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
rxLastCompile(): Get the last compiled model information as alist
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() assertRxUiIovNoCor() assertRxUiNoMix() 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
rxFixRes(): Literally fix residual 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
mexpit() dmexpit(): mexpit – Convert log-scale numbers to probabilities
mlogit(): mlogit – Convert multiple probabilities to log-scale numbers
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
rxNumLoaded(): Get the number of loaded rxode2 DLLs
rxParams() rxParam(): Parameters specified by the model
rxProgress() rxTick() rxProgressStop() rxProgressAbort(): rxode2 progress bar functions
rxState(): State variables
rxStateOde(): Get the ODE states only
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
mix(): Specify a mixture model of variables
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
rxUiDeparse(): This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDevelop(): rxUiDevelop - Enable/Disable rxUi development. Here all $ completions are given
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.

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