# R support for SBML, using libsbml

## Documentation for package ‘rsbml’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G H I K L M N O P R S T U V W X Y Z

## -- A --

additionalGraphicalObjects | SBML type "Layout"
additionalGraphicalObjects,Layout-method | SBML type "Layout"
additionalGraphicalObjects<-,Layout-method | SBML type "Layout"
AlgebraicRule-class | SBML type "AlgebraicRule"
annotation | SBML type "SBase"
annotation,SBase-method | SBML type "SBase"
annotation<-,SBase-method | SBML type "SBase"
as.character.SBML | SBML type "SBML"
as.character.SBMLDocument | "SBMLDocument" from libsbml
AssignmentRule-class | SBML type "AssignmentRule"

## -- B --

basePoint1 | SBML type "CubicBezier"
basePoint1,CubicBezier-method | SBML type "CubicBezier"
basePoint1<-,CubicBezier-method | SBML type "CubicBezier"
basePoint2 | SBML type "CubicBezier"
basePoint2,CubicBezier-method | SBML type "CubicBezier"
basePoint2<-,CubicBezier-method | SBML type "CubicBezier"
boundaryCondition | SBML type "Species"
boundaryCondition,Species-method | SBML type "Species"
boundaryCondition<-,Species-method | SBML type "Species"
boundingBox | SBML type "GraphicalObject"
boundingBox,GraphicalObject-method | SBML type "GraphicalObject"
BoundingBox-class | SBML type "BoundingBox"
boundingBox<-,GraphicalObject-method | SBML type "GraphicalObject"

## -- C --

charge | SBML type "Species"
charge,Species-method | SBML type "Species"
charge<-,Species-method | SBML type "Species"
coerce | SBML type "SBML"
coerce,SBML,SBMLDocument-method | SBML type "SBML"
coerce,SBMLDocument,graph-method | "SBMLDocument" from libsbml
coerce,SBMLDocument,SBML-method | "SBMLDocument" from libsbml
compartment | SBML type "Species"
compartment,CompartmentGlyph-method | SBML type "CompartmentGlyph"
compartment,CompartmentVolumeRule-method | SBML type "CompartmentVolumeRule"
compartment,Species-method | SBML type "Species"
Compartment-class | SBML type "Compartment"
compartment<-,CompartmentGlyph-method | SBML type "CompartmentGlyph"
compartment<-,CompartmentVolumeRule-method | SBML type "CompartmentVolumeRule"
compartment<-,Species-method | SBML type "Species"
CompartmentGlyph-class | SBML type "CompartmentGlyph"
compartmentGlyphs | SBML type "Layout"
compartmentGlyphs,Layout-method | SBML type "Layout"
compartmentGlyphs<-,Layout-method | SBML type "Layout"
compartments | SBML type "Model"
compartments,Model-method | SBML type "Model"
compartments<-,Model-method | SBML type "Model"
CompartmentType-class | SBML Type "CompartmentType"
compartmentTypes | SBML type "Model"
compartmentTypes,Model-method | SBML type "Model"
compartmentTypes<-,Model-method | SBML type "Model"
CompartmentVolumeRule-class | SBML type "CompartmentVolumeRule"
constant | SBML type "Species"
constant,Compartment-method | SBML type "Compartment"
constant,Parameter-method | SBML type "Parameter"
constant,Species-method | SBML type "Species"
constant<-,Compartment-method | SBML type "Compartment"
constant<-,Parameter-method | SBML type "Parameter"
constant<-,Species-method | SBML type "Species"
Constraint-class | SBML Type "Constraint"
constraints | SBML type "Model"
constraints,Model-method | SBML type "Model"
constraints<-,Model-method | SBML type "Model"
CubicBezier-class | SBML type "CubicBezier"
curve | SBML type "ReactionGlyph"
curve,ReactionGlyph-method | SBML type "ReactionGlyph"
curve,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
Curve-class | SBML type "Curve"
curve<-,ReactionGlyph-method | SBML type "ReactionGlyph"
curve<-,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
curveSegments | SBML type "Curve"
curveSegments,Curve-method | SBML type "Curve"
curveSegments<-,Curve-method | SBML type "Curve"

