rxode23.0.2 package

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 distributio...

boxCox

boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions

coef.rxode2

Return the rxode2 coefficients

cvPost

Sample a covariance Matrix from the Posterior Inverse Wishart distribu...

dfWishart

This uses simulations to match the rse

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 requires it

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 variables

dot-rxJacobian

Internal function for calculating the Jacobian

dot-rxLinCmtGen

Internal function to generate the model variables for a linCmt() model

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 transformation

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 funtions)

dot-udfEnvSetUdf

Use the udf model variable information to get the environment where th...

dot-udfExists

See if the UI function exists in given environment.

dot-udfMd5Info

Get the udf strings for creating model md5

dot-useUtf

Internal function to figure out if this session supports Unicode

dot-vecDf

Convert numeric vector to repeated data.frame

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 function

gammaq

Gammaq: normalized upper incomplete gamma function

gammaqInv

gammaqInv and gammaqInva: Inverses of normalized gammaq 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 underlyi...

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-set

Assign the ini block in the rxode2 related object

ini

Ini block for rxode2/nlmixr models

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 its derivat...

llikBinom

Calculate the log likelihood of the binomial function (and its derivat...

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 it...

llikNbinomMu

Calculate the log likelihood of the negative binomial function (and it...

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

meanProbs

Calculate expected confidence bands or prediction intreval with normal...

model-set

Assign the model block in the rxode2 related object

model

Model block for rxode2/nlmixr models

modelExtract

Extract model lines from a rxui model

odeMethodToInt

Conversion between character and integer ODE integration methods for r...

phi

Cumulative distribution of standard normal

plot.rxSolve

Plot rxode2 objects

plus-.rxSolve

Update Solved object with '+'

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

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 equations

rxCreateCache

This will create the cache directory for rxode2 to save between sessio...

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- compartment linear...

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_

Expand grid internal function

rxExpandGrid

Faster expand.grid

rxExpandIfElse

Expand if/else clauses into multiple different types of lines.

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 rxode2 si...

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 building

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 loaded

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-set

Set the function body of an rxUi object while retaining other object i...

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 dll is load...

rxode2parseAssignPointerTranslation

This sets function gets the currently assigned function pointer assign...

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 assignments

rxode2parseGetTranslation

This function gets the currently assigned translations

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 term

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.

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 random numb...

rxSetControl

rxSetControl options for UI object

rxSetCovariateNamesForPiping

Assign covariates for piping

rxSetIni0

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

rxSetPipingAuto

Set the variables for the model piping automatic covarite selection

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 derivatives

rxSymInvCholN

Return the dimension of the built-in derivatives/inverses

rxSyncOptions

Sync options with rxode2 variables

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 from the...

rxUdfUiData

Return the data.frame that is being processed or setup data.frame for ...

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 vari...

rxUdfUiNum

This gives the current number in the ui of the particular function bei...

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 printing...

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 nlmixr by...

rxVersion

Version and repository for this dparser package.

rxweibull

Simulate Weibull variable from threefry generator

rxWithSeed

Preserved seed and possibly set the seed

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

testIniDf

This function tests if this object is a iniDf as needed by the UI

testRxLinCmt

Test if rxode2 uses linear solved systems

testRxUnbounded

Test if the rxode2 model has any parameters with user defined boundari...

toTrialDuration

Convert event data to trial duration data A helper function to create ...

update.rxUi

Update for rxUi

uppergamma

uppergamma: upper incomplete gamma function

zeroRe

Set random effects and residual error to zero

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.

  • Maintainer: Matthew L. Fidler
  • License: GPL (>= 3)
  • Last published: 2024-10-30