Creating RxODE compiled objects

RxODE()

Create an ODE-based model specification

Creating RxODE event tables/data frames

et()

Event Table Function

etRbind() rbind(<rxEt>)

Combining event tables

etRep() rep(<rxEt>)

Repeat an RxODE event table

etSeq() seq(<rxEt>)

Sequence of event tables

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(<RxODE>) predict(<rxSolve>) predict(<rxEt>) predict(<rxParams>) simulate(<RxODE>) simulate(<rxSolve>) simulate(<rxParams>) solve(<rxSolve>) solve(<RxODE>) solve(<rxParams>) solve(<rxEt>) rxControl()

Solving & Simulation of a ODE/solved system (and solving options) equation

Exploring RxODE and creating models with Shiny

rxShiny()

Use Shiny to help develop an RxODE model

genShinyApp.template() write.template.server() write.template.ui()

Generate an example (template) of a dosing regimen shiny app

Using RxODE in Packages

rxUse()

Use model object in your package

rxPkg()

Creates a package from compiled RxODE models

Specialized Simulation functions

cvPost()

Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

rinvchisq()

Scaled Inverse Chi Squared distribution

rxPp()

Simulate a from a Poisson process

Optimizing models and/or adding precision

rxOptExpr()

Optimize RxODE for computer evaluation

rxSumProdModel()

Recast model in terms of sum/prod

rxSetProd()

Defunct setting of product

rxSetSum()

Defunct setting of sum

Running unit tests in RxODE

rxValidate() rxTest()

Validate RxODE This allows easy validation/qualification of nlmixr by running the testing suite on your system.

Internal functions

RxODE()

Create an ODE-based model specification

add.dosing()

Add dosing to eventTable

add.sampling()

Add sampling to eventTable

as.data.table.rxEt()

Convert an event table to a data.table

as.et()

Coerce object to data.frame

as_tibble.rxEt()

Convert to tbl

coef(<RxODE>)

Return the RxODE coefficients

cvPost()

Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

.clearPipe()

Clear/Set pipeline

.rxFinalizeInner()

Finalize inner RxODE based on symengine saved info

.rxFinalizePred()

Finalize RxODE pred based on symengine saved info

.rxGenEBE()

Generate pieces for EBE only problem

.rxGenEtaS()

Generate the ETA sensitivities for FO related methods

.rxGenFoce()

Generate FOCE without interaction

.rxGenFocei()

Generate pieces for FOCEi inner problem

.rxGenFunState()

Get the state information for the current model

.rxGenHdEta()

Generate the d(err)/d(eta) values for FO related methods

.rxGenPred()

Generate Augmented pred/err RxODE model

.rxRmPrint()

Remove print statements

.rxWinRtoolsPath()

Setup Rtools path

.rxWithOptions()

Temporarily set options then restore them while running code

.rxWithWd()

Temporarily set options then restore them while running code

.setWarnIdSort()

Turn on/off warnings for ID sorting.

et()

Event Table Function

etExpand()

Expand additional doses

etRbind() rbind(<rxEt>)

Combining event tables

etRep() rep(<rxEt>)

Repeat an RxODE event table

etSeq() seq(<rxEt>)

Sequence of event tables

eventTable()

Create an event table object

forderForceBase()

Force using base order for RxODE 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

genShinyApp.template() write.template.server() write.template.ui()

Generate an example (template) of a dosing regimen shiny app

getRxThreads() setRxThreads() rxCores()

Get/Set the number of threads that RxODE uses

guide_none()

Empty Guide

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.

logit() expit() logitNormInfo() probitNormInfo()

logit and inverse logit (expit) functions

lowergamma()

lowergamma: upper incomplete gamma function

phi()

Cumulative distribution of standard normal

print(<RxODE>)

Print information about the RxODE object.

probit() probitInv()

probit and inverse probit functions

rLKJ1()

One correlation sample from the LKJ distribution

rinvchisq()

Scaled Inverse Chi Squared distribution

rxAddReturn()

Add a return statment to a function.

rxAllowUnload()

