SBMLDocument-class {rsbml} | R Documentation |
Low-level libsbml document structure.
A virtual Class: No objects may be created from it.
Class "oldClass"
, directly.
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.
signature(doc = "SBMLDocument")
: Constructs an S4
object model from a libsbml document.
signature(doc = "SBMLDocument")
: Converts a
libsbml document to a graph
.
signature(object = "SBMLDocument")
:
reports problems encountered during parsing and/or validation.
signature(object = "SBMLDocument")
: writes this
document to a file as SBML.
signature(object = "SBMLDocument")
: converts this
document to a string as SBML.
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.
Michael Lawrence
# 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)