## -- D --

delay | SBML type "Event"
delay,Event-method | SBML type "Event"
Delay-class | SBML Type "Delay"
delay<-,Event-method | SBML type "Event"
depth | SBML type "Dimensions"
depth,Dimensions-method | SBML type "Dimensions"
depth<-,Dimensions-method | SBML type "Dimensions"
dimensions | SBML type "Layout"
dimensions,BoundingBox-method | SBML type "BoundingBox"
dimensions,Layout-method | SBML type "Layout"
Dimensions-class | SBML type "Dimensions"
dimensions<-,BoundingBox-method | SBML type "BoundingBox"
dimensions<-,Layout-method | SBML type "Layout"

## -- E --

end | SBML type "LineSegment"
end,LineSegment-method | SBML type "LineSegment"
end<-,LineSegment-method | SBML type "LineSegment"
Event-class | SBML type "Event"
EventAssignment-class | SBML type "EventAssignment"
eventAssignments | SBML type "Event"
eventAssignments,Event-method | SBML type "Event"
eventAssignments<-,Event-method | SBML type "Event"
events | SBML type "Model"
events,Model-method | SBML type "Model"
events<-,Model-method | SBML type "Model"
exponent | SBML type "Unit"
exponent,Unit-method | SBML type "Unit"
exponent<-,Unit-method | SBML type "Unit"

## -- F --

fast | SBML type "Reaction"
fast,Reaction-method | SBML type "Reaction"
fast<-,Reaction-method | SBML type "Reaction"
FunctionDefinition-class | SBML type "FunctionDefinition"
functionDefinitions | SBML type "Model"
functionDefinitions,Model-method | SBML type "Model"
functionDefinitions<-,Model-method | SBML type "Model"

## -- G --

graphicalObject | SBML type "TextGlyph"
graphicalObject,TextGlyph-method | SBML type "TextGlyph"
GraphicalObject-class | SBML type "GraphicalObject"
graphicalObject<-,TextGlyph-method | SBML type "TextGlyph"

## -- H --

hasOnlySubstanceUnits | SBML type "Species"
hasOnlySubstanceUnits,Species-method | SBML type "Species"
hasOnlySubstanceUnits<-,Species-method | SBML type "Species"
height | SBML type "Dimensions"
height,Dimensions-method | SBML type "Dimensions"
height<-,Dimensions-method | SBML type "Dimensions"

## -- I --

id | SBML type "UnitDefinition"
id,BoundingBox-method | SBML type "BoundingBox"
id,Compartment-method | SBML type "Compartment"
id,CompartmentType-method | SBML Type "CompartmentType"
id,Event-method | SBML type "Event"
id,FunctionDefinition-method | SBML type "FunctionDefinition"
id,GraphicalObject-method | SBML type "GraphicalObject"
id,Layout-method | SBML type "Layout"
id,Model-method | SBML type "Model"
id,Parameter-method | SBML type "Parameter"
id,Reaction-method | SBML type "Reaction"
id,SimpleSpeciesReference-method | SBML type "SimpleSpeciesReference"
id,Species-method | SBML type "Species"
id,SpeciesType-method | SBML Type "SpeciesType"
id,UnitDefinition-method | SBML type "UnitDefinition"
id<-,BoundingBox-method | SBML type "BoundingBox"
id<-,Compartment-method | SBML type "Compartment"
id<-,CompartmentType-method | SBML Type "CompartmentType"
id<-,Event-method | SBML type "Event"
id<-,FunctionDefinition-method | SBML type "FunctionDefinition"
id<-,GraphicalObject-method | SBML type "GraphicalObject"
id<-,Layout-method | SBML type "Layout"
id<-,Model-method | SBML type "Model"
id<-,Parameter-method | SBML type "Parameter"
id<-,Reaction-method | SBML type "Reaction"
id<-,SimpleSpeciesReference-method | SBML type "SimpleSpeciesReference"
id<-,Species-method | SBML type "Species"
id<-,SpeciesType-method | SBML Type "SpeciesType"
id<-,UnitDefinition-method | SBML type "UnitDefinition"
initialAmount | SBML type "Species"
initialAmount,Species-method | SBML type "Species"
initialAmount<-,Species-method | SBML type "Species"
InitialAssignment-class | SBML Type "InitialAssignment"
initialAssignments | SBML type "Model"
initialAssignments,Model-method | SBML type "Model"
initialAssignments<-,Model-method | SBML type "Model"
initialConcentration | SBML type "Species"
initialConcentration,Species-method | SBML type "Species"
initialConcentration<-,Species-method | SBML type "Species"

