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

Files in this package

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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