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RxODE (version 0.7.2-1)

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

236

Version

0.7.2-1

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/nlmixrdevelopment/RxODE

Homepage

https://www.r-project.org

Maintainer

Wenping Wang

Last Published

May 19th, 2018

Functions in RxODE (0.7.2-1)

Add sampling to eventTable

Return the RxODE coefficients

Jacobian and parameter derivatives

Format rxSolve and related objects as html.

Return the DLL associated with the RxODE object

Initial Values and State values for a RxODE object

Takes a model and expands it to log multiplication

Return the md5 of an RxODE object or file

Create an ODE-based model specification

Prepare Error function for inclusion in RxODE

Parameters specified by the model

Choose the type of product to use in RxODE. These are used in the RxODE prod blocks

Add dosing to eventTable

Choose the type of sums to use for RxODE.

print.rxCoefSolve

Print the rxCoefSolve object

Find the assignments in R expression

genShinyApp.template

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

Add a return statment to a function.

Assign pointer based on model variables

Use Shiny to help develop an RxODE model

Get Omega^-1 and derivatives

Print rxDll object

Second command in chaining commands

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Print information about the RxODE object.

rxSymInvCholCreate

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

Fix SymPy expressions to be R parsable expressions

Cleanup anonymous DLLs

Print the rxCoef object

Solves a ODE equation

Split line into multiple lines at + or - breaks

Compile a model if needed

Create an event table object

Check to see if this is an rxSolve object.

Creates a logical matrix for block matrixes.

Get RxODE model from object

Get model properties without compiling it.

Update Solved object with '+'

Return the C file associated with the RxODE object

rxWinPythonSetup

Setup Python and SymPy for windows

Does the varaible exist in the SymPy Python environment?

Return the expanded expression (via SymPy)

Delete the DLL for the model

Execute Python statement without getting the return value.

Get the number of cores in a system

Current Condition for RxODE object

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

rxWinRtoolsPath

Setup Rtools path

rxModelVars.character

All model variables for a RxODE object

Scaled Inverse Chi Squared distribution

Objects exported from other packages

rxChain Chain or add item to solved system of equations

Summary of rxDll object

Use cat when RxODE.verbose is TRUE

Remove sensitivity equations

Get the rxModels information

Permissive or Strict RxODE sytax options

Clear memoise cache for RxODE

rxPhysicalDrives

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

This translates the parameters specified by the model in the correct type of solving.

Left handed Variables

Load RxODE object

rxRtoolsBaseWin

Return Rtools base

Unload RxODE object

Parse PK function for inclusion in RxODE

Get the theta numbers for the diagonal elements.

Get Omega and Omega^-1 and derivatives

Setup SymPy environment if needed

Version and repository for this dparser package.

rxSymPySetupPred

Setup Pred function based on RxODE object.

Prepare Pred function for inclusion in RxODE

Invert matrix using Rcpp Armadilo.

rxSymPyFunctions

Setup SymPy functions

rxSymPySensitivity

Calculate the sensitivity equations for a model

Setup the initial conditions.

Checks if the RxODE object was built with the current build

Determine if the DLL associated with the RxODE object is loaded

Setup a SymPy environment that sets up the specified RxODE model.

Check the type of an object using Rcpp

Setup Windows components for RxODE

Get the normalized model

Print expanded information about the RxODE object.

Options for RxODE

Require namespace, otherwise throw error.

Print x using the message facility

Reload RxODE DLL

Remove Jacobian

Remove print statements

Return the dimension of the built-in derivatives/inverses

Setup the initial conditions.

Recast model in terms of sum/prod

This function splits a function based on + or - terms

Sync options with RxODE varaibles

State variables

Creates an object for caluclating Omega/Omega^-1 and dervatives

Format theta and eta for parameter estimate values in RxODE

Add undefined variables to SymPy

Delete variable if exists.

Calculate df/dy derivatives

Execute sympy statement.

Remove variables created by RxODE from the SymPy environment.

Return the version of SymPy that is running

Setup SymPy variables

rxSymPyJacobian

Calculate the full Jacobian for a model

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Converts model specification to/from a SymPy language

Translate the model to C code if needed