rodeo-class | R Documentation |
rodeo
ClassThis documents the rodeo
class to represent an ODE-based
model. See the rodeo-package
main page or type
help(package="rodeo")
for an introduction to the package of
the same name.
prosTbl
A data frame with fields 'name', 'unit', 'description', and 'expression' defining the process rates.
stoiTbl
A data frame with fields 'variable', 'process', and 'expression' reprenting the stoichiometry matrix in data base format.
varsTbl
A data frame with fields 'name', 'unit', 'description' declaring
the state variables of the model. The declared names become valid
identifiers to be used in the expression fields of prosTbl
or stoiTbl
.
parsTbl
A data frame of the same structure as vars
declaring the
parameters of the model. The declared names become valid
identifiers to be used in the expression fields of prosTbl
or stoiTbl
.
funsTbl
A data frame of the same structure as vars
declaring any
functions referenced in the expression fields of prosTbl
or stoiTbl
.
dim
Integer vector specifying the spatial dimensions.
vars
Numeric vector, holding values of state variables.
pars
Numeric vector, holding values of parameters.
For most of the methods below, a separate help page is available describing its arguments and usage.
initialize
Initialization method for new objects.
namesVars, namesPars, namesFuns, namesPros
Functions
returning the names of declared state variables, parameters,
functions, and processes, respectively (character vectors). No arguments.
lenVars, lenPars, lenFuns, lenPros
Functions
returning the number of declared state variables, parameters, functions
and processes, respectively (integer). No arguments.
getVarsTable, getParsTable, getFunsTable, getProsTable,
getStoiTable
Functions returning the data frames used to initialize
the object. No arguments
getDim
Returns the spatial dimensions as an integer vector.
No arguments.
compile
Compiles a Fortran library for use with
numerical methods from packages deSolve
or
rootSolve
.
generate
Translate the ODE-model specification into a
function that computes process rates and the state variables' derivatives
(either in R or Fortran). Consider to use the high-level method
compile
.
setVars
Assign values to state variables.
setPars
Assign values to parameters.
getVars
Returns the values of state variables.
getPars
Returns the values of parameters.
stoichiometry
Returns the stoichiometry matrix, either
evaluated (numeric) or as text.
plotStoichiometry
Plots qualitative stoichiometry
information.
See the rodeo-package
main page or type
help(package="rodeo")
to find the documentation of any non-class
methods contained in the rodeo
package.
# Bacteria growth in a continuous flow culture
library("deSolve")
# Creation of model object
data(vars, pars, funs, pros, stoi)
model <- rodeo$new(vars, pars, funs, pros, stoi, dim=c(1))
# Parameters, initial values
model$setPars(c(mu=0.8, half=0.1, yield= 0.1, vol=1000, flow=50, sub_in=1))
model$setVars(c(bac=0.01, sub=0))
# Implementation of functions declared in 'funs'
monod <- function(c,h) {c/(c+h)}
# Creation of derivatives function
code <- model$generate(name="derivs", lang="r")
derivs <- eval(parse(text=code))
# Integration
times <- 0:96
out <- deSolve::ode(y=model$getVars(), times=times, func=derivs,
parms=model$getPars())
colnames(out) <- c("time", model$namesVars(), model$namesPros())
plot(out)
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