| cbind Ome | .cbindOme |
| Collect warnings and just warn once. | .collectWarnings |
| This copies the rxode2 UI object so it can be modified | .copyUi |
| Handle the single error for normal or t distributions | .handleSingleErrTypeNormOrTFoceiBase |
| Check if a language object matches a template language object | .matchesLangTemplate |
| Handle model lines | .modelHandleModelLines |
| Returns quoted call information | .quoteCallInfoLines |
| Internal function to generate the model variables for a linCmt() model | .rxLinCmtGen |
| Get the rxode2 function pointers | .rxode2ptrs |
| Temporarily set options then restore them while running code | .rxWithOptions |
| Temporarily set options then restore them while running code | .rxWithWd |
| This converts NONMEM-style EVIDs to classic RxODE events | .toClassicEvid |
| Convert numeric vector to repeated data.frame | .vecDf |
| Add dosing to eventTable | add.dosing |
| Add sampling to eventTable | add.sampling |
| Convert to tbl | as_tibble.rxEt |
| Convert an event table to a data.table | as.data.table.rxEt |
| Coerce object to data.frame | as.et as.et.default |
| Turn into an ini block for initialization | as.ini as.ini.call as.ini.character as.ini.data.frame as.ini.default as.ini.lotriFix as.ini.matrix |
| Turn into a model expression | as.model as.model.call as.model.character as.model.default as.model.list |
| As rxode2 ui | as.rxUi as.rxUi.default as.rxUi.function as.rxUi.rxModelVars as.rxUi.rxode2 as.rxUi.rxode2tos as.rxUi.rxUi |
| Verify that the compartment exists in a model | assertCompartmentExists testCompartmentExists |
| Verify that a value is a valid nlmixr2 compartment name | assertCompartmentName assertExists assertParameterValue assertVariableName testExists |
| Verify that a compartment would be new to the model | assertCompartmentNew |
| Assert properties of the rxUi models | assertRxUi assertRxUiEstimatedResiduals assertRxUiIovNoCor assertRxUiMixedOnly assertRxUiMuRefOnly assertRxUiNoMix assertRxUiNormal assertRxUiPopulationOnly assertRxUiPrediction assertRxUiRandomOnIdOnly assertRxUiSingleEndpoint assertRxUiTransformNormal |
| Assert a variable exists in the model | assertVariableExists testVariableExists |
| Assert a variable would be new to the model | assertVariableNew |
| Calculate expected confidence bands with binomial sampling distribution | binomProbs binomProbs.default |
| Administer a bolus dose inside a rxode2 model | bolus |
| boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions | boxCox boxCoxInv yeoJohnson yeoJohnsonInv |
| Sample a covariance Matrix from the Posterior Inverse Wishart distribution. | cvPost |
| Delayed state for delay differential equations | delay |
| Derivatives of the Exponential Linear Unit (ELU) Activation Function | d2aELU d2ELU d2ELUa dELU dELUa |
| This uses simulations to match the rse | dfWishart |
| Derivatives of GELU | d2GELU d3GELU d4GELU dGELU |
| Derivative of Leaky ReLU activation function | dlReLU |
| Derivatives Parametric ReLU Activation Function | dPReLU dPReLUa dPReLUa1 |
| Derivative of the Rectified Linear Unit (ReLU) Activation Function | dReLU |
| Derivative of the Scaled Exponential Linear Unit (SELU) Activation Function | dSELU |
| Default Softplus Activation Function | d2softplus d3softplus d4softplus dsoftplus |
| Derivative of the Swish Activation Function | dSwish |
| Exponential Linear Unit (ELU) Activation Function | ELU |
| Error function | erf |
| Event Table Function | et et.default et.function et.rxode2 et.rxParams et.rxSolve et.rxUi |
| Expand additional doses | etExpand |
| Combining event tables | etRbind rbind.rxEt |
| Repeat an rxode2 event table | etRep rep.rxEt |
| Sequence of event tables | etSeq seq.rxEt |
| Create an event table object | eventTable |
| Push a future dose or observation event from within an rxode2 model | evid_ |
