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.
`unitDefinitions`:
  Object of class `"list"` containing `UnitDefinition`s.
`compartments`:
  Object of class `"list"` containing `Compartment`s.
`species`:
  Object of class `"list"` containing `Species`s.
`parameters`:
  Object of class `"list"` containing `Parameter`s.
`rules`:
  Object of class `"list"` containing `Rule`s.
`reactions`:
  Object of class `"list"` containing `Reaction`s.
`events`:
  Object of class `"list"` containing `Event`s.
`layouts`:
  Object of class `"list"` containing `Layout`s.
`speciesTypes`:
  Object of class `"list"` containing `SpeciesType`s.
`compartmentTypes`:
  Object of class `"list"` containing `CompartmentType`s.
`constraints`:
  Object of class `"list"` containing `Constraint`s.
`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

### Author(s)

Michael Lawrence

### References

http://sbml.org/documents/

[Package rsbml version 2.2.1 Index]