summary.SBML {SBMLR} | R Documentation |
This function extracts information from a model of class SBML
and returns it as a list. The list includes
species and reaction information tabularized as data frames.
## S3 method for class 'SBML': summary(object,...)
object |
A model object of class SBML from which information is to be extracted. |
... |
For compatibility with summary of the base package. |
no details
A list containing the following elements
BC |
A logical vector indicating which species are not state variables, i.e. which species are boundary conditions or auxillary variables. |
y0 |
The initial state (boundary conditions excluded!). |
nStates |
The length of the state vector, i.e. the number of system states. |
S0 |
The full set of species initial values. |
nReactions |
The number of reactions. |
nSpecies |
The number of species, including states, boundary conditions and possibly auxillary variables such as the total concentration of dihydofolate reductase in the morrison.r model. |
incid |
The incidence/stoichiometry matrix. This usually contains ones and minus ones corresponding to fluxes either synthesizing or degrading (respectively) a state variable chemical species. This matrix multiplied by the flux vector on its right yields the corresponding concentration state variable time derivatives. |
species |
Species information (i.e. names, ICs, BCs, and compartments) as a data frame. |
reactions |
Reaction information tabularized as a dataframe, including string laws and initial fluxes. |
The list output can be attached to immediately define many model variables of interest.
Tomas Radivoyevitch (radivot@hal.cwru.edu)
library(SBMLR) curto=readSBMLR(file.path(system.file(package="SBMLR"), "models/curto.r")) summary(curto)