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RxODE (version 0.9.0-8)

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

236

Version

0.9.0-8

License

GPL (>= 2)

Maintainer

Wenping Wang

Last Published

June 21st, 2019

Functions in RxODE (0.9.0-8)

Add sampling to eventTable

Return the RxODE coefficients

Clear/Set pipeline

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

Find power THETAs for appropriate scaling

Create an ODE-based model specification

Coerce object to data.frame

Add dosing to eventTable

Create an event table object

Find the assignments in R expression

Remove print statements

Update Solved object with '+'

Check to see if this is an rxSolve object.

Remove Jacobian

Repeat an RxODE event table

rxChain Chain or add item to solved system of equations

Combining event tables

Second command in chaining commands

Remove sensitivity equations

.rxWinRtoolsPath

Setup Rtools path

Add a return statment to a function.

print.rxCoefSolve

Print the rxCoefSolve object

Event Table Function

.rxSymPyJacobian

Calculate the full Jacobian for a model

Print information about the RxODE object.

Jacobian and parameter derivatives

Delete the DLL for the model

Print the rxCoef object

Setup C++14 support in windows (required for nlmixr)

Use cat when RxODE.verbose is TRUE

Current Condition for RxODE object

Checks if the RxODE object was built with the current build

Determine if the DLL associated with the RxODE object is loaded

Assign pointer based on model variables

genShinyApp.template

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

Event translation for RxODE

Sequence of event tables

Check to see if this is an rxEt object.

Scaled Inverse Chi Squared distribution

Unload RxODE object

Objects exported from other packages

Print rxDll object

All model variables for a RxODE object

Reload RxODE DLL

Return the md5 of an RxODE object or file

RxODE progress bar functions

Get the number of cores in a system

Check the type of an object using Rcpp

Invert matrix using Rcpp Armadilo.

First Order Expansion of ETA

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

Cleanup anonymous DLLs

Left handed Variables

Creates a logical matrix for block matrixes.

Return the C file associated with the RxODE object

Optimize RxODE for computer evaluation

Compile a model if needed

Clear memoise cache for RxODE

Parameters specified by the model

Require namespace, otherwise throw error.

Options for RxODE

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

Prepare Error function for inclusion in RxODE

Choose the type of sums to use for RxODE.

Setup the initial conditions.

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

Permissive or Strict RxODE sytax options

Load RxODE object

Return the DLL associated with the RxODE object

Get model properties without compiling it.

Format rxSolve and related objects as html.

Initial Values and State values for a RxODE object

rxPhysicalDrives

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

Add undefined variables to SymPy

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Solving \& Simulation of a ODE/solved system (and solving options) equation

Get Omega^-1 and derivatives

Recast model in terms of sum/prod

Return the dimension of the built-in derivatives/inverses

State variables

rxSymInvCholCreate

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

Setup the initial conditions.

Use Shiny to help develop an RxODE model

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Version and repository for this dparser package.

rxSymPySensitivity

Calculate the sensitivity equations for a model

rxWinPythonSetup

Setup Python and SymPy for windows

rxSymPySetupPred

Setup Pred function based on RxODE object.

Get RxODE model from object

Get the rxModels information

Delete variable if exists.

Parse PK function for inclusion in RxODE

Prepare Pred function for inclusion in RxODE

Calculate df/dy derivatives

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

Get the normalized model

This function splits a function based on + or - terms

Stack a solved object for things like ggplot

Split line into multiple lines at + or - breaks

Remove variables created by RxODE from the SymPy environment.

Free the C solving information.

Execute sympy statement.

Fix SymPy expressions to be R parsable expressions

Use model object in your package

Return the expanded expression (via SymPy)

Execute Python statement without getting the return value.

Setup SymPy variables

Setup SymPy environment if needed

Return the version of SymPy that is running

rxSymPyFunctions

Setup SymPy functions

rxSymPyLincmtDvdx

This creates the dv/dx RxODE model for a linear solved system

Does the varaible exist in the SymPy Python environment?

Sync options with RxODE varaibles

Get the RxODE temporary directory

Summary of rxDll object

type_sum function for units

Converts model specification to/from a SymPy language

Translate the model to C code if needed

Setup Windows components for RxODE

Print expanded information about the RxODE object.