Facilities for Simulating from ODE-Based Models


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Documentation for package ‘RxODE’ version 0.9.2-0

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A C E F G I P R S T U W misc

-- A --

add.dosing Add dosing to eventTable
add.sampling Add sampling to eventTable
as.character.rxEvid EVID formatting for tibble and other places.
as.data.table.rxEt Convert an event table to a data.table
as.et Coerce object to data.frame
as.et.default Coerce object to data.frame
as.rxEvid EVID formatting for tibble and other places.
as.rxRateDur Creates a rxRateDur object
as.tbl.rxEt Convert to tbl
as_tibble.rxEt Convert to tbl

-- C --

c.rxEvid EVID formatting for tibble and other places.
coef.RxCompilationManager Return the RxODE coefficients
coef.rxDll Return the RxODE coefficients
coef.RxODE Return the RxODE coefficients
coef.solveRxODE Return the RxODE coefficients
cvPost Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

-- E --

et Event Table Function
et.default Event Table Function
et.RxODE Event Table Function
et.rxParams Event Table Function
et.rxSolve Event Table Function
etExpand Expand additional doses
etRbind Combining event tables
etRep Repeat an RxODE event table
etSeq Sequence of event tables
eventTable Create an event table object

-- F --

forderForceBase Force using base order for RxODE radix sorting
format.rxEvid EVID formatting for tibble and other places.
format_type_sum.type_sum_units type_sum function for units

-- G --

genShinyApp.template Generate an example (template) of a dosing regimen shiny app
guide_none Empty Guide

-- I --

is.rxEt Check to see if this is an rxEt object.
is.rxSolve Check to see if this is an rxSolve object.

-- P --

pillar_shaft Re export of pillar_shaft
pillar_shaft.mixed_units type_sum function for units
pillar_shaft.rxEvid EVID formatting for tibble and other places.
pillar_shaft.rxRateDur Pillar shaft for rxRateDur
pillar_shaft.units type_sum function for units
predict.rxEt Solving & Simulation of a ODE/solved system (and solving options) equation
predict.RxODE Solving & Simulation of a ODE/solved system (and solving options) equation
predict.rxParams Solving & Simulation of a ODE/solved system (and solving options) equation
predict.rxSolve Solving & Simulation of a ODE/solved system (and solving options) equation
print.rxCoefSolve Print the rxCoefSolve object
print.rxEvid EVID formatting for tibble and other places.
print.RxODE Print information about the RxODE object.

