summary.SBMLR: Get summary information from an SBMLR model

In mdnestor/SBMLR: SBML-R Interface and Analysis Tools

Description

This function extracts information from a model of class SBMLR and returns it as a list. The list includes species and reaction information tabularized as data frames.

Usage

## S3 method for class 'SBMLR'
summary(object,...)

Arguments

object	A model object of class SBMLR from which information is to be extracted.
...	For compatibility with summary of the base package.

Details

no details

Value

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.

Note

The list output can be attached to immediately define many model variables of interest.

Author(s)

Tom Radivoyevitch

Examples

library(SBMLR)  
curto=readSBMLR(file.path(system.file(package="SBMLR"), "models/curto.r"))  
summary(curto)

mdnestor/SBMLR documentation built on Aug. 28, 2020, 12:06 a.m.