## -- K --

kind | SBML type "Unit"
kind,Unit-method | SBML type "Unit"
kind<-,Unit-method | SBML type "Unit"
kineticLaw | SBML type "Reaction"
kineticLaw,Reaction-method | SBML type "Reaction"
KineticLaw-class | SBML type "KineticLaw"
kineticLaw<-,Reaction-method | SBML type "Reaction"

## -- L --

Layout-class | SBML type "Layout"
layouts | SBML type "Model"
layouts,Model-method | SBML type "Model"
layouts<-,Model-method | SBML type "Model"
level | SBML type "SBML"
level,SBML-method | SBML type "SBML"
level<-,SBML-method | SBML type "SBML"
LineSegment-class | SBML type "LineSegment"

## -- M --

math | SBML type "KineticLaw"
math,Constraint-method | SBML Type "Constraint"
math,Delay-method | SBML Type "Delay"
math,EventAssignment-method | SBML type "EventAssignment"
math,FunctionDefinition-method | SBML type "FunctionDefinition"
math,InitialAssignment-method | SBML Type "InitialAssignment"
math,KineticLaw-method | SBML type "KineticLaw"
math,ParameterRule-method | SBML type "ParameterRule"
math,Rule-method | SBML type "Rule"
math,StoichiometryMath-method | SBML type "StoichiometryMath"
math,Trigger-method | SBML Type "Trigger"
math<-,Constraint-method | SBML Type "Constraint"
math<-,Delay-method | SBML Type "Delay"
math<-,EventAssignment-method | SBML type "EventAssignment"
math<-,FunctionDefinition-method | SBML type "FunctionDefinition"
math<-,InitialAssignment-method | SBML Type "InitialAssignment"
math<-,KineticLaw-method | SBML type "KineticLaw"
math<-,ParameterRule-method | SBML type "ParameterRule"
math<-,Rule-method | SBML type "Rule"
math<-,StoichiometryMath-method | SBML type "StoichiometryMath"
math<-,Trigger-method | SBML Type "Trigger"
message,Constraint-method | SBML Type "Constraint"
message<-,Constraint-method | SBML Type "Constraint"
metaId | SBML type "SBase"
metaId,SBase-method | SBML type "SBase"
metaId<-,SBase-method | SBML type "SBase"
model | SBML type "SBML"
model,SBML-method | SBML type "SBML"
Model-class | SBML type "Model"
model<-,SBML-method | SBML type "SBML"
modifiers | SBML type "Reaction"
modifiers,Reaction-method | SBML type "Reaction"
modifiers<-,Reaction-method | SBML type "Reaction"
ModifierSpeciesReference-class | SBML type "ModifierSpeciesReference"
multiplier | SBML type "Unit"
multiplier,Unit-method | SBML type "Unit"
multiplier<-,Unit-method | SBML type "Unit"