| Gammap: normalized lower incomplete gamma function | gammap |
| gammapDer: derivative of gammap | gammapDer |
| gammapInv and gammapInva: Inverses of normalized gammap function | gammapInv gammapInva |
| Gammaq: normalized upper incomplete gamma function | gammaq |
| gammaqInv and gammaqInva: Inverses of normalized gammaq function | gammaqInv gammaqInva |
| GELU activation function | GELU |
| Generate an example (template) of a dosing regimen shiny app | genShinyApp.template write.template.server write.template.ui |
| Get/Set the number of threads that rxode2 uses | getRxThreads rxCores setRxThreads |
| Transition ODEs written in d/dt() format to matrix exponential / inductive linearization format | indLin rxOdeToIndLin rxToIndLin |
| Administer a infusion (with rate being fixed) inside a rxode2 model | infuse |
| Administer a infusion (with duration being fixed) inside a rxode2 model | infuseDur |
| Ini block for rxode2/nlmixr models | ini ini.default ini.rxUi |
| Assign the ini block in the rxode2 related object | ini<- |
| Check if object is an rxEt event table | is.rxEt |
| Return if the object can be stacked | is.rxStackData |
| Linear model to replace in rxode2 ui model | linMod linMod0 linModA linModA0 linModB linModB0 linModD linModD0 linModM linModM0 |
| Convert linCmt rxUi models to ODE rxUi models | linToOde |
| Calculate the log likelihood of the binomial function (and its derivatives) | llikBeta |
| Calculate the log likelihood of the binomial function (and its derivatives) | llikBinom |
| log likelihood of Cauchy distribution and it's derivatives (from stan) | llikCauchy |
| log likelihood and derivatives for chi-squared distribution | llikChisq |
| log likelihood and derivatives for exponential distribution | llikExp |
| log likelihood and derivatives for F distribution | llikF |
| log likelihood and derivatives for Gamma distribution | llikGamma |
| log likelihood and derivatives for Geom distribution | llikGeom |
| Calculate the log likelihood of the negative binomial function (and its derivatives) | llikNbinom |
| Calculate the log likelihood of the negative binomial function (and its derivatives) | llikNbinomMu |
| Log likelihood for normal distribution | llikNorm |
| log-likelihood for the Poisson distribution | llikPois |
| Log likelihood of T and it's derivatives (from stan) | llikT |
| log likelihood and derivatives for Unif distribution | llikUnif |
| log likelihood and derivatives for Weibull distribution | llikWeibull |
| logit and inverse logit (expit) functions | expit logit logitNormInfo probitNormInfo |
| lowergamma: upper incomplete gamma function | lowergamma |
| Leaky ReLU activation function | lReLU |
| Calculate expected confidence bands or prediction intreval with normal or t sampling distribution | meanProbs meanProbs.default |
| mexpit - Convert log-scale numbers to probabilities | dmexpit mexpit |
| Specify a mixture model of variables | mix |
| mlogit - Convert multiple probabilities to log-scale numbers | mlogit |
| Model block for rxode2/nlmixr models | model model.default model.function model.rxModelVars model.rxode2 model.rxUi |
| Assign the model block in the rxode2 related object | model<- |
| Extract model lines from a rxui model | modelExtract modelExtract.default modelExtract.function modelExtract.rxModelVars modelExtract.rxode2 modelExtract.rxUi |
| Multiply dose the rxode2 system in the model | multiply |
| Add observations to a model | obs |
| Conversion between character and integer ODE integration methods for rxode2 | odeMethodToInt |
| Convert ODE-based linear compartment models to analytical linCmt() form | odeToLin |
| Administer a phantom/transit dose inside a rxode2 model | phantom |
| Cumulative distribution of standard normal | phi |
| Plot rxode2 objects | plot.rxSolve plot.rxSolveConfint1 plot.rxSolveConfint2 |