Allow unloading of dlls

rxAssignPtr()

Assign pointer based on model variables

rxChain() `+`(<solveRxDll>)

rxChain Chain or add item to solved system of equations

rxClean()

Cleanup anonymous DLLs by unloading them

rxCompile()

Compile a model if needed

rxCreateCache()

This will create the cache directory for RxODE to save between sessions

rxD()

Add to RxODE's derivative tables

rxDelete()

Delete the DLL for the model

rxDerived()

Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.

rxDfdy()

Jacobian and parameter derivatives

rxEvid() as.rxEvid() c(<rxEvid>) `[`(<rxEvid>) as.character(<rxEvid>) `[[`(<rxEvid>) type_sum.rxEvid() pillar_shaft.rxEvid() c(<rxRateDur>) format(<rxEvid>) format(<rxRateDur>) print(<rxEvid>)

EVID formatting for tibble and other places.

rxFun() rxRmFun()

Add user function to RxODE

rxGenSaem()

Generate pred-only SAEM RxODE model

rxGetLin()

Get the linear compartment model true function

rxGetRxODE()

Get RxODE 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

rxInv()

Invert matrix using RcppArmadillo.

rxIsCurrent()

Checks if the RxODE object was built with the current build

rxLhs()

Left handed Variables

rxLock() rxUnlock()

Lock/unlocking of RxODE dll file

rxNorm()

Get the normalized model

rxOptExpr()

Optimize RxODE for computer evaluation

rxParams() rxParam()

Parameters specified by the model

rxPkg()

Creates a package from compiled RxODE models

rxPp()

Simulate a from a Poisson process

rxProgress() rxTick() rxProgressStop() rxProgressAbort()

RxODE progress bar functions

rxRandNV()

Create a random "normal" matrix using vandercorput generator

rxRateDur() `[`(<rxRateDur>) as.rxRateDur() as.character(<rxRateDur>) `[[`(<rxRateDur>) type_sum.rxRateDur() pillar_shaft.rxRateDur()

Creates a rxRateDur object

rxRmvn()

Simulate from a (truncated) multivariate normal

rxS()

Load a model into a symengine environment

rxSetIni0()

Set Initial conditions to time zero instead of the first observed/dosed time

rxSetProd()

Defunct setting of product

rxSetProgressBar()

Set timing for progress bar

rxSetSum()

Defunct setting of sum

rxShiny()

Use Shiny to help develop an RxODE model

rxSimThetaOmega()

Simulate Parameters from a Theta/Omega specification

rxSolve() update(<rxSolve>) predict(<RxODE>) predict(<rxSolve>) predict(<rxEt>) predict(<rxParams>) simulate(<RxODE>) simulate(<rxSolve>) simulate(<rxParams>) solve(<rxSolve>) solve(<RxODE>) solve(<rxParams>) solve(<rxEt>) rxControl()

Solving & Simulation of a ODE/solved system (and solving options) equation

rxStack()

Stack a solved object for things like ggplot

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

rxSyncOptions()

Sync options with RxODE variables

rxTempDir()

Get the RxODE temporary directory

rxTheme()

rxTheme is the RxODE theme for plots

rxToSE() .rxToSE() rxFromSE() .rxFromSE()

RxODE to symengine environment

rxTrans()

Translate the model to C code if needed

rxUnloadAll()

Unloads all RxODE compiled DLLs

rxUse()

Use model object in your package

rxValidate() rxTest()

Validate RxODE This allows easy validation/qualification of nlmixr by running the testing suite on your system.

rxWinSetup()

Setup Windows components for RxODE

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

rxnorm() rxnormV()

Simulate random normal variable from threefry/vandercorput generator

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

stat_amt() geom_amt()

Dosing/Amt geom/stat

stat_cens() geom_cens()

Censoring geom/stat

summary(<RxODE>)

Print expanded information about the RxODE object.

type_sum.units() format_type_sum.type_sum_units() pillar_shaft.units() type_sum.mixed_units() pillar_shaft.mixed_units()

type_sum function for units

uppergamma()

uppergamma: upper incomplete gamma function