rodeo: A Code Generator for ODE-Based Models
Version 0.7.1

Provides an R6 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'.

AuthorDavid Kneis <david.kneis@tu-dresden.de>
Date of publication2017-01-06 11:34:12
MaintainerDavid Kneis <david.kneis@tu-dresden.de>
LicenseGPL (>= 2)
Version0.7.1
URL https://github.com/dkneis/rodeo
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rodeo")

Getting started

Package overview
README.md
R package rodeo: Basic Use and Sample Applications

Popular man pages

funs: Declaration of Functions
initialize: Initialize a 'rodeo' Object
libFunc: Return name of library function
setVars: Assign Values to State Variables
step: Numerical Integration Over a Single Time Step
stoi: Specification of Stoichiometry
stoichiometry: Return the Stoichiometry Matrix
See all...

All man pages Function index File listing

Man pages

compile: Generate Executable Code
dynamics: Numerical Integration
exportDF: Export a Data Frame as HTML/TEX Code
finalize: Clean-up a 'rodeo' Object
forcingFunctions: Generation of Forcing Functions in Fortran
funs: Declaration of Functions
generate: Code Generator
getPars: Query Values of Parameters
getVars: Query Values of State Variables
initialize: Initialize a 'rodeo' Object
initStepper: Initialize Internal ODE Solver
libFunc: Return name of library function
libName: Return library name
pars: Declaration of Parameters
plotStoichiometry: Plot Qualitative Stoichiometry Matrix
pros: Declaration of Processes
rodeo-class: 'rodeo' Class
rodeo-package: Package to Facilitate ODE-Based Modeling
setPars: Assign Values to Parameters
setVars: Assign Values to State Variables
step: Numerical Integration Over a Single Time Step
stoi: Specification of Stoichiometry
stoiCheck: Validation of a Stoichiometry Matrix
stoichiometry: Return the Stoichiometry Matrix
stoiCreate: Stoichiometry Matrix from Reaction Equations
vars: Declaration of Variables

Functions

checkTbl Source code
codeElem Source code
compile Man page
dynamics Man page
elNames Source code
exportDF Man page Source code
extractIdentifiers Source code
finalize Man page
forcingFunctions Man page Source code
fortran.breakLine Source code
fortran.doubleConst Source code
fortran.powerOperator Source code
funs Man page
generate Man page
getPars Man page
getVars Man page
initStepper Man page
initialize Man page
libFunc Man page
libName Man page
new Man page
parenthesized Source code
pars Man page
plotStoichiometry Man page
pros Man page
rodeo Man page
rodeo-class Man page
rodeo-package Man page
setOpt Source code
setPars Man page
setVars Man page
solverInterface Source code
splitComponents Source code
splitEquation Source code
splitFactor Source code
step Man page
stoi Man page
stoiBuildSingle Source code
stoiCheck Man page Source code
stoiCreate Man page Source code
stoichiometry Man page
substituteIdentifiers Source code
undeclared Source code
vars Man page
xapply Source code

