rodeo ObjectInitializes an object of the rodeo-class with data frames
holding the specification of an ODE system.
The method is called implicitly for its side effects when a
rodeo object is instantiated with new.
It has no accessible return value.
Declaration of state variables appearing in the ODE system. Data frame with mandatory columns 'name', 'unit', 'description'.
Declaration of parameters (i.e. constants) appearing in the ODE
system. Data frame with the same mandatory columns as vars.
Declaration of functions being referenced in the ODE
system. Data frame with the same mandatory columns as vars or
NULL if no function calls are present at the ODEs' right-hand sides.
Declaration of process rates. Data frame with mandatory columns 'name', 'unit', 'description', 'expression'.
Declaration of stoichiometric factors. A data frame with
mandatory columns 'variable', 'process', 'expression', if asMatrix
is FALSE. The 'expression' colum holds the stoichiometric factors.
If asMatrix is TRUE, this must be a matrix of type character
with row names (processes) and colum names (variables). Empty or NA
matrix elements are interpreted as zero stoichiometry factors.
Logical. Specifies whether stoichiometry information is given in matrix or data base format.
An integer vector, specifying the number of boxes in each spatial
dimension. Use c(1) to create a zero-dimensional
(i.e. single-box) model. This is the default.
Use, e.g. c(5) to create a 1-dimensional model with 5 boxes.
To create, e.g., a 2-dimensional model with 4 x 5 boxes, use c(4,5).
See the package vignette for examples.
data(vars, pars, funs, pros, stoi)
model <- rodeo$new(vars, pars, funs, pros, stoi, dim=c(1))
print(model)
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