Man pages for nlmixr2/rxode2
Facilities for Simulating from ODE-Based Models
| add.dosing | Add dosing to eventTable |
| add.sampling | Add sampling to eventTable |
| as.et | Coerce object to data.frame |
| as.ini | Turn into an ini block for initialization |
| as.model | Turn into a model expression |
| as.rxUi | As rxode2 ui |
| assertCompartmentExists | Verify that the compartment exists in a model |
| assertCompartmentName | Verify that a value is a valid nlmixr2 compartment name |
| assertCompartmentNew | Verify that a compartment would be new to the model |
| assertRxUi | Assert properties of the rxUi models |
| assertVariableExists | Assert a variable exists in the model |
| assertVariableNew | Assert a variable would be new to the model |
| binomProbs | Calculate expected confidence bands with binomial sampling... |
| boxCox | boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions |
| coef.rxode2 | Return the rxode2 coefficients |
| cvPost | Sample a covariance Matrix from the Posterior Inverse Wishart... |
| dELU | Derivatives of the Exponential Linear Unit (ELU) Activation... |
| dfWishart | This uses simulations to match the rse |
| dGELU | Derivatives of GELU |
| dlReLU | Derivative of Leaky ReLU activation function |
| dot-assertRenameErrorModelLine | This function asserts the requested rename makes sense |
| dot-cbindOme | cbind Ome |
| dot-clearPipe | Clear/Set pipeline |
| dot-collectWarnings | Collect warnings and just warn once. |
| dot-convertId | Convert a factor/char to an id |
| dot-copyUi | This copies the rxode2 UI object so it can be modified |
| dot-expandPars | Expand parameters |
| dot-extraC | Generate extraC information for rxode2 models |
| dot-extraCnow | Get the extraCnow for compiling |
| dot-getLastIdLvl | Get the last 'idLvl' |
| dot-getWh | Get the internal breakdown of an evid |
| dot-handleSingleErrTypeNormOrTFoceiBase | Handle the single error for normal or t distributions |
| dot-iniGetAppendArg | This gets the append arg for the ini() piping |
| dot-iniHandleAppend | Reorder rows in iniDf |
| dot-iniHandleLine | Update the iniDf of a model |
| dot-linCmtSensB | Is the linear systems with gradients built-in |
| dot-matchesLangTemplate | Check if a language object matches a template language object |
| dot-minfo | Internal messaging statements |
| dot-modelHandleModelLines | Handle model lines |
| dot-pipeRx | Assign in the rxode2 pipeline |
| dot-quoteCallInfoLines | Returns quoted call information |
| dot-rxBlankIni | Get a blank, theta1, or eta1 initialization block for iniDf |
| dot-rxC | Return the C code of an internal function |
| dot-rxDocTable | Print out a table in the documentation |
| dot-rxGetHiBoundaryPred1AndIni | Get the upper boundary condition when the transformation it |
| dot-rxGetLambdaFromPred1AndIni | Get the lambda value based on the pred information |
| dot-rxGetLowBoundaryPred1AndIni | Get the lower boundary condition when the transformation... |
| dot-rxGetPredictionDVTransform | Get the Observation transformation |
| dot-rxGetPredictionF | Get the prediction name |
| dot-rxGetPredictionFTransform | Get the prediction transformation |
| dot-rxGetVarianceForErrorType | Get Variance for error type |
| dot-rxIsLinCmt | Internal function to tell if the linCmt() is the model... |
| dot-rxJacobian | Internal function for calculating the Jacobian |
| dot-rxLinCmtGen | Internal function to generate the model variables for a... |
| dot-rxode2ptrs | Get the rxode2 function pointers |
| dot-rxPrune | Internal Pruning function |
| dot-rxSEeqUsr | Return the equivalents symengine user functions from C |
| dot-rxSens | Sensitivity for model |
| dot-rxTransform | rxode2 general transformation function |
| dot-rxTransInfo | Get the information about the rxode2 derived parameter... |
| dot-rxWithOptions | Temporarily set options then restore them while running code |
| dot-rxWithSink | With one sink, then release |
| dot-rxWithWd | Temporarily set options then restore them while running code |
| dot-s3register | Register a method for a suggested dependency |
| dot-symengineFs | Return symengineFs from user functions |
| dot-toClassicEvid | This converts NONMEM-style EVIDs to classic RxODE events |
| dot-udfCallFunArg | Get the function name with the current arguments as a string |
| dot-udfEnvReset | Lock/Unlock environment for getting R user functions |
| dot-udfEnvSet | Setup the UDF environment (for querying user defined... |
| dot-udfEnvSetUdf | Use the udf model variable information to get the environment... |
| dot-udfExists | See if the UI function exists in given environment. |
| dot-udfMd5Info | Get the udf strings for creating model md5 |