Files

inst
inst/fortran
inst/fortran/forcingsInclude.f95
inst/fortran/integrators.f95
inst/fortran/forcingsGenericMethods.f95
inst/doc
inst/doc/examples
inst/doc/examples/0D
inst/doc/examples/0D/twoZonesStirredTank
inst/doc/examples/0D/twoZonesStirredTank/pars.txt
inst/doc/examples/0D/twoZonesStirredTank/fig
inst/doc/examples/0D/twoZonesStirredTank/fig/system.odg
inst/doc/examples/0D/twoZonesStirredTank/fig/system.png
inst/doc/examples/0D/twoZonesStirredTank/stoi.txt
inst/doc/examples/0D/twoZonesStirredTank/xecute.r
inst/doc/examples/0D/twoZonesStirredTank/pros.txt
inst/doc/examples/0D/twoZonesStirredTank/vars.txt
inst/doc/examples/0D/streeterPhelpsLike
inst/doc/examples/0D/streeterPhelpsLike/pars.txt
inst/doc/examples/0D/streeterPhelpsLike/fig
inst/doc/examples/0D/streeterPhelpsLike/fig/system.odp
inst/doc/examples/0D/streeterPhelpsLike/fig/system.png
inst/doc/examples/0D/streeterPhelpsLike/stoi.txt
inst/doc/examples/0D/streeterPhelpsLike/funs.txt
inst/doc/examples/0D/streeterPhelpsLike/xecute.r
inst/doc/examples/0D/streeterPhelpsLike/pros.txt
inst/doc/examples/0D/streeterPhelpsLike/vars.txt
inst/doc/examples/1D
inst/doc/examples/1D/groundwater
inst/doc/examples/1D/groundwater/pars.txt
inst/doc/examples/1D/groundwater/fig
inst/doc/examples/1D/groundwater/fig/watershed.png
inst/doc/examples/1D/groundwater/fig/watershed.odg
inst/doc/examples/1D/groundwater/functions.f95
inst/doc/examples/1D/groundwater/stoi.txt
inst/doc/examples/1D/groundwater/funs.txt
inst/doc/examples/1D/groundwater/xecute.r
inst/doc/examples/1D/groundwater/pros.txt
inst/doc/examples/1D/groundwater/vars.txt
inst/doc/examples/1D/advectionDispersion
inst/doc/examples/1D/advectionDispersion/pars.txt
inst/doc/examples/1D/advectionDispersion/fig
inst/doc/examples/1D/advectionDispersion/fig/reach.png
inst/doc/examples/1D/advectionDispersion/fig/reach.odg
inst/doc/examples/1D/advectionDispersion/functions.f95
inst/doc/examples/1D/advectionDispersion/stoi.txt
inst/doc/examples/1D/advectionDispersion/funs.txt
inst/doc/examples/1D/advectionDispersion/xecute.r
inst/doc/examples/1D/advectionDispersion/pros.txt
inst/doc/examples/1D/advectionDispersion/vars.txt
inst/doc/examples/1D/diffusion
inst/doc/examples/1D/diffusion/pars.txt
inst/doc/examples/1D/diffusion/fig
inst/doc/examples/1D/diffusion/fig/diffusion.png
inst/doc/examples/1D/diffusion/fig/diffusion.odg
inst/doc/examples/1D/diffusion/stoi.txt
inst/doc/examples/1D/diffusion/xecute.r
inst/doc/examples/1D/diffusion/pros.txt
inst/doc/examples/1D/diffusion/vars.txt
inst/doc/examples/1D/tetracycline
inst/doc/examples/1D/tetracycline/pars.txt
inst/doc/examples/1D/tetracycline/fig
inst/doc/examples/1D/tetracycline/fig/tanksInSeries.png
inst/doc/examples/1D/tetracycline/fig/tanksInSeries.odg
inst/doc/examples/1D/tetracycline/functions.f95
inst/doc/examples/1D/tetracycline/stoi.txt
inst/doc/examples/1D/tetracycline/funs.txt
inst/doc/examples/1D/tetracycline/xecute.r
inst/doc/examples/1D/tetracycline/pros.txt
inst/doc/examples/1D/tetracycline/vars.txt
inst/doc/examples/linked
inst/doc/examples/linked/waterSediment
inst/doc/examples/linked/waterSediment/fig
inst/doc/examples/linked/waterSediment/fig/system.odp
inst/doc/examples/linked/waterSediment/fig/system.png
inst/doc/examples/linked/waterSediment/functions.f95
inst/doc/examples/linked/waterSediment/multiObject
inst/doc/examples/linked/waterSediment/multiObject/sed_pars.txt
inst/doc/examples/linked/waterSediment/multiObject/sed_funs.txt
inst/doc/examples/linked/waterSediment/multiObject/wat_pros.txt
inst/doc/examples/linked/waterSediment/multiObject/sed_stoi.txt
inst/doc/examples/linked/waterSediment/multiObject/wat_stoi.txt
