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RxODE (version 0.8.0-9)

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

0.8.0-9

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

December 10th, 2018

Functions in RxODE (0.8.0-9)

Return the RxODE coefficients

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

Check to see if this is an rxSolve object.

Remove print statements

.rxRtoolsBaseWin

Return Rtools base

Update Solved object with '+'

Creates a logical matrix for block matrixes.

Print information about the RxODE object.

.rxSymPyJacobian

Calculate the full Jacobian for a model

.rxWinRtoolsPath

Setup Rtools path

Return the C file associated with the RxODE object

Print the rxCoef object

Get the number of cores in a system

Objects exported from other packages

Scaled Inverse Chi Squared distribution

Second command in chaining commands

Cleanup anonymous DLLs

Compile a model if needed

Current Condition for RxODE object

Delete the DLL for the model

Clear memoise cache for RxODE

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

First Order Expansion of ETA

Add sampling to eventTable

Generalized Cholesky Matrix Decomposition

Initial Values and State values for a RxODE object

Check the type of an object using Rcpp

Create an ODE-based model specification

Get model properties without compiling it.

Create an event table object

Permissive or Strict RxODE sytax options

Checks if the RxODE object was built with the current build

Left handed Variables

Prepare Pred function for inclusion in RxODE

Determine if the DLL associated with the RxODE object is loaded

rxPhysicalDrives

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

Find the assignments in R expression

Add dosing to eventTable

print.rxCoefSolve

Print the rxCoefSolve object

Invert matrix using Rcpp Armadilo.

Print x using the message facility

RxODE progress bar functions

Fit/Evaulate FOCEi

genShinyApp.template

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

Return the md5 of an RxODE object or file

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

Add a return statment to a function.

Assign pointer based on model variables

Print rxDll object

Free the C solving information.

Jacobian and parameter derivatives

Reload RxODE DLL

Choose the type of sums to use for RxODE.

Use cat when RxODE.verbose is TRUE

rxChain Chain or add item to solved system of equations

Get Omega^-1 and derivatives

Setup the initial conditions.

rxSymInvCholCreate

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

Require namespace, otherwise throw error.

Get RxODE model from object

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Split line into multiple lines at + or - breaks

Return the DLL associated with the RxODE object

rxSymPySensitivity

Calculate the sensitivity equations for a model

Format rxSolve and related objects as html.

Delete variable if exists.

Remove variables created by RxODE from the SymPy environment.

Load RxODE object

Does the varaible exist in the SymPy Python environment?

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

Return the expanded expression (via SymPy)

Get the normalized model

Unload RxODE object

Recast model in terms of sum/prod

Version and repository for this dparser package.

Add undefined variables to SymPy

All model variables for a RxODE object

Get the rxModels information

Prepare Error function for inclusion in RxODE

Optimize RxODE for computer evaluation

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

Sync options with RxODE varaibles

Parse PK function for inclusion in RxODE

Options for RxODE

Summary of rxDll object

Yeo-Johnson Transformation

Setup SymPy environment if needed

Parameters specified by the model

rxSymPySetupPred

Setup Pred function based on RxODE object.

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Setup the initial conditions.

Format theta and eta for parameter estimate values in RxODE

Solves a ODE equation

This function splits a function based on + or - terms

Use Shiny to help develop an RxODE model

Fix SymPy expressions to be R parsable expressions

State variables

Return the square root of general square matrix A

rxSymPyFunctions

Setup SymPy functions

Return the dimension of the built-in derivatives/inverses

Print expanded information about the RxODE object.

Execute sympy statement.

Calculate df/dy derivatives

Execute Python statement without getting the return value.

Return the version of SymPy that is running

Setup SymPy variables

Translate the model to C code if needed

Converts model specification to/from a SymPy language

rxWinPythonSetup

Setup Python and SymPy for windows

Setup Windows components for RxODE

Remove Jacobian

Cox Box transformation

Remove sensitivity equations