Learn R Programming

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

RxODE (version 0.6-1)

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.

Copy Link

Version

Install

install.packages('RxODE')

Monthly Downloads

121

Version

0.6-1

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

October 13th, 2017

Functions in RxODE (0.6-1)

Create an ODE-based model specification

Add dosing to eventTable

Add sampling to eventTable

arrange_ for solveRxDll object

Return the RxODE coefficients

distinct_ for solveRxDll object

as_data_frame for solveRxODE

$ Assign for RxODE solved objects

Create an event table object

filter_ for solveRxDll object

genShinyApp.template

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

group_by_ for solveRxDll object

A compilation manager for RxODE models

Add a return statment to a function.

Jacobain and parameter derivates

Return the DLL associated with the RxODE object

Find the assignments in R expression

gather_ for solveRxDll object

rename_ for solveRxDll object

do.call while setting up windows path for compiling

Cleanup anonymous DLLs

Print the rxCoef object

print.rxCoefSolve

Print the rxCoefSolve object

Creates a logical matrix for block matrixes.

Use cat when RxODE.verbose is TRUE

mutate_ for solveRxDll object

Update Solved object with '+'

Print rxDll object

Predict an RxODE object

Print information about the RxODE object.

rxChain Chain or add item to solved system of equations

Second command in chaining commands

Determine if the rxDll is loaded or not.

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

Initial Values and State values for a RxODE object

Invert matrix using Rcpp Armadilo.

Takes a model and expands it to log multiplication

Return the md5 of an RxODE object or file

Get the normalized model

Return an accurate floating point sum of values

Parameters specified by the model

rxPhysicalDrives

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

Print x using the message facility

rxRtoolsBaseWin

Return Rtools base

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

Execute sympy statement.

Remove variables created by RxODE from the SymPy environment.

Return the expanded expression (via SymPy)

Using the Kahan method, take a more accurate sum

Left handed Variables

Prepare Error function for inclusion in RxODE

Parse PK function for inclusion in RxODE

Remove print statements

Remove sensitivity equations

Compile a model if needed

Echo cout to console for a number

Delete the DLL for the model

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

Load the DLL for the object

Prepare Pred function for inclusion in RxODE

Fix SymPy expressions to be R parsable expressions

Sync options with RxODE varaibles

Format theta and eta for parameter estimate values in RxODE

sample_n for solveRxDll object

select_ for solveRxDll object

Objects exported from other packages

Current Condition for RxODE object

Give the cout string for a number

Clear memoise cache for RxODE

Get model properties without compiling it.

Choose the type of sums to use for RxODE.

This setups the memoized functions.

Execute Python statement without getting the return value.

Does the varaible exist in the SymPy Python environment?

rxSymPySetupPred

Setup Pred function based on RxODE object.

Permissive or Strict RxODE sytax options

Using RxODE's default method, take a product

Return an accurate floating point sum of values

All model variables for a RxODE object

Using the Neumaier method, take a more accurate sum

Remove Jacobian

Using RxODE's default method, take a sum

Options for RxODE

Reload RxODE DLL

Require namespace, otherwise throw error.

This function splits a function based on + or - terms

State variables

Recast model in terms of sum/prod

Delete variable if exists.

Calculate df/dy derivatives

rxSymPyReserved

Return a list of reserved functions and variables from sympy

rxSymPySensitivity

Calculate the sensitivity equations for a model

Version and repository for this dparser package.

rxWinPythonSetup

Setup Python and SymPy for windows

separate_ for solveRxDll object

Unload the DLL for the object

Solve RxODE objects

spread_ for solveRxDll object

unite_ for solveRxDll object

update.solveRxODE

Update the solved object with any of the new parameters.

slice_ for solveRxDll object

summarise_ for solveRxDll object

Print expanded information about the RxODE object.

Get Omega and Omega^-1 and derivatives

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

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

Setup SymPy environment if needed

Solves a ODE equation

Split line into multiple lines at + or - breaks

Add undefined variables to SymPy

Get the theta numbers for the diagonal elements.

Setup SymPy variables

Return the version of SymPy that is running

rxWinRtoolsPath

Setup Rtools path

Setup Windows components for RxODE

Summary of rxDll object

transmute_ for solveRxDll object

rxSymPyFunctions

Setup SymPy functions

rxSymPyJacobian

Calculate the full Jacobian for a model

Converts model specification to/from a SymPy language

Translate the model to C code if needed

Garbage Collection for RxODE objects

sample_frac for solveRxDll object

[[<-.solveRxODE

Assign solved objects using the [[]] syntax

Assign solved objects using the [] syntax