inst/doc/examples/linked/waterSediment/multiObject/wat_vars.txt
inst/doc/examples/linked/waterSediment/multiObject/sed_pros.txt
inst/doc/examples/linked/waterSediment/multiObject/sed_vars.txt
inst/doc/examples/linked/waterSediment/multiObject/wat_funs.txt
inst/doc/examples/linked/waterSediment/multiObject/wat_pars.txt
inst/doc/examples/linked/waterSediment/xecute_multiObject.r
inst/doc/examples/linked/waterSediment/singleObject
inst/doc/examples/linked/waterSediment/singleObject/pars.txt
inst/doc/examples/linked/waterSediment/singleObject/stoi.txt
inst/doc/examples/linked/waterSediment/singleObject/funs.txt
inst/doc/examples/linked/waterSediment/singleObject/pros.txt
inst/doc/examples/linked/waterSediment/singleObject/vars.txt
inst/doc/examples/linked/waterSediment/xecute_singleObject.r
inst/doc/vignetteData
inst/doc/vignetteData/fortran
inst/doc/vignetteData/fortran/functionsCode.f95
inst/doc/vignetteData/fortran/fortranForcingsTest.f95
inst/doc/vignetteData/fig
inst/doc/vignetteData/fig/reactor.odg
inst/doc/vignetteData/fig/reactor.png
inst/doc/vignetteData/fig/overview.png
inst/doc/vignetteData/fig/overview.odg
inst/doc/rodeoVignette.Rmd
inst/doc/rodeoVignette.pdf
inst/doc/rodeoVignette.R
NAMESPACE
data
data/pros.r
data/pars.r
data/stoi.r
data/vars.r
data/funs.r
R
R/classMethod_step.r
R/classMethods_setValues.r
R/classMethod_initStepper.r
R/internal_functions.r
R/classMethod_getDim.r
R/classMethod_stoichiometry.r
R/classMethods_getValues.r
R/classMethod_initialize.r
R/plainMethods_stoiBuild_stoiCheck.r
R/classMethod_dynamics.r
R/classMethod_plotStoichiometry.r
R/plainMethod_forcingFunctions.r
R/classMethod_compile.r
R/classMethods_getTables.r
R/internal_constants.r
R/classMethods_lib.r
R/classMethod_generate.r
R/0_package.r
R/class.r
R/data.r
R/plainMethod_exportDF.r
R/classMethod_finalize.r
vignettes
vignettes/examples
vignettes/examples/0D
vignettes/examples/0D/twoZonesStirredTank
vignettes/examples/0D/twoZonesStirredTank/pars.txt
vignettes/examples/0D/twoZonesStirredTank/fig
vignettes/examples/0D/twoZonesStirredTank/fig/system.odg
vignettes/examples/0D/twoZonesStirredTank/fig/system.png
vignettes/examples/0D/twoZonesStirredTank/stoi.txt
vignettes/examples/0D/twoZonesStirredTank/xecute.r
vignettes/examples/0D/twoZonesStirredTank/pros.txt
vignettes/examples/0D/twoZonesStirredTank/vars.txt
vignettes/examples/0D/streeterPhelpsLike
vignettes/examples/0D/streeterPhelpsLike/pars.txt
vignettes/examples/0D/streeterPhelpsLike/fig
vignettes/examples/0D/streeterPhelpsLike/fig/system.odp
vignettes/examples/0D/streeterPhelpsLike/fig/system.png
vignettes/examples/0D/streeterPhelpsLike/stoi.txt
vignettes/examples/0D/streeterPhelpsLike/funs.txt
vignettes/examples/0D/streeterPhelpsLike/xecute.r
vignettes/examples/0D/streeterPhelpsLike/pros.txt
vignettes/examples/0D/streeterPhelpsLike/vars.txt
vignettes/examples/1D
vignettes/examples/1D/groundwater
vignettes/examples/1D/groundwater/pars.txt
vignettes/examples/1D/groundwater/fig
vignettes/examples/1D/groundwater/fig/watershed.png
vignettes/examples/1D/groundwater/fig/watershed.odg
vignettes/examples/1D/groundwater/functions.f95
vignettes/examples/1D/groundwater/stoi.txt
vignettes/examples/1D/groundwater/funs.txt
vignettes/examples/1D/groundwater/xecute.r
vignettes/examples/1D/groundwater/pros.txt
vignettes/examples/1D/groundwater/vars.txt
vignettes/examples/1D/advectionDispersion
vignettes/examples/1D/advectionDispersion/pars.txt
vignettes/examples/1D/advectionDispersion/fig
vignettes/examples/1D/advectionDispersion/fig/reach.png
vignettes/examples/1D/advectionDispersion/fig/reach.odg
vignettes/examples/1D/advectionDispersion/functions.f95
