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RxODE (version 0.7.2-2)

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

0.7.2-2

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/nlmixrdevelopment/RxODE

Homepage

https://www.r-project.org

Maintainer

Wenping Wang

Last Published

June 3rd, 2018

Functions in RxODE (0.7.2-2)

Get the normalized model

Options for RxODE

Compile a model if needed

Remove print statements

Fix SymPy expressions to be R parsable expressions

State variables

Second command in chaining commands

Use cat when RxODE.verbose is TRUE

Current Condition for RxODE object

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

Clear memoise cache for RxODE

Parse PK function for inclusion in RxODE

rxSymPyFunctions

Setup SymPy functions

Objects exported from other packages

This function splits a function based on + or - terms

Execute Python statement without getting the return value.

Prepare Pred function for inclusion in RxODE

Remove Jacobian

Get the number of cores in a system

Jacobian and parameter derivatives

rxWinRtoolsPath

Setup Rtools path

Format rxSolve and related objects as html.

rxChain Chain or add item to solved system of equations

Cleanup anonymous DLLs

Takes a model and expands it to log multiplication

Initial Values and State values for a RxODE object

rxWinPythonSetup

Setup Python and SymPy for windows

Delete the DLL for the model

Parameters specified by the model

Load RxODE object

Unload RxODE object

Return the md5 of an RxODE object or file

Check the type of an object using Rcpp

Invert matrix using Rcpp Armadilo.

Prepare Error function for inclusion in RxODE

Return the DLL associated with the RxODE object

Left handed Variables

Get model properties without compiling it.

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

Get RxODE model from object

Checks if the RxODE object was built with the current build

rxModelVars.character

All model variables for a RxODE object

Get the rxModels information

Determine if the DLL associated with the RxODE object is loaded

Remove sensitivity equations

Reload RxODE DLL

rxRtoolsBaseWin

Return Rtools base

Permissive or Strict RxODE sytax options

Setup the initial conditions.

Print x using the message facility

Get Omega^-1 and derivatives

Require namespace, otherwise throw error.

Setup the initial conditions.

Get the theta numbers for the diagonal elements.

rxPhysicalDrives

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

rxSymInvCholCreate

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

Get Omega and Omega^-1 and derivatives

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Use Shiny to help develop an RxODE model

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

Choose the type of sums to use for RxODE.

Delete variable if exists.

Solves a ODE equation

Recast model in terms of sum/prod

Calculate df/dy derivatives

rxSymPyJacobian

Calculate the full Jacobian for a model

Translate the model to C code if needed

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Summary of rxDll object

Add undefined variables to SymPy

Converts model specification to/from a SymPy language

Remove variables created by RxODE from the SymPy environment.

Does the varaible exist in the SymPy Python environment?

rxSymPySensitivity

Calculate the sensitivity equations for a model

Execute sympy statement.

Split line into multiple lines at + or - breaks

Return the dimension of the built-in derivatives/inverses

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

Setup SymPy environment if needed

Return the expanded expression (via SymPy)

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

Sync options with RxODE varaibles

rxSymPySetupPred

Setup Pred function based on RxODE object.

Format theta and eta for parameter estimate values in RxODE

Setup SymPy variables

Return the version of SymPy that is running

Setup Windows components for RxODE

Version and repository for this dparser package.

Print expanded information about the RxODE object.

Check to see if this is an rxSolve object.

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

Add dosing to eventTable

Add sampling to eventTable

Assign pointer based on model variables

genShinyApp.template

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

Find the assignments in R expression

Update Solved object with '+'

Print rxDll object

Return the RxODE coefficients

Return the C file associated with the RxODE object

Create an ODE-based model specification

Create an event table object

Add a return statment to a function.

Print information about the RxODE object.

Scaled Inverse Chi Squared distribution

print.rxCoefSolve

Print the rxCoefSolve object

Print the rxCoef object

Creates a logical matrix for block matrixes.