| Parametric ReLU Activation Function | PReLU |
| Print Values | print.rxModelVars |
| probit and inverse probit functions | probit probitInv |
| Rectified Linear Unit (ReLU) Activation Function | ReLU |
| Replace dose the rxode2 system in the model | replace |
| Reset the rxode2 system in the model | reset |
| Scaled Inverse Chi Squared distribution | rinvchisq |
| Allow unloading of dlls | rxAllowUnload |
| Append two rxui models together | rxAppendModel |
| Assign Control Variable | rxAssignControlValue |
| Assign pointer based on model variables | rxAssignPtr |
| Simulate beta variable from threefry generator | rxbeta |
| Simulate Binomial variable from threefry generator | rxbinom |
| Simulate Cauchy variable from threefry generator | rxcauchy |
| Bind the study parameters and individual parameters | rxCbindStudyIndividual |
| Simulate chi-squared variable from threefry generator | rxchisq |
| Cleanup anonymous DLLs by unloading them | rxClean |
| Compile a model if needed | rxCompile rxCompile.character rxCompile.rxDll rxCompile.rxModelVars rxCompile.rxode2 |
| This updates the tolerances based on the sensitivity equations | rxControlUpdateSens |
| This will create the cache directory for rxode2 to save between sessions | rxCreateCache |
| Add to rxode2's derivative tables | rxD |
| Delete the DLL for the model | rxDelete |
| Calculate derived parameters for the 1-, 2-, and 3- compartment linear models. | rxDerived |
| Jacobian and parameter derivatives | rxDfdy |
| Dispatch solve to 'rxode2' solve | rxEtDispatchSolve rxEtDispatchSolve.default |
| EVID formatting for tibble and other places. | as.character.rxEvid as.rxEvid c.rxEvid c.rxRateDur format.rxEvid format.rxRateDur print.rxEvid rxEvid units<-.rxEvid [.rxEvid [[.rxEvid |
| Simulate exponential variable from threefry generator | rxexp |
| Simulate F variable from threefry generator | rxf |
| Apply the fixed population estimated parameters | rxFixPop |
| Literally fix residual parameters | rxFixRes |
| Add/Create C functions for use in rxode2 | rxFun rxRmFun |
| Simulate gamma variable from threefry generator | rxgamma |
| Simulate geometric variable from threefry generator | rxgeom |
| rxGetControl option from ui | rxGetControl |
| Get the Default Serialization Type | rxGetDefaultSerialize |
| Get the linear compartment model true function | rxGetLin |
| Get rxode2 model from object | rxGetrxode2 |
| Get the rxode2 seed | rxGetSeed |
| Format rxSolve and related objects as html. | rxHtml rxHtml.rxSolve |
| Set the preferred factoring by state | rxIndLinState |
| This sets the inductive linearization strategy for matrix building | rxIndLinStrategy |
| Convert a positive base | rxIntToBase |
| Convert a positive integer to a letter series | rxIntToLetter |
| Invert matrix using RcppArmadillo. | rxInv |
| Check whether an ODE method string is an AutoSwitch composite pair | rxIsAutoSwitch |
| Checks if the rxode2 object was built with the current build | rxIsCurrent |
| Check whether an ODE solving method supports dense output | rxIsDense |
| Check whether an ODE solving method requires a Jacobian (is implicit) | rxIsImplicit |
| Check whether an ODE solving method is a purely non-stiff solver | rxIsNonStiff |
| Check whether an ODE solving method is a purely stiff solver | rxIsStiff |
| Get the last compiled model information as alist | rxLastCompile |
| Left handed Variables | rxLhs |
| Lock/unlocking of rxode2 dll file | rxLock rxUnlock |
| Estimate memory required by rxSolve() for a given dataset and model | rxMemoryEstimate |
| Create a per-ID event summary for memory estimation | rxMemSummary |
| Simulate Binomial variable from threefry generator | rxnbinom rxnbinomMu |
| Get the normalized model | rxNorm |
| Simulate random normal variable from threefry generator | rxnorm rxnormV |
