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RxODE (version 0.7.2-4)

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

12

Version

0.7.2-4

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 16th, 2018

Functions in RxODE (0.7.2-4)

Invert matrix using Rcpp Armadilo.

Objects exported from other packages

Get RxODE model from object

rxChain Chain or add item to solved system of equations

Checks if the RxODE object was built with the current build

Scaled Inverse Chi Squared distribution

Format rxSolve and related objects as html.

Compile a model if needed

Return the C file associated with the RxODE object

Initial Values and State values for a RxODE object

Current Condition for RxODE object

All model variables for a RxODE object

Get model properties without compiling it.

Use cat when RxODE.verbose is TRUE

Get the rxModels information

Get the normalized model

Check the type of an object using Rcpp

Parse PK function for inclusion in RxODE

Options for RxODE

Parameters specified by the model

Cleanup anonymous DLLs

Return the dimension of the built-in derivatives/inverses

Second command in chaining commands

State variables

Prepare Error function for inclusion in RxODE

This function splits a function based on + or - terms

Recast model in terms of sum/prod

Load RxODE object

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

Free the C solving information.

Get the number of cores in a system

Prepare Pred function for inclusion in RxODE

Split line into multiple lines at + or - breaks

Unload RxODE object

Add undefined variables to SymPy

Delete the DLL for the model

Left handed Variables

Require namespace, otherwise throw error.

Determine if the DLL associated with the RxODE object is loaded

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

Delete variable if exists.

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

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

Permissive or Strict RxODE sytax options

Takes a model and expands it to log multiplication

Clear memoise cache for RxODE

Setup the initial conditions.

Return the md5 of an RxODE object or file

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

rxPhysicalDrives

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

Calculate df/dy derivatives

Use Shiny to help develop an RxODE model

Print x using the message facility

Solves a ODE equation

Choose the type of sums to use for RxODE.

Reload RxODE DLL

Execute sympy statement.

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Setup SymPy variables

rxSymPySetupPred

Setup Pred function based on RxODE object.

Get the theta numbers for the diagonal elements.

Get Omega and Omega^-1 and derivatives

Remove variables created by RxODE from the SymPy environment.

rxSymPySensitivity

Calculate the sensitivity equations for a model

Fix SymPy expressions to be R parsable expressions

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

rxSymPyFunctions

Setup SymPy functions

Setup the initial conditions.

Translate the model to C code if needed

Return the version of SymPy that is running

Does the varaible exist in the SymPy Python environment?

Return the expanded expression (via SymPy)

rxSymInvCholCreate

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

Get Omega^-1 and derivatives

Summary of rxDll object

Setup SymPy environment if needed

Sync options with RxODE varaibles

Execute Python statement without getting the return value.

Setup Windows components for RxODE

Format theta and eta for parameter estimate values in RxODE

Print expanded information about the RxODE object.

rxWinPythonSetup

Setup Python and SymPy for windows

Converts model specification to/from a SymPy language

Version and repository for this dparser package.

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

Find the assignments in R expression

Return the RxODE coefficients

Add dosing to eventTable

Check to see if this is an rxSolve object.

genShinyApp.template

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

Update Solved object with '+'

Create an event table object

Print information about the RxODE object.

Print the rxCoef object

Add sampling to eventTable

Add a return statment to a function.

Assign pointer based on model variables

Creates a logical matrix for block matrixes.

Create an ODE-based model specification

print.rxCoefSolve

Print the rxCoefSolve object

Print rxDll object

Jacobian and parameter derivatives

Return the DLL associated with the RxODE object