Package index • r2sbml

Reading a model

Everything except convertReactions() works in two phases: read the file once, then query the pointer that comes back.

getModel(): Read an SBML model

Querying components

These return R objects. Note that a query for a component the model does not have raises an error rather than returning an empty result.

getSpeciesTable(): Table of the species in a model
getParameterTable(): Table of the parameters in a model
getReactionTable(): Table of the reactions in a model
getSpeciesNames(): Names of the species in a model
getSpeciesIC(): Initial values of the species in a model
getNumSpecies(): Number of species in a model
getCmtNames(): Names of the compartments in a model
getCmtSizes(): Sizes of the compartments in a model

Printing the mathematics

These write to the console and return 0 invisibly, so capture them with capture.output() rather than assigning them.

getRuleMath(): Print the rules of a model
getReactionMath(): Print the rate laws of a model
getFunctionDefinition(): Print the function definitions of a model
getEventMath(): Print the events of a model

Printing the document

The exception to the two-phase rule: these take a filename, not a model pointer.

printSBML(): Summarise an SBML file
echoSBML(): Check an SBML file for errors

Exporting mass balances

Writes ready-to-simulate code for one of six ODE targets. Reads the SBML file itself, so it takes no model pointer.

convertReactions(): Convert an SBML model to simulation code