| dot-uiArg | Handle arguments for ui functions |
| dot-useUtf | Internal function to figure out if this session supports... |
| dot-vecDf | Convert numeric vector to repeated data.frame |
| dPReLU | Derivatives Parametric ReLU Activation Function |
| dReLU | Derivative of the Rectified Linear Unit (ReLU) Activation... |
| dSELU | Derivative of the Scaled Exponential Linear Unit (SELU)... |
| dsoftplus | Default Softplus Activation Function |
| dSwish | Derivative of the Swish Activation Function |
| ELU | Exponential Linear Unit (ELU) Activation Function |
| erf | Error function |
| et | Event Table Function |
| etExpand | Expand additional doses |
| etRbind | Combining event tables |
| etRep | Repeat an rxode2 event table |
| etSeq | Sequence of event tables |
| etTrans | Event translation for rxode2 |
| eventTable | Create an event table object |
| findLhs | Find the assignments in R expression |
| forderForceBase | Force using base order for rxode2 radix sorting |
| gammap | Gammap: normalized lower incomplete gamma function |
| gammapDer | gammapDer: derivative of gammap |
| gammapInv | gammapInv and gammapInva: Inverses of normalized gammap... |
| gammaq | Gammaq: normalized upper incomplete gamma function |
| gammaqInv | gammaqInv and gammaqInva: Inverses of normalized gammaq... |
| GELU | GELU activation function |
| genShinyApp.template | Generate an example (template) of a dosing regimen shiny app |
| getBaseIniSimModel | Get the base simulation model for simulation with inis in the... |
| getBaseSimModel | Get the base simulation model for simulation |
| getBaseSymengineModel | Get the symengine for loading into symengine with 'rxS()' |
| getRxThreads | Get/Set the number of threads that rxode2 uses |
| guide_none | Empty Guide |
| ini | Ini block for rxode2/nlmixr models |
| ini-set | Assign the ini block in the rxode2 related object |
| invWR1d | One correlation sample from the Inverse Wishart distribution |
| is.rxEt | Check to see if this is an rxEt object. |
| is.rxSolve | Check to see if this is an rxSolve object. |
| is.rxStackData | Return if the object can be stacked |
| linMod | Linear model to replace in rxode2 ui model |
| llikBeta | Calculate the log likelihood of the binomial function (and... |
| llikBinom | Calculate the log likelihood of the binomial function (and... |
| llikCauchy | log likelihood of Cauchy distribution and it's derivatives... |
| 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... |
| llikNbinomMu | Calculate the log likelihood of the negative binomial... |
| 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 |
| logit | logit and inverse logit (expit) functions |
| lowergamma | lowergamma: upper incomplete gamma function |
| lReLU | Leaky ReLU activation function |
| meanProbs | Calculate expected confidence bands or prediction intreval... |
| model | Model block for rxode2/nlmixr models |
| modelExtract | Extract model lines from a rxui model |
| model-set | Assign the model block in the rxode2 related object |
| odeMethodToInt | Conversion between character and integer ODE integration... |
| phi | Cumulative distribution of standard normal |
| plot.rxSolve | Plot rxode2 objects |
| plus-.rxSolve | Update Solved object with '+' |
| PReLU | Parametric ReLU Activation Function |
| print.rxCoef | Print the rxCoef object |
| print.rxDll | Print rxDll object |
| print.rxModelVars | Print Values |
| print.rxode2 | Print information about the rxode2 object. |
| probit | probit and inverse probit functions |
| reexports | Objects exported from other packages |
| ReLU | Rectified Linear Unit (ReLU) Activation Function |
| rinvchisq | Scaled Inverse Chi Squared distribution |
| rLKJ1 | One correlation sample from the LKJ distribution |
| rxAllowUnload | Allow unloading of dlls |
| rxAppendModel | Append two rxui models together |
| rxAssignControlValue | Assign Control Variable |
| rxAssignPtr | Assign pointer based on model variables |
| rxbeta | Simulate beta variable from threefry generator |
| rxbinom | Simulate Binomial variable from threefry generator |
| rxBlockZeros | Creates a logical matrix for block matrixes. |
| rxC | Return the C file associated with the rxode2 object |
| rxCat | Use cat when rxode2.verbose is TRUE |
| rxcauchy | Simulate Cauchy variable from threefry generator |
| rxCbindStudyIndividual | Bind the study parameters and individual parameters |
| rxChain | rxChain Chain or add item to solved system of equations |
| rxChain2 | Second command in chaining commands |
| rxchisq | Simulate chi-squared variable from threefry generator |
| rxClean | Cleanup anonymous DLLs by unloading them |
