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'.

Install the latest version of this package by entering the following in R:
install.packages("rodeo")
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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