-- R --

rbind.rxEt Combining event tables
rep.rxEt Repeat an RxODE event table
rinvchisq Scaled Inverse Chi Squared distribution
rxAddReturn Add a return statement to a function.
rxAllowUnload Allow unloading of dlls
rxAssignPtr Assign pointer based on model variables
rxC14 Setup C++14 support in windows (required for nlmixr)
rxChain rxChain Chain or add item to solved system of equations
rxClean Cleanup anonymous DLLs by unloading them
rxCompile Compile a model if needed
rxCompile.character Compile a model if needed
rxCompile.rxDll Compile a model if needed
rxCompile.RxODE Compile a model if needed
rxControl Solving & Simulation of a ODE/solved system (and solving options) equation
rxCores Get the number of cores in a system
rxDelete Delete the DLL for the model
rxDfdy Jacobian and parameter derivatives
rxEvid EVID formatting for tibble and other places.
rxFoExpandEta First Order Expansion of ETA
rxGetRxODE Get RxODE model from object
rxHtml Format rxSolve and related objects as html.
rxHtml.rxSolve Format rxSolve and related objects as html.
rxInv Invert matrix using RcppArmadillo.
rxIsCurrent Checks if the RxODE object was built with the current build
rxLhs Left handed Variables
rxLock Lock/unlocking of RxODE dll file
rxNorm Get the normalized model
RxODE Create an ODE-based model specification
rxOptExpr Optimize RxODE for computer evaluation
rxOptions Options for RxODE
rxParam Parameters specified by the model
rxParams Parameters specified by the model
rxParams.rxEt Parameters specified by the model
rxParams.RxODE Parameters specified by the model
rxParams.rxSolve Parameters specified by the model
rxPermissive Permissive or Strict RxODE syntax options
rxProgress RxODE progress bar functions
rxProgressAbort RxODE progress bar functions
rxProgressStop RxODE progress bar functions
rxRateDur Creates a rxRateDur object
rxSetIni0 Set Initial conditions to time zero instead of the first observed/dosed time
rxSetProd Choose the type of product to use in RxODE. These are used in the RxODE 'prod' blocks
rxSetProgressBar Set timing for progress bar
rxSetSum Choose the type of sums to use for RxODE.
rxShiny Use Shiny to help develop an RxODE model
rxShiny.default Use Shiny to help develop an RxODE model
rxShiny.rxSolve Use Shiny to help develop an RxODE model
rxSimThetaOmega Simulate Parameters from a Theta/Omega specification
rxSolve Solving & Simulation of a ODE/solved system (and solving options) equation
rxSolve.default Solving & Simulation of a ODE/solved system (and solving options) equation
rxStack Stack a solved object for things like ggplot
rxState State variables
rxStrict Permissive or Strict RxODE syntax options
rxSumProdModel Recast model in terms of sum/prod
rxSymInvChol Get Omega^-1 and derivatives
rxSymPyFix Fix SymPy expressions to be R parsable expressions
rxSymPySensitivity Calculate the sensitivity equations for a model
rxSymPyVersion Return the version of SymPy that is running
rxSyncOptions Sync options with RxODE variables
rxTempDir Get the RxODE temporary directory
rxTest Validate RxODE
rxTick RxODE progress bar functions
rxTrans Translate the model to C code if needed
rxTrans.character Translate the model to C code if needed
rxTrans.default Translate the model to C code if needed
rxUnloadAll Unload all RxODE Dlls that are not locked for solving.
rxUnlock Lock/unlocking of RxODE dll file
rxUse Use model object in your package
rxUseRadixSort Use Radix Sort when possible
rxValidate Validate RxODE
rxWinPythonSetup Setup Python and SymPy for windows
rxWinSetup Setup Windows components for RxODE

-- S --

seq.rxEt Sequence of event tables
simulate.RxODE Solving & Simulation of a ODE/solved system (and solving options) equation
simulate.rxParams Solving & Simulation of a ODE/solved system (and solving options) equation
simulate.rxSolve Solving & Simulation of a ODE/solved system (and solving options) equation
solve.rxEt Solving & Simulation of a ODE/solved system (and solving options) equation
solve.RxODE Solving & Simulation of a ODE/solved system (and solving options) equation
solve.rxParams Solving & Simulation of a ODE/solved system (and solving options) equation
solve.rxSolve Solving & Simulation of a ODE/solved system (and solving options) equation
summary.RxODE Print expanded information about the RxODE object.

-- T --

tibble type_sum function for units
type_sum.mixed_units type_sum function for units
type_sum.rxEvid EVID formatting for tibble and other places.
type_sum.rxRateDur Creates a rxRateDur object
type_sum.units type_sum function for units

-- U --

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

-- W --

write.template.server Generate an example (template) of a dosing regimen shiny app
write.template.ui Generate an example (template) of a dosing regimen shiny app

-- misc --

+.solveRxDll rxChain Chain or add item to solved system of equations
.clearPipe Clear/Set pipeline
.rxFindPow Find power THETAs for appropriate scaling
.rxRmPrint Remove print statements
.rxRmSens Remove sensitivity equations
.rxSymPyJacobian Calculate the full Jacobian for a model
.rxWinRtoolsPath Setup Rtools path
.setWarnIdSort Turn on/off warnings for ID sorting.
[.rxEvid EVID formatting for tibble and other places.
[[.rxEvid EVID formatting for tibble and other places.