| rxCombineErrorLines | Combine Error Lines and create rxode2 expression |
| rxCompile | Compile a model if needed |
| rxCondition | Current Condition for rxode2 object |
| rxControlUpdateSens | This updates the tolerances based on the sensitivity... |
| rxCreateCache | This will create the cache directory for rxode2 to save... |
| rxD | Add to rxode2's derivative tables |
| rxDelete | Delete the DLL for the model |
| rxDemoteAddErr | Demote the error type |
| rxDerived | Calculate derived parameters for the 1-, 2-, and 3-... |
| rxDfdy | Jacobian and parameter derivatives |
| rxDll | Return the DLL associated with the rxode2 object |
| rxDynLoad | Load rxode2 object |
| rxDynUnload | Unload rxode2 object |
| rxErrTypeCombine | Combine transformations and error structures |
| rxEtDispatchSolve | Dispatch solve to 'rxode2' solve |
| rxEvid | EVID formatting for tibble and other places. |
| rxexp | Simulate exponential variable from threefry generator |
| rxExpandFEta_ | Expand d(f)/d(eta) |
| rxExpandGrid | Faster expand.grid |
| rxExpandGrid_ | Expand grid internal function |
| rxExpandIfElse | Expand if/else clauses into multiple different types of... |
| rxExpandSens_ | Expand sensitivity |
| rxExpandSens2_ | Expand second order sensitivity |
| rxf | Simulate F variable from threefry generator |
| rxFixPop | Apply the fixed population estimated parameters |
| rxForget | Clear memoise cache for rxode2 |
| rxFun | Add/Create C functions for use in rxode2 |
| rxFunParse | Add user function to rxode2 |
| rxgamma | Simulate gamma variable from threefry generator |
| rxgeom | Simulate geometric variable from threefry generator |
| rxGetControl | rxGetControl option from ui |
| rxGetDistributionSimulationLines | This is a S3 method for getting the distribution lines for a... |
| rxGetLin | Get the linear compartment model true function |
| rxGetModel | Get model properties without compiling it. |
| rxGetrxode2 | Get rxode2 model from object |
| rxGetSeed | Get the rxode2 seed |
| rxHtml | Format rxSolve and related objects as html. |
| rxIndLinState | Set the preferred factoring by state |
| rxIndLinStrategy | This sets the inductive linearization strategy for matrix... |
| rxInits | Initial Values and State values for a rxode2 object |
| rxIntToBase | Convert a positive base |
| rxIntToLetter | Convert a positive integer to a letter series |
| rxInv | Invert matrix using RcppArmadillo. |
| rxIs | Check the type of an object using Rcpp |
| rxIsCurrent | Checks if the rxode2 object was built with the current build |
| rxIsLoaded | Determine if the DLL associated with the rxode2 object is... |
| rxLhs | Left handed Variables |
| rxLock | Lock/unlocking of rxode2 dll file |
| rxMd5 | Return the md5 of an rxode2 object or file |
| rxModels_ | Get the rxModels information |
| rxModelVars | All model variables for a rxode2 object |
| rxnbinom | Simulate Binomial variable from threefry generator |
| rxNorm | Get the normalized model |
| rxnormV | Simulate random normal variable from threefry generator |
| rxode2 | Create an ODE-based model specification |
| rxode2parse | Internal translation to get model variables list |
| rxode2parseAssignPackagesToLoad | Control the packages that are loaded when a 'rxode2' model... |
| rxode2parseAssignPointerTranslation | This sets function gets the currently assigned function... |
| rxode2parseAssignTranslation | This assigns the c level linkages for a roxde2 model |
| rxode2parseD | This gives the derivative table for rxode2 |
| rxode2parseGetPointerAssignment | This function gets the currently assigned function pointer... |
| rxode2parseGetTranslation | This function gets the currently assigned translations |
| rxode2-set | Set the function body of an rxUi object while retaining other... |
| rxOptExpr | Optimize rxode2 for computer evaluation |
| rxord | Simulate ordinal value |
| rxParams | Parameters specified by the model |
| rxParseErr | Prepare Error function for inclusion in rxode2 |
| rxParsePk | Parse PK function for inclusion in rxode2 |
| rxParsePred | Prepare Pred function for inclusion in rxode2 |
| rxParseSetSilentErr | Silence some of rxode2's C/C++ messages |
| rxParseSuppressMsg | Respect suppress messages |
| rxPkg | Creates a package from compiled rxode2 models |
| rxpois | Simulate random Poisson variable from threefry generator |
| rxPp | Simulate a from a Poisson process |
| rxPreferredDistributionName | Change distribution name to the preferred distribution name... |
| rxProgress | rxode2 progress bar functions |
| rxPrune | Prune branches (ie if/else) from rxode2 |
| rxRateDur | Creates a rxRateDur object |
| rxReload | Reload rxode2 DLL |
