SBMLDocument-class {rsbml} | R Documentation

## "SBMLDocument" from libsbml

### Description

Low-level libsbml document structure.

### Instantiation

A virtual Class: No objects may be created from it.

### Extends

Class `"oldClass"`, directly.

### Methods

rsbml\_check

  `signature(object = "SBMLDocument")`: `rsbml_check(object, strict = FALSE, consistency = TRUE)`: Check for problems with the document and signal R conditions if any errors are detected. If `strict` is `TRUE`, libsbml warnings will be emitted as R warnings (these are often too pedantic). If `consistency` is also `TRUE`, reports problems regarding internal model inconsistencies. This can be time consuming.

rsbml\_dom

  `signature(doc = "SBMLDocument")`: Constructs an S4 object model from a libsbml document.

rsbml\_graph

  `signature(doc = "SBMLDocument")`: Converts a libsbml document to a `graph`.

rsbml\_problems

  `signature(object = "SBMLDocument")`: reports problems encountered during parsing and/or validation.

rsbml\_write

  `signature(object = "SBMLDocument")`: writes this document to a file as SBML.

rsbml\_xml

  `signature(object = "SBMLDocument")`: converts this document to a string as SBML.

simulate

  `signature(object = "SBMLDocument")`: `simulate(object, nsim = 10, seed, ...)`: a shortcut for simulating the model in this document using the SBML ODE Solver library. Arguments in `...` should match slots of `SOSProtocol`. See `simulate` for more details.

### Author(s)

Michael Lawrence

### References

http://sbml.org/documents/

### Examples

      # Read a document into an R DOM
      dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package
    = "rsbml"))

      # Convert to a graph
      graph <- rsbml_graph(dom)

      # Write it out to a file
      ## Not run: rsbml_write(dom, "my.xml")

      # Or convert it to a string of XML
      rsbml_xml(dom)

      # Read into external libsbml data structure
      doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package
    = "rsbml"), dom = FALSE)

      # Convert it explicitly to an S4 DOM
      dom <- rsbml_dom(doc)

[Package rsbml version 2.44.0 Index]