved system of equations

rxControlUpdateSens(): This updates the tolerances based on the sensitivity equations

rxDfdy(): Jacobian and parameter derivatives

rxFun() rxRmFun(): Add user function to rxode2

rxGetControl(): rxGetControl option from ui

rxGetLin(): Get the linear compartment model true function

rxGetrxode2(): Get rxode2 model from object

rxHtml(): Format rxSolve and related objects as html.

rxIndLinState(): Set the preferred factoring by state

rxIndLinStrategy(): This sets the inductive linearization strategy for matrix building

rxIndLin_: Inductive linearization solver

rxPreferredDistributionName(): Change distribution name to the preferred distribution name term

rxRemoveControl(): rxRemoveControl options for UI object

rxReservedKeywords: A list and description of Rode supported reserved keywords

rxS(): Load a model into a symengine environment

rxSetControl(): rxSetControl options for UI object

rxSetProgressBar(): Set timing for progress bar

rxSupportedFuns(): Get list of supported functions

rxSuppressMsg(): Respect suppress messages

rxSyncOptions(): Sync options with rxode2 variables

rxSyntaxFunctions: A list and description of Rode supported syntax functions

rxTempDir(): Get the rxode2 temporary directory

rxTheme(): rxTheme is the ggplot2 theme for rxode2 plots

rxToSE() .rxToSE() rxFromSE() .rxFromSE(): rxode2 to symengine environment

rxTrans(): Translate the model to C code if needed

rxUiGet(): S3 for getting information from UI model

summary(<rxode2>): Print expanded information about the rxode2 object.