| rxRemoveControl | rxRemoveControl options for UI object |
| rxRename | Rename items inside of a 'rxode2' ui model |
| rxRepR0_ | Rep R0 for foce |
| rxReq | Require namespace, otherwise throw error. |
| rxReservedKeywords | A list and description of rxode2 supported reserved keywords |
| rxResidualError | A description of Rode2 supported residual errors |
| rxRmvn | Simulate from a (truncated) multivariate normal |
| rxS | Load a model into a symengine environment |
| rxSeedEng | This seeds the engine based on the number of cores used in... |
| rxSetControl | rxSetControl options for UI object |
| rxSetCovariateNamesForPiping | Assign covariates for piping |
| rxSetIni0 | Set Initial conditions to time zero instead of the first... |
| rxSetPipingAuto | Set the variables for the model piping automatic covarite... |
| rxSetProd | Defunct setting of product |
| rxSetProgressBar | Set timing for progress bar |
| rxSetSeed | Set the parallel seed for rxode2 random number generation |
| rxSetSilentErr | Silence some of rxode2's C/C++ messages |
| rxSetSum | Defunct setting of sum |
| rxSetupIni | Setup the initial conditions. |
| rxSetupScale | Setup the initial conditions. |
| rxShiny | Use Shiny to help develop an rxode2 model |
| rxSimThetaOmega | Simulate Parameters from a Theta/Omega specification |
| rxSolve | Options, Solving & Simulation of an ODE/solved system |
| rxSolveFree | Free the C solving/parsing information. |
| rxSolveSetup | See if the memory is installed for a solve |
| rxSplitPlusQ | This function splits a function based on + or - terms |
| rxStack | Stack a solved object for things like default ggplot2 plot |
| rxState | State variables |
| rxSumProdModel | Recast model in terms of sum/prod |
| rxSupportedFuns | Get list of supported functions |
| rxSuppressMsg | Respect suppress messages |
| rxSymInvChol | Get Omega^-1 and derivatives |
| rxSymInvCholCreate | Creates an object for calculating Omega/Omega^-1 and... |
| rxSymInvCholN | Return the dimension of the built-in derivatives/inverses |
| rxSyncOptions | Sync options with rxode2 variables |
| rxSyntaxFunctions | A list and description of Rode supported syntax functions |
| rxt | Simulate student t variable from threefry generator |
| rxTempDir | Get the rxode2 temporary directory |
| rxTheme | rxTheme is the ggplot2 theme for rxode2 plots |
| rxToSE | rxode2 to symengine environment |
| rxTrans | Translate the model to C code if needed |
| rxUdfUi | This function is called when processing rxode2 user functions... |
| rxUdfUiControl | Return the control that is being processed or setup control... |
| rxUdfUiData | Return the data.frame that is being processed or setup... |
| rxUdfUiEst | Return the current estimation method for the UI processing |
| rxUdfUiIniDf | Get the rxode2 iniDf of the current UI being processed (or... |
| rxUdfUiIniLhs | Return the lhs parsed language expression |
| rxUdfUiMv | Return the model variables that is being processed or setup... |
| rxUdfUiNum | This gives the current number in the ui of the particular... |
| rxUdfUiParsing | Returns if the current ui function is being parsed |
| rxUdfUiReset | Reset the rxode2 ui environment variables |
| rxUiDecompress | Compress/Decompress 'rxode2' ui |
| rxUiDeparse | This is a generic function for deparsing certain objects when... |
| rxUiGet | S3 for getting information from UI model |
| rxunif | Simulate uniform variable from threefry generator |
| rxUnloadAll | Unloads all rxode2 compiled DLLs |
| rxUse | Use model object in your package |
| rxValidate | Validate rxode2 This allows easy validation/qualification of... |
| rxVersion | Version and repository for this dparser package. |
| rxweibull | Simulate Weibull variable from threefry generator |
| rxWithSeed | Preserved seed and possibly set the seed |
| SELU | Scaled Exponential Linear Unit (SELU) Activation Function |
| softplus | Softplus Activation Function |
| stat_amt | Dosing/Amt geom/stat |
| stat_cens | Censoring geom/stat |
| summary.rxDll | Summary of rxDll object |
| summary.rxode2 | Print expanded information about the rxode2 object. |
| swapMatListWithCube | Swaps the matrix list with a cube |
| Swish | Switch Activation Function |
| testIniDf | This function tests if this object is a iniDf as needed by... |
| testRxLinCmt | Test if rxode2 uses linear solved systems |
| testRxUnbounded | Test if the rxode2 model has any parameters with user defined... |
| toTrialDuration | Convert event data to trial duration data A helper function... |
| update.rxUi | Update for rxUi |
| uppergamma | uppergamma: upper incomplete gamma function |
| zeroRe | Set random effects and residual error to zero |