## -- N --

name | SBML type "UnitDefinition"
name,Compartment-method | SBML type "Compartment"
name,CompartmentType-method | SBML Type "CompartmentType"
name,Event-method | SBML type "Event"
name,FunctionDefinition-method | SBML type "FunctionDefinition"
name,Model-method | SBML type "Model"
name,Parameter-method | SBML type "Parameter"
name,ParameterRule-method | SBML type "ParameterRule"
name,Reaction-method | SBML type "Reaction"
name,Species-method | SBML type "Species"
name,SpeciesType-method | SBML Type "SpeciesType"
name,UnitDefinition-method | SBML type "UnitDefinition"
name<-,Compartment-method | SBML type "Compartment"
name<-,CompartmentType-method | SBML Type "CompartmentType"
name<-,Event-method | SBML type "Event"
name<-,FunctionDefinition-method | SBML type "FunctionDefinition"
name<-,Model-method | SBML type "Model"
name<-,Parameter-method | SBML type "Parameter"
name<-,ParameterRule-method | SBML type "ParameterRule"
name<-,Reaction-method | SBML type "Reaction"
name<-,Species-method | SBML type "Species"
name<-,SpeciesType-method | SBML Type "SpeciesType"
name<-,UnitDefinition-method | SBML type "UnitDefinition"
notes | SBML type "SBase"
notes,SBase-method | SBML type "SBase"
notes<-,SBase-method | SBML type "SBase"

## -- O --

offset | SBML type "Unit"
offset,Unit-method | SBML type "Unit"
offset<-,Unit-method | SBML type "Unit"
originOfText | SBML type "TextGlyph"
originOfText,TextGlyph-method | SBML type "TextGlyph"
originOfText<-,TextGlyph-method | SBML type "TextGlyph"
outside | SBML type "Compartment"
outside,Compartment-method | SBML type "Compartment"
outside<-,Compartment-method | SBML type "Compartment"

## -- P --

Parameter-class | SBML type "Parameter"
ParameterRule-class | SBML type "ParameterRule"
parameters | SBML type "Model"
parameters,KineticLaw-method | SBML type "KineticLaw"
parameters,Model-method | SBML type "Model"
parameters<-,KineticLaw-method | SBML type "KineticLaw"
parameters<-,Model-method | SBML type "Model"
Point-class | SBML type "Point"
position | SBML type "BoundingBox"
position,BoundingBox-method | SBML type "BoundingBox"
position<-,BoundingBox-method | SBML type "BoundingBox"
products | SBML type "Reaction"
products,Reaction-method | SBML type "Reaction"
products<-,Reaction-method | SBML type "Reaction"

## -- R --

RateRule-class | SBML type "RateRule"
reactants | SBML type "Reaction"
reactants,Reaction-method | SBML type "Reaction"
reactants<-,Reaction-method | SBML type "Reaction"
reaction | SBML type "ReactionGlyph"
reaction,ReactionGlyph-method | SBML type "ReactionGlyph"
Reaction-class | SBML type "Reaction"
reaction<-,ReactionGlyph-method | SBML type "ReactionGlyph"
ReactionGlyph-class | SBML type "ReactionGlyph"
reactionGlyphs | SBML type "Layout"
reactionGlyphs,Layout-method | SBML type "Layout"
reactionGlyphs<-,Layout-method | SBML type "Layout"
reactions | SBML type "Model"
reactions,Model-method | SBML type "Model"
reactions<-,Model-method | SBML type "Model"
reversible | SBML type "Reaction"
reversible,Reaction-method | SBML type "Reaction"
reversible<-,Reaction-method | SBML type "Reaction"
role | SBML type "SpeciesReferenceGlyph"
role,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
role<-,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
rsbml_check | "SBMLDocument" from libsbml
rsbml_check,SBMLDocument-method | "SBMLDocument" from libsbml
rsbml_doc | SBML type "SBML"
rsbml_doc,SBML-method | SBML type "SBML"
rsbml_dom | "SBMLDocument" from libsbml
rsbml_dom,SBMLDocument-method | "SBMLDocument" from libsbml
rsbml_graph | "SBMLDocument" from libsbml
rsbml_graph,SBMLDocument-method | "SBMLDocument" from libsbml
rsbml_problems | "SBMLDocument" from libsbml
rsbml_problems,SBMLDocument-method | "SBMLDocument" from libsbml
rsbml_read | Read in an SBML file (start here)
rsbml_write | SBML type "SBML"
rsbml_write,SBML-method | SBML type "SBML"
rsbml_write,SBMLDocument-method | "SBMLDocument" from libsbml
rsbml_xml | SBML type "SBML"
rsbml_xml,SBML-method | SBML type "SBML"
rsbml_xml,SBMLDocument-method | "SBMLDocument" from libsbml
Rule-class | SBML type "Rule"
rules | SBML type "Model"
rules,Model-method | SBML type "Model"
rules<-,Model-method | SBML type "Model"

