Learn R Programming

⚠️There's a newer version (1.1.5) of this package.Take me there.

RxODE (version 0.7.2-5)

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.

Copy Link

Version

Install

install.packages('RxODE')

Monthly Downloads

121

Version

0.7.2-5

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

June 19th, 2018

Functions in RxODE (0.7.2-5)

Add sampling to eventTable

Objects exported from other packages

Scaled Inverse Chi Squared distribution

Find the assignments in R expression

genShinyApp.template

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

print.rxCoefSolve

Print the rxCoefSolve object

rxChain Chain or add item to solved system of equations

Use cat when RxODE.verbose is TRUE

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

Print rxDll object

Clear memoise cache for RxODE

Left handed Variables

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

Delete the DLL for the model

Get the number of cores in a system

Require namespace, otherwise throw error.

Checks if the RxODE object was built with the current build

Get RxODE model from object

Get model properties without compiling it.

Determine if the DLL associated with the RxODE object is loaded

Load RxODE object

Parameters specified by the model

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

Unload RxODE object

Prepare Error function for inclusion in RxODE

Check to see if this is an rxSolve object.

Free the C solving information.

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Update Solved object with '+'

Solves a ODE equation

Print the rxCoef object

Print information about the RxODE object.

Split line into multiple lines at + or - breaks

Cleanup anonymous DLLs

Get the theta numbers for the diagonal elements.

Second command in chaining commands

Format rxSolve and related objects as html.

Get Omega and Omega^-1 and derivatives

All model variables for a RxODE object

Return the expanded expression (via SymPy)

Get the rxModels information

Fix SymPy expressions to be R parsable expressions

Recast model in terms of sum/prod

Sync options with RxODE varaibles

Permissive or Strict RxODE sytax options

Return the version of SymPy that is running

Add undefined variables to SymPy

Version and repository for this dparser package.

Initial Values and State values for a RxODE object

Execute Python statement without getting the return value.

rxPhysicalDrives

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

rxWinPythonSetup

Setup Python and SymPy for windows

Setup the initial conditions.

Does the varaible exist in the SymPy Python environment?

Use Shiny to help develop an RxODE model

Create an ODE-based model specification

Converts model specification to/from a SymPy language

Format theta and eta for parameter estimate values in RxODE

Setup Windows components for RxODE

Add dosing to eventTable

Print expanded information about the RxODE object.

Execute sympy statement.

Get the normalized model

Options for RxODE

Print x using the message facility

Remove variables created by RxODE from the SymPy environment.

rxSymPyFunctions

Setup SymPy functions

Add a return statment to a function.

Assign pointer based on model variables

Translate the model to C code if needed

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Reload RxODE DLL

Choose the type of sums to use for RxODE.

Jacobian and parameter derivatives

Summary of rxDll object

Return the DLL associated with the RxODE object

Setup the initial conditions.

Get Omega^-1 and derivatives

rxSymInvCholCreate

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

Invert matrix using Rcpp Armadilo.

Check the type of an object using Rcpp

Calculate df/dy derivatives

Delete variable if exists.

Takes a model and expands it to log multiplication

Setup SymPy variables

Return the md5 of an RxODE object or file

Parse PK function for inclusion in RxODE

This function splits a function based on + or - terms

Prepare Pred function for inclusion in RxODE

State variables

Return the dimension of the built-in derivatives/inverses

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

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

rxSymPySensitivity

Calculate the sensitivity equations for a model

Setup SymPy environment if needed

rxSymPySetupPred

Setup Pred function based on RxODE object.

Return the RxODE coefficients

Create an event table object

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

Creates a logical matrix for block matrixes.

Return the C file associated with the RxODE object

Compile a model if needed

Current Condition for RxODE object