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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

Solving, Simulating and Solving options

Functions for working with nlmixr2/rxode2 functions

model.function model.rxUi model.rxode2 model.rxModelVars model model.default
Model block for rxode2/nlmixr models
modelExtract modelExtract.function modelExtract.rxUi modelExtract.rxode2 modelExtract.rxModelVars modelExtract.default
Extract model lines from a rxui model
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.rxode2tos 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
rxSetPipingAuto()
Set the variables for the model piping automatic covarite selection
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

binomProbs()
Calculate expected confidence bands with binomial sampling distribution
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 toTrialDuration
Objects exported from other packages
meanProbs()
Calculate expected confidence bands or prediction intreval with normal or t sampling distribution
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 toTrialDuration
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

Internal Functions

.copyUi()
This copies the rxode2 UI object so it can be modified
.handleSingleErrTypeNormOrTFoceiBase()
Handle the single error for normal or t distributions
.matchesLangTemplate()
Check if a language object matches a template language object
.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 toTrialDuration
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/Create C functions for use in 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 rxode2 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.

Rxode2 data sets

rxResidualError
A description of Rode2 supported residual errors