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RxODE (version 0.9.2-1)

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. 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

121

Version

0.9.2-1

License

GPL (>= 3)

Maintainer

Wenping Wang

Last Published

October 15th, 2020

Functions in RxODE (0.9.2-1)

Add sampling to eventTable

as.data.table.rxEt

Convert an event table to a data.table

Find power THETAs for appropriate scaling

Coerce object to data.frame

Create an ODE-based model specification

Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

Add dosing to eventTable

Return the RxODE coefficients

Clear/Set pipeline

Event Table Function

Remove Jacobian

Remove sensitivity equations

Repeat an RxODE event table

.rxSymPyJacobian

Calculate the full Jacobian for a model

Remove print statements

.rxWinRtoolsPath

Setup Rtools path

Turn on/off warnings for ID sorting.

Expand additional doses

Sequence of event tables

forderForceBase

Force using base order for RxODE radix sorting

Second command in chaining commands

rxChain Chain or add item to solved system of equations

Create an event table object

Re export of pillar_shaft

First Order Expansion of ETA

Combining event tables

Event translation for RxODE

Print the rxCoef object

Compile a model if needed

Cleanup anonymous DLLs by unloading them

pillar_shaft.rxRateDur

Pillar shaft for rxRateDur

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

Get RxODE model from object

Print information about the RxODE object.

Invert matrix using RcppArmadillo.

genShinyApp.template

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

Allow unloading of dlls

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

Objects exported from other packages

print.rxCoefSolve

Print the rxCoefSolve object

Find the assignments in R expression

Update Solved object with '+'

Initial Values and State values for a RxODE object

Permissive or Strict RxODE syntax options

Check to see if this is an rxEt object.

Current Condition for RxODE object

Print rxDll object

Options for RxODE

Optimize RxODE for computer evaluation

Format rxSolve and related objects as html.

Get the number of cores in a system

Split line into multiple lines at + or - breaks

Scaled Inverse Chi Squared distribution

Use Shiny to help develop an RxODE model

rxSimThetaOmega

Simulate Parameters from a Theta/Omega specification

Check to see if this is an rxSolve object.

Add a return statement to a function.

Stack a solved object for things like ggplot

Use cat when RxODE.verbose is TRUE

Prepare Pred function for inclusion in RxODE

Parse PK function for inclusion in RxODE

Return the DLL associated with the RxODE object

Return the md5 of an RxODE object or file

This function splits a function based on + or - terms

rxSymPyLincmtDvdx

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

rxPhysicalDrives

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

Left handed Variables

Determine if the DLL associated with the RxODE object is loaded

Load RxODE object

Lock/unlocking of RxODE dll file

Jacobian and parameter derivatives

RxODE progress bar functions

Creates a rxRateDur object

Assign pointer based on model variables

Delete the DLL for the model

Setup SymPy variables

rxSymPyReserved

Return a list of reserved functions and variables from sympy

Return the C file associated with the RxODE object

Fix SymPy expressions to be R parsable expressions

EVID formatting for tibble and other places.

State variables

rxSymPyFunctions

Setup SymPy functions

Creates a logical matrix for block matrixes.

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

Choose the type of sums to use for RxODE.

Checks if the RxODE object was built with the current build

Get the normalized model

Version and repository for this dparser package.

Parameters specified by the model

rxSetProgressBar

Set timing for progress bar

Setup SymPy environment if needed

Unload RxODE object

rxSymPySensitivity

Calculate the sensitivity equations for a model

Execute sympy statement.

Setup the initial conditions.

Get the rxModels information

Get model properties without compiling it.

Clear memoise cache for RxODE

Setup the initial conditions.

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

Use model object in your package

Check the type of an object using Rcpp

Prepare Error function for inclusion in RxODE

Require namespace, otherwise throw error.

Reload RxODE DLL

Return the dimension of the built-in derivatives/inverses

Recast model in terms of sum/prod

Add undefined variables to SymPy

Calculate df/dy derivatives

Sync options with RxODE variables

rxSymPySetupPred

Setup Pred function based on RxODE object.

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

Return the version of SymPy that is running

rxWinPythonSetup

Setup Python and SymPy for windows

Get Omega^-1 and derivatives

Get the RxODE temporary directory

type_sum function for units

Execute Python statement without getting the return value.

rxSymInvCholCreate

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

Use Radix Sort when possible

All model variables for a RxODE object

Setup Windows components for RxODE

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

Remove variables created by RxODE from the SymPy environment.

Return the expanded expression (via SymPy)

Converts model specification to/from a SymPy language

Free the C solving/parsing information.

Translate the model to C code if needed

Print expanded information about the RxODE object.

Unload all RxODE Dlls that are not locked for solving.

Summary of rxDll object

Does the variable exist in the SymPy Python environment?

Delete variable if exists.