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(): getModel Outputs an external pointer to the Model from SBML file

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(): getspeciesTable Outputs the Information Table for Species
getParameterTable(): getParameterTable Outputs the Information Table for Paremeters
getReactionTable(): getReactionTable Outputs the Information Table for Reactions
getSpeciesNames(): getSpeciesNames Names of the species in a model
getSpeciesIC(): getSpeciesIC Initial values of the species in a model
getNumSpecies(): getSpeciesNum Outputs the number of Species in the model
getCmtNames(): getCmtNames Names of the compartments in a model
getCmtSizes(): getCmtSizes Outputs the Sizes of Compartments

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

getRuleMath(): getRuleMath Outputs Model which can be simulated
getReactionMath(): getReactionMath Outputs Model which can be simulated
getFunctionDefinition(): getFunctionDefinition Outputs Model which can be simulated
getEventMath(): getEventMath Outputs Model which can be simulated

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

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