
Function reference
-
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
-
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
-
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.function
solve.rxode2
solve.rxParams
solve.rxEt
rxControl
- Options, Solving & Simulation of an ODE/solved system
-
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
-
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.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
-
stat_cens()
geom_cens()
- Censoring geom/stat
-
stat_amt()
geom_amt()
- Dosing/Amt geom/stat
-
plot(<rxSolve>)
plot(<rxSolveConfint1>)
plot(<rxSolveConfint2>)
- Plot rxode2 objects
-
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
-
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
-
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
-
rxOptExpr()
- Optimize rxode2 for computer evaluation
-
rxSumProdModel()
- Recast model in terms of sum/prod
-
rxSetProd()
- Defunct setting of product
-
rxSetSum()
- Defunct setting of sum
-
rxD()
- Add to rxode2's derivative tables
-
rxValidate()
rxTest()
- Validate rxode2 This allows easy validation/qualification of nlmixr by running the testing suite on your system.
-
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
-
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
-
getRxThreads()
setRxThreads()
rxCores()
- Get/Set the number of threads that rxode2 uses
-
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
-
.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
- 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
-
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.