## -- S --

SBase-class | SBML type "SBase"
SBML-class | SBML type "SBML"
SBMLDocument-class | "SBMLDocument" from libsbml
scale | SBML type "Unit"
scale,Unit-method | SBML type "Unit"
scale<-,Unit-method | SBML type "Unit"
SimpleSpeciesReference-class | SBML type "SimpleSpeciesReference"
size | SBML type "Compartment"
size,Compartment-method | SBML type "Compartment"
size<-,Compartment-method | SBML type "Compartment"
spatialDimensions | SBML type "Compartment"
spatialDimensions,Compartment-method | SBML type "Compartment"
spatialDimensions<-,Compartment-method | SBML type "Compartment"
spatialSizeUnits | SBML type "Species"
spatialSizeUnits,Species-method | SBML type "Species"
spatialSizeUnits<-,Species-method | SBML type "Species"
species | SBML type "SpeciesGlyph"
species,Model-method | SBML type "Model"
species,SimpleSpeciesReference-method | SBML type "SimpleSpeciesReference"
species,SpeciesConcentrationRule-method | SBML type "SpeciesConcentrationRule"
species,SpeciesGlyph-method | SBML type "SpeciesGlyph"
Species-class | SBML type "Species"
species<-,Model-method | SBML type "Model"
species<-,SimpleSpeciesReference-method | SBML type "SimpleSpeciesReference"
species<-,SpeciesConcentrationRule-method | SBML type "SpeciesConcentrationRule"
species<-,SpeciesGlyph-method | SBML type "SpeciesGlyph"
SpeciesConcentrationRule-class | SBML type "SpeciesConcentrationRule"
speciesGlyph | SBML type "SpeciesReferenceGlyph"
speciesGlyph,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
SpeciesGlyph-class | SBML type "SpeciesGlyph"
speciesGlyph<-,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
speciesGlyphs | SBML type "Layout"
speciesGlyphs,Layout-method | SBML type "Layout"
speciesGlyphs<-,Layout-method | SBML type "Layout"
speciesReference | SBML type "SpeciesReferenceGlyph"
speciesReference,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
SpeciesReference-class | SBML type "SpeciesReference"
speciesReference<-,SpeciesReferenceGlyph-method | SBML type "SpeciesReferenceGlyph"
SpeciesReferenceGlyph-class | SBML type "SpeciesReferenceGlyph"
speciesReferenceGlyphs | SBML type "ReactionGlyph"
speciesReferenceGlyphs,ReactionGlyph-method | SBML type "ReactionGlyph"
speciesReferenceGlyphs<-,ReactionGlyph-method | SBML type "ReactionGlyph"
SpeciesType-class | SBML Type "SpeciesType"
speciesTypes | SBML type "Model"
speciesTypes,Model-method | SBML type "Model"
speciesTypes<-,Model-method | SBML type "Model"
start | SBML type "LineSegment"
start,LineSegment-method | SBML type "LineSegment"
start<-,LineSegment-method | SBML type "LineSegment"
stoichiometry | SBML type "SpeciesReference"
stoichiometry,SpeciesReference-method | SBML type "SpeciesReference"
stoichiometry<-,SpeciesReference-method | SBML type "SpeciesReference"
stoichiometryMath | SBML type "SpeciesReference"
stoichiometryMath,SpeciesReference-method | SBML type "SpeciesReference"
StoichiometryMath-class | SBML type "StoichiometryMath"
stoichiometryMath<-,SpeciesReference-method | SBML type "SpeciesReference"
substanceUnits | SBML type "KineticLaw"
substanceUnits,KineticLaw-method | SBML type "KineticLaw"
substanceUnits,Species-method | SBML type "Species"
substanceUnits<-,KineticLaw-method | SBML type "KineticLaw"
substanceUnits<-,Species-method | SBML type "Species"
symbol | SBML Type "InitialAssignment"
symbol,InitialAssignment-method | SBML Type "InitialAssignment"
symbol<-,InitialAssignment-method | SBML Type "InitialAssignment"

