Package index • rxode2

Creating/Deleting/Loading rxode2 compiled objects

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

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

Creating rxode2 event tables/data frames

et(): Event Table Function

toTrialDuration(): Convert event data to trial duration data A helper function to create a custom event table. The observation time will start from the first event time (baseline) and end at trial duration. The interval is the spacing between each observation.

etRbind() rbind(<rxEt>): Combining event tables

etRep() rep(<rxEt>): Repeat an rxode2 event table

etSeq() seq(<rxEt>): Sequence of event tables

etExpand(): Expand additional doses

as.et(): Coerce object to data.frame

eventTable(): Create an event table object

add.dosing(): Add dosing to eventTable

add.sampling(): Add sampling to eventTable

Solving, Simulating and Solving options

rxSolve() update(<rxSolve>) predict(<rxode2>) predict(<function>) predict(<rxUi>) 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

rxCbindStudyIndividual(): Bind the study parameters and individual parameters

Functions for working with nlmixr2/rxode2 functions

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

as.model(): Turn into a model expression

as.rxUi(): As rxode2 ui

assertCompartmentExists() testCompartmentExists(): Verify that the compartment exists in a model

assertCompartmentName() assertVariableName() assertParameterValue() assertExists() testExists(): Verify that a value is a valid nlmixr2 compartment name

assertCompartmentNew(): Verify that a compartment would be new to the model

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

assertVariableExists() testVariableExists(): Assert a variable exists in the model

assertVariableNew(): Assert a variable would be new to the model

ini(): Ini block for rxode2/nlmixr models

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

model(): Model block for rxode2/nlmixr models

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

modelExtract(): Extract model lines from a rxui model

rxAppendModel(): Append two rxui models together

rxFixPop(): Apply the fixed population estimated parameters

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

rxSetCovariateNamesForPiping(): Assign covariates for piping

rxSetPipingAuto(): Set the variables for the model piping automatic covarite selection

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

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

testIniDf() assertIniDf(): This function tests if this object is a iniDf as needed by the UI

testRxLinCmt() assertRxLinCmt(): Test if rxode2 uses linear solved systems

testRxUnbounded() assertRxUnbounded() warnRxBounded(): Test if the rxode2 model has any parameters with user defined boundaries

update(<rxUi>): Update for rxUi

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

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

cvPost(): Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

dfWishart(): This uses simulations to match the rse

meanProbs(): Calculate expected confidence bands or prediction intreval with normal or t sampling distribution

rinvchisq(): Scaled Inverse Chi Squared distribution

rxGetSeed(): Get the rxode2 seed

rxPp(): Simulate a from a Poisson process

rxSetSeed(): Set the parallel seed for rxode2 random number generation

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

rxWithSeed() rxWithPreserveSeed(): Preserved seed and possibly set the seed

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

boxCox() boxCoxInv() yeoJohnson() yeoJohnsonInv(): boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions

erf(): Error function

forderForceBase(): Force using base order for rxode2 radix sorting

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

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

lowergamma(): lowergamma: upper incomplete gamma function

phi(): Cumulative distribution of standard normal

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

rxRmvn(): Simulate from a (truncated) multivariate normal

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

rxDerived(): Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.

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

swapMatListWithCube(): Swaps the matrix list with a cube

uppergamma(): uppergamma: upper incomplete gamma function

User functions

linMod() linMod0() linModB() linModB0() linModA() linModA0() linModD() linModD0() linModM() linModM0(): Linear model to replace in rxode2 ui model

rxIntToBase(): Convert a positive base

rxIntToLetter(): Convert a positive integer to a letter series

rxUdfUiControl(): Return the control that is being processed or setup control for processing

rxUdfUiData(): Return the data.frame that is being processed or setup data.frame for processing

rxUdfUiEst(): Return the current estimation method for the UI processing

rxUdfUiIniDf(): Get the rxode2 iniDf of the current UI being processed (or return NULL)

rxUdfUiIniLhs(): Return the lhs parsed language expression

rxUdfUiMv(): Return the model variables that is being processed or setup model variables for processing

rxUdfUiNum(): This gives the current number in the ui of the particular function being called.

rxUdfUiParsing(): Returns if the current ui function is being parsed

Internal Functions

.cbindOme(): cbind Ome

.collectWarnings(): Collect warnings and just warn once.

.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

.rxode2ptrs(): Get the rxode2 function pointers

.toClassicEvid(): This converts NONMEM-style EVIDs to classic RxODE events

.vecDf(): Convert numeric vector to repeated data.frame

invWR1d(): One correlation sample from the Inverse Wishart distribution

is.rxStackData(): Return if the object can be stacked

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

print(<rxModelVars>): Print Values

rLKJ1(): One correlation sample from the LKJ distribution

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

rxEtDispatchSolve(): Dispatch solve to 'rxode2' solve

rxEvid() as.rxEvid() c(<rxEvid>) `[`(<rxEvid>) as.character(<rxEvid>) `[[`(<rxEvid>) `units<-`(<rxEvid>) c(<rxRateDur>) format(<rxEvid>) format(<rxRateDur>) print(<rxEvid>): EVID formatting for tibble and other places.

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

rxParseSuppressMsg(): Respect suppress messages

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

rxRateDur() `[`(<rxRateDur>) as.rxRateDur() as.character(<rxRateDur>) `[[`(<rxRateDur>): Creates a rxRateDur object

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

rxSetIni0(): Set Initial conditions to time zero instead of the first observed/dosed time

rxSetProgressBar(): Set timing for progress bar

rxStack(): Stack a solved object for things like default ggplot2 plot

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

rxode2parse(): Internal translation to get model variables list

rxode2parseAssignTranslation(): This assigns the c level linkages for a roxde2 model

rxode2parseD(): This gives the derivative table for rxode2

rxode2parseGetPackagesToLoad() rxode2parseAssignPackagesToLoad(): Control the packages that are loaded when a rxode2 model dll is loaded

rxode2parseGetPointerAssignment(): This function gets the currently assigned function pointer assignments

rxode2parseGetTranslation(): This function gets the currently assigned translations

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

rxUiDeparse(): This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information

Neural Network Activation functions

ELU(): Exponential Linear Unit (ELU) Activation Function

GELU(): GELU activation function

PReLU(): Parametric ReLU Activation Function

ReLU(): Rectified Linear Unit (ReLU) Activation Function

SELU(): Scaled Exponential Linear Unit (SELU) Activation Function

Swish(): Switch Activation Function

dELU() d2ELU() d2aELU() dELUa() d2ELUa(): Derivatives of the Exponential Linear Unit (ELU) Activation Function

dGELU() d2GELU() d3GELU() d4GELU(): Derivatives of GELU

dPReLU() dPReLUa() dPReLUa1(): Derivatives Parametric ReLU Activation Function

dReLU(): Derivative of the Rectified Linear Unit (ReLU) Activation Function

dSELU(): Derivative of the Scaled Exponential Linear Unit (SELU) Activation Function

dSwish(): Derivative of the Swish Activation Function

dlReLU(): Derivative of Leaky ReLU activation function

dsoftplus() d2softplus() d3softplus() d4softplus(): Default Softplus Activation Function

lReLU(): Leaky ReLU activation function

softplus(): Softplus Activation Function

Rxode2 data sets

rxResidualError: A description of Rode2 supported residual errors