R support for SBML, using libsbml


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Documentation for package ‘rsbml’ version 1.4.0

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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"