| Get the number of loaded rxode2 DLLs | rxNumLoaded |
| Create an ODE-based model specification | RxODE rxode rxode2 |
| Set the function body of an rxUi object while retaining other object information (like data) | rxode2<- rxode2<-.default rxode2<-.function RxODE<- rxode<- |
| Internal translation to get model variables list | rxode2parse |
| This assigns the c level linkages for a roxde2 model | rxode2parseAssignTranslation |
| This gives the derivative table for rxode2 | rxode2parseD |
| Control the packages that are loaded when a 'rxode2' model dll is loaded | rxode2parseAssignPackagesToLoad rxode2parseGetPackagesToLoad |
| This function gets the currently assigned function pointer assignments | rxode2parseGetPointerAssignment |
| This function gets the currently assigned translations | rxode2parseGetTranslation |
| Variance-covariance (non-Cholesky) Omega parameterization derivatives | rxOmegaVarCovDeriv |
| Optimize rxode2 for computer evaluation | rxOptExpr |
| Simulate ordinal value | rxord |
| Parameters specified by the model | rxParam rxParams rxParams.rxEt rxParams.rxode2 rxParams.rxSolve |
| Respect suppress messages | rxParseSuppressMsg |
| Creates a package from compiled rxode2 models | rxPkg |
| Simulate random Poisson variable from threefry generator | rxpois |
| Simulate a from a Poisson process | rxPp |
| Change distribution name to the preferred distribution name term | rxPreferredDistributionName |
| rxode2 progress bar functions | rxProgress rxProgressAbort rxProgressStop rxTick |
| Creates a rxRateDur object | as.character.rxRateDur as.rxRateDur rxRateDur [.rxRateDur [[.rxRateDur |
| rxRemoveControl options for UI object | rxRemoveControl |
| Rename items inside of a 'rxode2' ui model | .rxRename rename.function rename.rxUi rxRename rxRename.default rxRename.function rxRename.rxUi |
| A list and description of rxode2 supported reserved keywords | rxReservedKeywords |
| A description of Rode2 supported residual errors | rxResidualError |
| Simulate from a (truncated) multivariate normal | rxRmvn |
| Load a model into a symengine environment | rxS |
| Differentiate and expand a matrix exponential model with forward sensitivities | rxSensMatExp |
| rxSetControl options for UI object | rxSetControl |
| Assign covariates for piping | rxSetCovariateNamesForPiping |
| Set Initial conditions to time zero instead of the first observed/dosed time | rxSetIni0 |
| Set the variables for the model piping automatic covarite selection | rxSetPipingAuto |
| Defunct setting of product | rxSetProd |
| Set timing for progress bar | rxSetProgressBar |
| Set the parallel seed for rxode2 random number generation | rxSetSeed |
| Defunct setting of sum | rxSetSum |
| Use Shiny to help develop an rxode2 model | rxShiny rxShiny.default rxShiny.rxSolve |
| Simulate Parameters from a Theta/Omega specification | rxSimThetaOmega |
| Options, Solving & Simulation of an ODE/solved system | predict.function predict.rxEt predict.rxode2 predict.rxParams predict.rxSolve predict.rxUi rxControl rxSolve rxSolve.default rxSolve.function rxSolve.nlmixr2FitCore rxSolve.nlmixr2FitData rxSolve.rxode2tos rxSolve.rxSolve rxSolve.rxUi simulate.rxode2 simulate.rxParams simulate.rxSolve solve.function solve.rxEt solve.rxode2 solve.rxParams solve.rxSolve solve.rxUi update.rxSolve |
| Stack a solved object for things like default ggplot2 plot | rxStack |
| State variables | rxState |
| Get the ODE states only | rxStateOde |
| Recast model in terms of sum/prod | rxSumProdModel |
| Get list of supported functions | rxSupportedFuns |
| Respect suppress messages | rxSuppressMsg |
| Get Omega^-1 and derivatives | rxSymInvChol |
| Sync options with rxode2 variables | rxSyncOptions |
| A list and description of Rode supported syntax functions | rxSyntaxFunctions |
