rodeo: A Code Generator for ODE-Based Models

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
https://github.com/dkneis/rodeo

View on CRAN

Functions

compile Man page
dynamics Man page
exportDF Man page
finalize Man page
forcingFunctions Man page
funs Man page
generate Man page
getPars Man page
getVars Man page
initialize Man page
initStepper Man page
libFunc Man page
libName Man page
new Man page
pars Man page
plotStoichiometry Man page
pros Man page
rodeo Man page
rodeo-class Man page
rodeo-package Man page
setPars Man page
setVars Man page
step Man page
stoi Man page
stoiCheck Man page
stoichiometry Man page
stoiCreate Man page
vars Man page

Files

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

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