Model-class {rsbml} | R Documentation

## SBML type "Model"

### Description

The central SBML element. Contains the `Species`, `Reaction`s, `Compartment`s and other components of the model. See the SBML specification, at the reference, for further details.

### Instantiation

Objects can be created by calls of the form `new("Model", ...)`.

### Slots

`id`:

  Object of class `"character"` uniquely identifying this component.

`name`:

  Object of class `"character"` naming this component.

`functionDefinitions`:

  Object of class `"list"` containing `FunctionDefinition`s. The names of the list correspond to the IDs of the elements.

`unitDefinitions`:

  Object of class `"list"` containing `UnitDefinition`s. The names of the list correspond to the IDs of the elements.

`compartments`:

  Object of class `"list"` containing `Compartment`s. The names of the list correspond to the IDs of the elements.

`species`:

  Object of class `"list"` containing `Species`s. The names of the list correspond to the IDs of the elements.

`parameters`:

  Object of class `"list"` containing `Parameter`s. The names of the list correspond to the IDs of the elements.

`rules`:

  Object of class `"list"` containing `Rule`s.

`reactions`:

  Object of class `"list"` containing `Reaction`s. The names of the list correspond to the IDs of the elements.

`events`:

  Object of class `"list"` containing `Event`s. The names of the list correspond to the IDs of the elements.

`layouts`:

  Object of class `"list"` containing `Layout`s. The names of the list correspond to the IDs of the elements.

`speciesTypes`:

  Object of class `"list"` containing `SpeciesType`s. The names of the list correspond to the IDs of the elements.

`compartmentTypes`:

  Object of class `"list"` containing `CompartmentType`s. The names of the list correspond to the IDs of the elements.

`constraints`:

  Object of class `"list"` containing `Constraint`s. The names of the list correspond to the IDs of the elements.

`initialAssignments`:

  Object of class `"list"` containing `InitialAssignment`s.

`modelHistory`:

  Object of class `ModelHistory` recording the history of the model.

`metaId`:

  Object of class `"character"` that is an XML ID "described" by an RDF resource. This links an SBML element to an RDF resource. RDF may appear anywhere in an SBML element, but is usually placed inside the `annotation` element.

`notes`:

  Object of class `"character"` containing user-readable XHTML notes about an element.

`annotation`:

  Object of class `"character"` containing additional machine-readable information about an element, usually as RDF, such as BioPAX. This is where application-specific data belongs.

`cvTerms`:

  Object of class `"list"` containing instances of `CVTerm` associated with this element.

`sboTerm`:

  Object of class `"integer"` identifying a term in the Systems Biology Ontology (SBO).

### Extends

Class `"SBase"`, directly.

### Methods

id

  `signature(object = "Model")`: gets the `id` slot

id<-

  `signature(object = "Model")`: sets the `id` slot

name

  `signature(object = "Model")`: gets the `name` slot

name<-

  `signature(object = "Model")`: sets the `name` slot

compartments

  `signature(object = "Model")`: gets the `compartments` slot

compartments<-

  `signature(object = "Model")`: sets the `compartments` slot

events

  `signature(object = "Model")`: gets the `events` slot

events<-

  `signature(object = "Model")`: sets the `events` slot

functionDefinitions

  `signature(object = "Model")`: gets the `functionDefinitions` slot

functionDefinitions<-

  `signature(object = "Model")`: sets the `functionDefinitions` slot

layouts

  `signature(object = "Model")`: gets the `layouts` slot

layouts<-

  `signature(object = "Model")`: sets the `layouts` slot

parameters

  `signature(object = "Model")`: gets the `parameters` slot

parameters<-

  `signature(object = "Model")`: sets the `parameters` slot

species

  `signature(object = "Model")`: gets the `species` slot

species<-

  `signature(object = "Model")`: sets the `species` slot

reactions

  `signature(object = "Model")`: gets the `reactions` slot

reactions<-

  `signature(object = "Model")`: sets the `reactions` slot

rules

  `signature(object = "Model")`: gets the `rules` slot

rules<-

  `signature(object = "Model")`: sets the `rules` slot

unitDefinitions

  `signature(object = "Model")`: gets the `unitDefinitions` slot

unitDefinitions<-

  `signature(object = "Model")`: sets the `unitDefinitions` slot

compartmentTypes

  `signature(object = "Model")`: gets the `compartmentTypes` slot

compartmentTypes<-

  `signature(object = "Model")`: sets the `compartmentTypes` slot

constraints

  `signature(object = "Model")`: gets the `constraints` slot

constraints<-

  `signature(object = "Model")`: sets the `constraints` slot

initialAssignments

  `signature(object = "Model")`: gets the `initialAssignments` slot

initialAssignments<-

  `signature(object = "Model")`: sets the `initialAssignments` slot

speciesTypes

  `signature(object = "Model")`: gets the `speciesTypes` slot

speciesTypes<-

  `signature(object = "Model")`: sets the `speciesTypes`slot

modelHistory

  `signature(object = "Model")`: gets the `modelHistory` slot

modelHistory<-

  `signature(object = "Model")`: sets the `modelHistory` slot

stoichiometryMatrix

  `signature(object = "Model")`: calculates the stoichiometry matrix of the model

### Author(s)

Michael Lawrence

### References

http://sbml.org/documents/

[Package rsbml version 2.52.0 Index]