## -- T --

text | SBML type "TextGlyph"
text,TextGlyph-method | SBML type "TextGlyph"
text<-,TextGlyph-method | SBML type "TextGlyph"
TextGlyph-class | SBML type "TextGlyph"
textGlyphs | SBML type "Layout"
textGlyphs,Layout-method | SBML type "Layout"
textGlyphs<-,Layout-method | SBML type "Layout"
timeUnits | SBML type "KineticLaw"
timeUnits,Event-method | SBML type "Event"
timeUnits,KineticLaw-method | SBML type "KineticLaw"
timeUnits<-,Event-method | SBML type "Event"
timeUnits<-,KineticLaw-method | SBML type "KineticLaw"
trigger | SBML type "Event"
trigger,Event-method | SBML type "Event"
Trigger-class | SBML Type "Trigger"
trigger<-,Event-method | SBML type "Event"
type | SBML type "AssignmentRule"
type,AssignmentRule-method | SBML type "AssignmentRule"
type,ParameterRule-method | SBML type "ParameterRule"
type<-,AssignmentRule-method | SBML type "AssignmentRule"
type<-,ParameterRule-method | SBML type "ParameterRule"

## -- U --

Unit-class | SBML type "Unit"
UnitDefinition-class | SBML type "UnitDefinition"
unitDefinitions | SBML type "Model"
unitDefinitions,Model-method | SBML type "Model"
unitDefinitions<-,Model-method | SBML type "Model"
units | SBML type "UnitDefinition"
units,Compartment-method | SBML type "Compartment"
units,Parameter-method | SBML type "Parameter"
units,ParameterRule-method | SBML type "ParameterRule"
units,Species-method | SBML type "Species"
units,UnitDefinition-method | SBML type "UnitDefinition"
units<-,Compartment-method | SBML type "Compartment"
units<-,Parameter-method | SBML type "Parameter"
units<-,ParameterRule-method | SBML type "ParameterRule"
units<-,Species-method | SBML type "Species"
units<-,UnitDefinition-method | SBML type "UnitDefinition"

## -- V --

value | SBML type "Parameter"
value,Parameter-method | SBML type "Parameter"
value<-,Parameter-method | SBML type "Parameter"
variable | SBML type "RateRule"
variable,AssignmentRule-method | SBML type "AssignmentRule"
variable,EventAssignment-method | SBML type "EventAssignment"
variable,ParameterRule-method | SBML type "ParameterRule"
variable,RateRule-method | SBML type "RateRule"
variable<-,AssignmentRule-method | SBML type "AssignmentRule"
variable<-,EventAssignment-method | SBML type "EventAssignment"
variable<-,ParameterRule-method | SBML type "ParameterRule"
variable<-,RateRule-method | SBML type "RateRule"
ver | SBML type "SBML"
ver,SBML-method | SBML type "SBML"
ver<-,SBML-method | SBML type "SBML"

## -- W --

width | SBML type "Dimensions"
width,Dimensions-method | SBML type "Dimensions"
width<-,Dimensions-method | SBML type "Dimensions"

## -- X --

x | SBML type "Point"
x,Point-method | SBML type "Point"
x<-,Point-method | SBML type "Point"

## -- Y --

y | SBML type "Point"
y,Point-method | SBML type "Point"
y<-,Point-method | SBML type "Point"

## -- Z --

z | SBML type "Point"
z,Point-method | SBML type "Point"
z<-,Point-method | SBML type "Point"