rodeo: A Code Generator for ODE-Based Models

Share:

Provides a reference class and several utility methods to facilitate the implementation of models based on ordinary differential equations. The heart of the package is a code generator that creates compiled 'Fortran' (or 'R') code which can be passed to a numerical solver. There is direct support for solvers contained in packages 'deSolve' and 'rootSolve'.

Author
David Kneis <david.kneis@tu-dresden.de>
Date of publication
2016-04-24 16:37:40
Maintainer
David Kneis <david.kneis@tu-dresden.de>
License
GPL (>= 2)
Version
0.3

View on CRAN

Man pages

arrangePars
Assign Values to Parameters
arrangeVars
Assign Values to State Variables
compile
Create Fortran Library
exampleIdentifiers
Declaration of Identifiers
exampleProcesses
Declaration of Processes
exampleStoichiometry
Specification of Stoichiometry
exportDF
Export a Data Frame as HTML/TEX Code
forcingFunctions
Generation of Forcing Functions in Fortran
generate
Code Generator
initialize
Initialize a 'rodeo' Object
plotStoichiometry
Plot Qualitative Stoichiometry Matrix
rodeo-class
'rodeo' Reference Class
rodeo-package
Package to Facilitate ODE-Based Modeling
solverInterface
Wrapping of Generated Fortran for Use with Solver Packages
stoichiometry
Return the Stoichiometry Matrix

Files in this package

rodeo
rodeo/inst
rodeo/inst/fortran
rodeo/inst/fortran/forcingsInclude.f95
rodeo/inst/fortran/forcingsGenericMethods.f95
rodeo/inst/examples
rodeo/inst/examples/create_documentation.rnw
rodeo/inst/doc
rodeo/inst/doc/rodeo.pdf
rodeo/inst/doc/rodeo.rnw
rodeo/inst/doc/rodeo.R
rodeo/NAMESPACE
rodeo/data
rodeo/data/exampleProcesses.txt.gz
rodeo/data/exampleIdentifiers.txt.gz
rodeo/data/exampleStoichiometry.txt.gz
rodeo/R
rodeo/R/libraries.r
rodeo/R/classMethods_get.r
rodeo/R/internal_functions.r
rodeo/R/plainMethod_solverInterface.r
rodeo/R/classMethod_stoichiometry.r
rodeo/R/classMethod_initialize.r
rodeo/R/classMethod_plotStoichiometry.r
rodeo/R/plainMethod_forcingFunctions.r
rodeo/R/classMethod_compile.r
rodeo/R/internal_constants.r
rodeo/R/classMethods_arrange.r
rodeo/R/classMethod_generate.r
rodeo/R/0_package.r
rodeo/R/class.r
rodeo/R/data.r
rodeo/R/plainMethod_exportDF.r
rodeo/vignettes
rodeo/vignettes/reactor.odg
rodeo/vignettes/functionsCode.f95
rodeo/vignettes/rodeo.rnw
rodeo/vignettes/reactor.eps
rodeo/vignettes/reactor.pdf
rodeo/vignettes/fortranForcingsTest.f95
rodeo/README.md
rodeo/MD5
rodeo/build
rodeo/build/vignette.rds
rodeo/DESCRIPTION
rodeo/man
rodeo/man/rodeo-package.Rd
rodeo/man/arrangeVars.Rd
rodeo/man/forcingFunctions.Rd
rodeo/man/plotStoichiometry.Rd
rodeo/man/exampleProcesses.Rd
rodeo/man/rodeo-class.Rd
rodeo/man/arrangePars.Rd
rodeo/man/stoichiometry.Rd
rodeo/man/compile.Rd
rodeo/man/solverInterface.Rd
rodeo/man/generate.Rd
rodeo/man/exampleIdentifiers.Rd
rodeo/man/exportDF.Rd
rodeo/man/initialize.Rd
rodeo/man/exampleStoichiometry.Rd