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RxODE (version 1.0.4)

Facilities for Simulating from ODE-Based Models

Description

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.

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Version

Install

install.packages('RxODE')

Monthly Downloads

121

Version

1.0.4

License

GPL (>= 3)

Maintainer

Wenping Wang

Last Published

February 24th, 2021

Functions in RxODE (1.0.4)

Register a method for a suggested dependency

Expand additional doses

genShinyApp.template

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

forderForceBase

Force using base order for RxODE radix sorting

.rxFinalizePred

Finalize RxODE pred based on symengine saved info

Gammap: normalized lower incomplete gamma function

Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

Generate pieces for EBE only problem

Event Table Function

Get/Set the number of threads that RxODE uses

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

Scaled Inverse Chi Squared distribution

Get the state information for the current model

Generate pieces for FOCEi inner problem

Setup Pred function based on RxODE object.

Combining event tables

Turn on/off warnings for ID sorting.

Allow unloading of dlls

One correlation sample from the Inverse Wishart distribution

Create an event table object

Repeat an RxODE event table

Find the assignments in R expression

Generate the ETA sensitivities for FO related methods

With one sink, then release

Add a return statment to a function.

Determine if the DLL associated with the RxODE object is loaded

Parameters specified by the model

Objects exported from other packages

Generate FOCE without interaction

Gammaq: normalized upper incomplete gamma function

Check to see if this is an rxEt object.

gammaqInv and gammaqInva: Inverses of normalized gammaq function

Sequence of event tables

Generate Augmented pred/err RxODE model

Setup the initial conditions.

Use cat when RxODE.verbose is TRUE

Simulate chi-squared variable from threefry generator

Set the preferred factoring by state

EVID formatting for tibble and other places.

Return the dimension of the built-in derivatives/inverses

Get the linear compartment model true function

rxChain Chain or add item to solved system of equations

Faster expand.grid

Return the md5 of an RxODE object or file

Event translation for RxODE

Get model properties without compiling it.

One correlation sample from the LKJ distribution

Reload RxODE DLL

logit and inverse logit (expit) functions

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

Check to see if this is an rxSolve object.

rxTheme is the RxODE theme for plots

lowergamma: upper incomplete gamma function

Setup Windows components for RxODE

Add to RxODE's derivative tables

Delete the DLL for the model

Load a model into a symengine environment

Prune branches (ie if/else) from RxODE

Simulate exponential variable from threefry generator

Compile a model if needed

Initial Values and State values for a RxODE object

Lock/unlocking of RxODE dll file

Creates a rxRateDur object

Assign pointer based on model variables

Left handed Variables

rxSupportedFuns

Get list of supported functions

Invert matrix using RcppArmadillo.

Current Condition for RxODE object

rxSymInvCholCreate

Creates an object for calculating Omega/Omega^-1 and derivatives

Parse PK function for inclusion in RxODE

rxSetProgressBar

Set timing for progress bar

Recast model in terms of sum/prod

Remove print statements

Print information about the RxODE object.

Prepare Pred function for inclusion in RxODE

Defunct setting of sum

Silence some of RxODE's C/C++ messages

Simulate F variable from threefry generator

Simulate beta variable from threefry generator

probit and inverse probit functions

gammapInv and gammapInva: Inverses of normalized gammap function

gammapDer: derivative of gammap

Simulate Binomial variable from threefry generator

Temporarily set options then restore them while running code

Simulate uniform variable from threefry generator

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

Format rxSolve and related objects as html.

Cumulative distribution of standard normal

Update Solved object with '+'

Print rxDll object

Simulate geometric variable from threefry generator

Use Shiny to help develop an RxODE model

Return the C file associated with the RxODE object

Creates a logical matrix for block matrixes.

Checks if the RxODE object was built with the current build

Simulate Cauchy variable from threefry generator

Simulate random normal variable from threefry/vandercorput generator

Load RxODE object

Simulate random Poisson variable from threefry generator

Jacobian and parameter derivatives

Wrap a test in RxODE

Get the normalized model

Return the DLL associated with the RxODE object

Setup the initial conditions.

Simulate student t variable from threefry generator

rxIndLinStrategy

This sets the inductive linearization strategy for matrix building

Prepare Error function for inclusion in RxODE

Sync options with RxODE variables

Stack a solved object for things like ggplot

Dosing/Amt geom/stat

State variables

Simulate a from a Poisson process

Get the RxODE temporary directory

Temporarily set options then restore them while running code

.rxWinRtoolsPath

Setup Rtools path

Creates a package from compiled RxODE models

Censoring geom/stat

Version and repository for this dparser package.

Unload RxODE object

This function splits a function based on + or - terms

Check the type of an object using Rcpp

Get RxODE model from object

Create a random "normal" matrix using vandercorput generator

Optimize RxODE for computer evaluation

Unloads all RxODE compiled DLLs

RxODE progress bar functions

Print the rxCoef object

Print expanded information about the RxODE object.

Cleanup anonymous DLLs by unloading them

Second command in chaining commands

RxODE to symengine environment

Translate the model to C code if needed

Free the C solving/parsing information.

Add user function to RxODE

Clear memoise cache for RxODE

Simulate gamma variable from threefry generator

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

Simulate Weibull variable from threefry generator

Simulate from a (truncated) multivariate normal

Summary of rxDll object

Require namespace, otherwise throw error.

Generate pred-only SAEM RxODE model

rxPhysicalDrives

Returns a list of physical drives that have been or currently are mounted to the computer.

All model variables for a RxODE object

Get the rxModels information

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

Defunct setting of product

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

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Respect suppress messages

Use model object in your package

type_sum function for units

uppergamma: upper incomplete gamma function

Get Omega^-1 and derivatives

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

Clear/Set pipeline

.rxFinalizeInner

Finalize inner RxODE based on symengine saved info

Add sampling to eventTable

as.data.table.rxEt

Convert an event table to a data.table

Return the RxODE coefficients

Coerce object to data.frame

Create an ODE-based model specification

Add dosing to eventTable