vignettes/examples/1D/advectionDispersion/stoi.txt
vignettes/examples/1D/advectionDispersion/funs.txt
vignettes/examples/1D/advectionDispersion/xecute.r
vignettes/examples/1D/advectionDispersion/pros.txt
vignettes/examples/1D/advectionDispersion/vars.txt
vignettes/examples/1D/diffusion
vignettes/examples/1D/diffusion/pars.txt
vignettes/examples/1D/diffusion/fig
vignettes/examples/1D/diffusion/fig/diffusion.png
vignettes/examples/1D/diffusion/fig/diffusion.odg
vignettes/examples/1D/diffusion/stoi.txt
vignettes/examples/1D/diffusion/xecute.r
vignettes/examples/1D/diffusion/pros.txt
vignettes/examples/1D/diffusion/vars.txt
vignettes/examples/1D/tetracycline
vignettes/examples/1D/tetracycline/pars.txt
vignettes/examples/1D/tetracycline/fig
vignettes/examples/1D/tetracycline/fig/tanksInSeries.png
vignettes/examples/1D/tetracycline/fig/tanksInSeries.odg
vignettes/examples/1D/tetracycline/functions.f95
vignettes/examples/1D/tetracycline/stoi.txt
vignettes/examples/1D/tetracycline/funs.txt
vignettes/examples/1D/tetracycline/xecute.r
vignettes/examples/1D/tetracycline/pros.txt
vignettes/examples/1D/tetracycline/vars.txt
vignettes/examples/linked
vignettes/examples/linked/waterSediment
vignettes/examples/linked/waterSediment/fig
vignettes/examples/linked/waterSediment/fig/system.odp
vignettes/examples/linked/waterSediment/fig/system.png
vignettes/examples/linked/waterSediment/functions.f95
vignettes/examples/linked/waterSediment/multiObject
vignettes/examples/linked/waterSediment/multiObject/sed_pars.txt
vignettes/examples/linked/waterSediment/multiObject/sed_funs.txt
vignettes/examples/linked/waterSediment/multiObject/wat_pros.txt
vignettes/examples/linked/waterSediment/multiObject/sed_stoi.txt
vignettes/examples/linked/waterSediment/multiObject/wat_stoi.txt
vignettes/examples/linked/waterSediment/multiObject/wat_vars.txt
vignettes/examples/linked/waterSediment/multiObject/sed_pros.txt
vignettes/examples/linked/waterSediment/multiObject/sed_vars.txt
vignettes/examples/linked/waterSediment/multiObject/wat_funs.txt
vignettes/examples/linked/waterSediment/multiObject/wat_pars.txt
vignettes/examples/linked/waterSediment/xecute_multiObject.r
vignettes/examples/linked/waterSediment/singleObject
vignettes/examples/linked/waterSediment/singleObject/pars.txt
vignettes/examples/linked/waterSediment/singleObject/stoi.txt
vignettes/examples/linked/waterSediment/singleObject/funs.txt
vignettes/examples/linked/waterSediment/singleObject/pros.txt
vignettes/examples/linked/waterSediment/singleObject/vars.txt
vignettes/examples/linked/waterSediment/xecute_singleObject.r
vignettes/.install_extras
vignettes/vignetteData
vignettes/vignetteData/fortran
vignettes/vignetteData/fortran/functionsCode.f95
vignettes/vignetteData/fortran/fortranForcingsTest.f95
vignettes/vignetteData/fig
vignettes/vignetteData/fig/reactor.odg
vignettes/vignetteData/fig/reactor.png
vignettes/vignetteData/fig/overview.png
vignettes/vignetteData/fig/overview.odg
vignettes/references.bib
vignettes/preamble-latex.tex
vignettes/rodeoVignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/rodeo-package.Rd
man/forcingFunctions.Rd
man/getVars.Rd
man/plotStoichiometry.Rd
man/rodeo-class.Rd
man/pros.Rd
man/getPars.Rd
man/setVars.Rd
man/vars.Rd
man/stoichiometry.Rd
man/step.Rd
man/compile.Rd
man/stoiCreate.Rd
man/dynamics.Rd
man/funs.Rd
man/stoiCheck.Rd
man/stoi.Rd
man/libName.Rd
man/setPars.Rd
man/libFunc.Rd
man/generate.Rd
man/finalize.Rd
man/initStepper.Rd
man/exportDF.Rd
man/initialize.Rd
man/pars.Rd
.Rinstignore
rodeo documentation built on May 19, 2017, 7:59 a.m.

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