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RxODE (version 0.9.2-0)

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. You can also obtain the archived SnakeCharmR for python integration from CRAN archives or .

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Version

Install

install.packages('RxODE')

Monthly Downloads

236

Version

0.9.2-0

License

GPL (>= 3)

Maintainer

Wenping Wang

Last Published

March 13th, 2020

Functions in RxODE (0.9.2-0)

Expand additional doses

Remove sensitivity equations

Remove print statements

as.data.table.rxEt

Convert an event table to a data.table

Add sampling to eventTable

Event Table Function

Turn on/off warnings for ID sorting.

Create an ODE-based model specification

Add dosing to eventTable

Combining event tables

Remove Jacobian

Repeat an RxODE event table

genShinyApp.template

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

Print information about the RxODE object.

forderForceBase

Force using base order for RxODE radix sorting

Update Solved object with '+'

Event translation for RxODE

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

.rxSymPyJacobian

Calculate the full Jacobian for a model

Create an event table object

.rxWinRtoolsPath

Setup Rtools path

Print rxDll object

Find the assignments in R expression

Creates a logical matrix for block matrixes.

Check to see if this is an rxEt object.

Get the number of cores in a system

Check to see if this is an rxSolve object.

Return the C file associated with the RxODE object

Objects exported from other packages

Use cat when RxODE.verbose is TRUE

Current Condition for RxODE object

Clear memoise cache for RxODE

Get the normalized model

Setup the initial conditions.

Reload RxODE DLL

Setup the initial conditions.

Get model properties without compiling it.

Re export of pillar_shaft

Sequence of event tables

Get the rxModels information

Execute sympy statement.

rxChain Chain or add item to solved system of equations

Require namespace, otherwise throw error.

Return the dimension of the built-in derivatives/inverses

Delete the DLL for the model

EVID formatting for tibble and other places.

Print the rxCoef object

Return the expanded expression (via SymPy)

Left handed Variables

print.rxCoefSolve

Print the rxCoefSolve object

Unload RxODE object

pillar_shaft.rxRateDur

Pillar shaft for rxRateDur

Does the variable exist in the SymPy Python environment?

Compile a model if needed

Determine if the DLL associated with the RxODE object is loaded

Second command in chaining commands

Cleanup anonymous DLLs by unloading them

Parameters specified by the model

Return the DLL associated with the RxODE object

Sync options with RxODE variables

Return the version of SymPy that is running

Permissive or Strict RxODE syntax options

Prepare Error function for inclusion in RxODE

Jacobian and parameter derivatives

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

Scaled Inverse Chi Squared distribution

Add a return statement to a function.

Free the C solving/parsing information.

Version and repository for this dparser package.

Optimize RxODE for computer evaluation

Load RxODE object

Checks if the RxODE object was built with the current build

Check the type of an object using Rcpp

rxPhysicalDrives

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

Options for RxODE

Parse PK function for inclusion in RxODE

Assign pointer based on model variables

Allow unloading of dlls

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

Recast model in terms of sum/prod

Use Shiny to help develop an RxODE model

Stack a solved object for things like ggplot

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Prepare Pred function for inclusion in RxODE

Get RxODE model from object

Format rxSolve and related objects as html.

State variables

First Order Expansion of ETA

Calculate df/dy derivatives

Get the RxODE temporary directory

Execute Python statement without getting the return value.

rxWinPythonSetup

Setup Python and SymPy for windows

Converts model specification to/from a SymPy language

Return the md5 of an RxODE object or file

Add undefined variables to SymPy

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

Invert matrix using RcppArmadillo.

Lock/unlocking of RxODE dll file

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

Set Initial conditions to time zero instead of the first observed/dosed time

Initial Values and State values for a RxODE object

rxSetProgressBar

Set timing for progress bar

RxODE progress bar functions

Setup Windows components for RxODE

Fix SymPy expressions to be R parsable expressions

All model variables for a RxODE object

Split line into multiple lines at + or - breaks

Creates a rxRateDur object

Remove variables created by RxODE from the SymPy environment.

Delete variable if exists.

This function splits a function based on + or - terms

Setup SymPy environment if needed

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Translate the model to C code if needed

rxSymPyLincmtDvdx

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

Choose the type of sums to use for RxODE.

Unload all RxODE Dlls that are not locked for solving.

Use model object in your package

rxSymPyFunctions

Setup SymPy functions

Use Radix Sort when possible

Get Omega^-1 and derivatives

rxSymInvCholCreate

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

rxSymPySetupPred

Setup Pred function based on RxODE object.

type_sum function for units

rxSymPySensitivity

Calculate the sensitivity equations for a model

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

Print expanded information about the RxODE object.

Setup SymPy variables

Summary of rxDll object

Clear/Set pipeline

Find power THETAs for appropriate scaling

Coerce object to data.frame

Return the RxODE coefficients

Sample a covariance Matrix from the Posterior Inverse Wishart distribution.