| Simulate student t variable from threefry generator | rxt |
| Get the rxode2 temporary directory | rxTempDir |
| rxTheme is the ggplot2 theme for rxode2 plots | rxTheme |
| rxode2 to symengine environment | .rxFromSE .rxToSE rxFromSE rxToSE |
| Translate the model to C code if needed | rxTrans rxTrans.character rxTrans.default |
| Return the control that is being processed or setup control for processing | rxUdfUiControl |
| Return the data.frame that is being processed or setup data.frame for processing | rxUdfUiData |
| Return the current estimation method for the UI processing | rxUdfUiEst |
| Give the expression as a compressed model or expression | rxUdfUiExpr |
| Is the expression actually a flag that can be used in the rxUdfUi functions? | rxUdfUiFlag |
| Get the rxode2 iniDf of the current UI being processed (or return NULL) | rxUdfUiIniDf |
| Return the lhs parsed language expression | rxUdfUiIniLhs |
| Is the expression actually equal to a value? | rxUdfUiIsValue |
| Return the model variables that is being processed or setup model variables for processing | rxUdfUiMv |
| This gives the current number in the ui of the particular function being called. | rxUdfUiNum |
| Returns if the current ui function is being parsed | rxUdfUiParsing |
| Compress/Decompress 'rxode2' ui | rxUiCompress rxUiDecompress |
| This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information | rxUiDeparse rxUiDeparse.default rxUiDeparse.lotriFix rxUiDeparse.rxControl |
| rxUiDevelop - Enable/Disable rxUi development. Here all $ completions are given | rxUiDevelop |
| S3 for getting information from UI model | rxUiGet rxUiGet.allCovs rxUiGet.cmtLines rxUiGet.covLhs rxUiGet.default rxUiGet.dvidLine rxUiGet.etaLhs rxUiGet.fun rxUiGet.funPartsDigest rxUiGet.funPrint rxUiGet.funTxt rxUiGet.ini rxUiGet.iniFun rxUiGet.interpLines rxUiGet.levelLhs rxUiGet.levels rxUiGet.lhsCov rxUiGet.lhsEta rxUiGet.lhsTheta rxUiGet.lhsVar rxUiGet.lstChr rxUiGet.md5 rxUiGet.model rxUiGet.modelDesc rxUiGet.modelFun rxUiGet.multipleEndpoint rxUiGet.muRefTable rxUiGet.omega rxUiGet.paramsLine rxUiGet.props rxUiGet.sha1 rxUiGet.simulationIniModel rxUiGet.simulationModel rxUiGet.simulationSigma rxUiGet.splitDose rxUiGet.splitDoseLines rxUiGet.state rxUiGet.stateDf rxUiGet.statePropDf rxUiGet.symengineModelNoPrune rxUiGet.symengineModelPrune rxUiGet.theta rxUiGet.thetaLhs rxUiGet.thetaLower rxUiGet.thetaUpper rxUiGet.varLhs |
| Simulate uniform variable from threefry generator | rxunif |
| Unloads all rxode2 compiled DLLs | rxUnloadAll |
| Use model object in your package | rxUse |
| Validate rxode2 This allows easy validation/qualification of nlmixr by running the testing suite on your system. | rxTest rxValidate |
| Simulate Weibull variable from threefry generator | rxweibull |
| Preserved seed and possibly set the seed | rxWithPreserveSeed rxWithSeed |
| Scaled Exponential Linear Unit (SELU) Activation Function | SELU |
| Softplus Activation Function | softplus |
| Split bolus doses across compartments inside an rxode2 model | splitBolus |
| Dosing/Amt geom/stat | geom_amt stat_amt |
| Censoring geom/stat | geom_cens stat_cens |
| Print expanded information about the rxode2 object. | summary.rxode2 |
| Swaps the matrix list with a cube | swapMatListWithCube |
| Switch Activation Function | Swish |
| This function tests if this object is a iniDf as needed by the UI | assertIniDf testIniDf |
| Test if rxode2 uses linear solved systems | assertRxLinCmt testRxLinCmt |
| Test if the rxode2 model has any parameters with user defined boundaries | assertRxUnbounded testRxUnbounded warnRxBounded |
| 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. | toTrialDuration |
| Update for rxUi | update.rxUi |
| uppergamma: upper incomplete gamma function | uppergamma |
| Set random effects and residual error to zero | zeroRe |
