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RxODE (version 0.9.0-6)

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

0.9.0-6

License

GPL (>= 2)

Maintainer

Wenping Wang

Last Published

May 30th, 2019

Functions in RxODE (0.9.0-6)

Add dosing to eventTable

Remove print statements

Remove Jacobian

print.rxCoefSolve

Print the rxCoefSolve object

Print rxDll object

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

Combining event tables

Sequence of event tables

Jacobian and parameter derivatives

Delete the DLL for the model

.rxWinRtoolsPath

Setup Rtools path

Use cat when RxODE.verbose is TRUE

Get RxODE model from object

Event translation for RxODE

Get the normalized model

Create an event table object

Get model properties without compiling it.

Get the rxModels information

Find the assignments in R expression

rxChain Chain or add item to solved system of equations

Event Table Function

Repeat an RxODE event table

Choose the type of sums to use for RxODE.

Remove sensitivity equations

Print information about the RxODE object.

Second command in chaining commands

Setup the initial conditions.

Unload RxODE object

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

Print the rxCoef object

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

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

Cleanup anonymous DLLs

Return the C file associated with the RxODE object

Creates a logical matrix for block matrixes.

Compile a model if needed

Checks if the RxODE object was built with the current build

.rxSymPyJacobian

Calculate the full Jacobian for a model

Determine if the DLL associated with the RxODE object is loaded

Return the md5 of an RxODE object or file

genShinyApp.template

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

First Order Expansion of ETA

All model variables for a RxODE object

Check to see if this is an rxSolve object.

Clear memoise cache for RxODE

Delete variable if exists.

Update Solved object with '+'

Permissive or Strict RxODE sytax options

Optimize RxODE for computer evaluation

Check to see if this is an rxEt object.

Add a return statment to a function.

rxPhysicalDrives

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

Assign pointer based on model variables

Current Condition for RxODE object

Calculate df/dy derivatives

Get the number of cores in a system

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

Invert matrix using Rcpp Armadilo.

Free the C solving information.

Setup SymPy environment if needed

Objects exported from other packages

Scaled Inverse Chi Squared distribution

Check the type of an object using Rcpp

Version and repository for this dparser package.

Options for RxODE

Split line into multiple lines at + or - breaks

Fix SymPy expressions to be R parsable expressions

Get Omega^-1 and derivatives

Add undefined variables to SymPy

Return the expanded expression (via SymPy)

rxWinPythonSetup

Setup Python and SymPy for windows

Setup SymPy variables

Parameters specified by the model

Return the DLL associated with the RxODE object

Return the version of SymPy that is running

RxODE progress bar functions

Load RxODE object

Prepare Error function for inclusion in RxODE

Format rxSolve and related objects as html.

This function splits a function based on + or - terms

Reload RxODE DLL

Initial Values and State values for a RxODE object

Stack a solved object for things like ggplot

Execute Python statement without getting the return value.

Does the varaible exist in the SymPy Python environment?

Parse PK function for inclusion in RxODE

Left handed Variables

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

Prepare Pred function for inclusion in RxODE

Setup the initial conditions.

Use Shiny to help develop an RxODE model

rxSymInvCholCreate

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

Require namespace, otherwise throw error.

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

rxSymPySetupPred

Setup Pred function based on RxODE object.

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Return the dimension of the built-in derivatives/inverses

rxSymPySensitivity

Calculate the sensitivity equations for a model

Translate the model to C code if needed

Converts model specification to/from a SymPy language

Setup Windows components for RxODE

Sync options with RxODE varaibles

State variables

Get the RxODE temporary directory

Print expanded information about the RxODE object.

Recast model in terms of sum/prod

Remove variables created by RxODE from the SymPy environment.

Execute sympy statement.

rxSymPyLincmtDvdx

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

rxSymPyFunctions

Setup SymPy functions

Use model object in your package

Summary of rxDll object

type_sum function for units

Sample a covariance Matrix from the Posteior Inverse Wishart distribution.

Coerce object to data.frame

Add sampling to eventTable

Find power THETAs for appropriate scaling

Return the RxODE coefficients

Clear/Set pipeline

Create an ODE-based model specification