rsbml: R support for SBML, using libsbml
Version 2.34.0

Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.

AuthorMichael Lawrence <michafla@gene.com>
Bioconductor views GraphAndNetwork Network Pathways
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseArtistic-2.0
Version2.34.0
URL http://www.sbml.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rsbml")

Popular man pages

AlgebraicRule-class: SBML type "AlgebraicRule"
CompartmentVolumeRule-class: SBML type "CompartmentVolumeRule"
Experiment-class: Experiment
KineticLaw-class: SBML type "KineticLaw"
Reaction-class: SBML type "Reaction"
SpeciesReference-class: SBML type "SpeciesReference"
Trigger-class: SBML Type "Trigger"
See all...

All man pages Function index File listing

Man pages

AlgebraicRule-class: SBML type "AlgebraicRule"
AssignmentRule-class: SBML type "AssignmentRule"
BoundingBox-class: SBML type "BoundingBox"
Compartment-class: SBML type "Compartment"
CompartmentGlyph-class: SBML type "CompartmentGlyph"
CompartmentType-class: SBML Type "CompartmentType"
CompartmentVolumeRule-class: SBML type "CompartmentVolumeRule"
Constraint-class: SBML Type "Constraint"
CubicBezier-class: SBML type "CubicBezier"
Curve-class: SBML type "Curve"
CVTerm-class: SBML Type "CVTerm"
Delay-class: SBML Type "Delay"
Describable-class: Describing objects
Dimensions-class: SBML type "Dimensions"
EventAssignment-class: SBML type "EventAssignment"
Event-class: SBML type "Event"
Experiment-class: Experiment
FunctionDefinition-class: SBML type "FunctionDefinition"
GraphicalObject-class: SBML type "GraphicalObject"
InitialAssignment-class: SBML Type "InitialAssignment"
KineticLaw-class: SBML type "KineticLaw"
Layout-class: SBML type "Layout"
LineSegment-class: SBML type "LineSegment"
math: MathML Utilities
Model-class: SBML type "Model"
ModelCreator-class: SBML Type "ModelCreator"
ModelHistory-class: SBML Type "ModelHistory"
ModifierSpeciesReference-class: SBML type "ModifierSpeciesReference"
Parameter-class: SBML type "Parameter"
ParameterRule-class: SBML type "ParameterRule"
Point-class: SBML type "Point"
RateRule-class: SBML type "RateRule"
Reaction-class: SBML type "Reaction"
ReactionGlyph-class: SBML type "ReactionGlyph"
read: Read in an SBML file (start here)
Rule-class: SBML type "Rule"
SBase-class: SBML type "SBase"
SBML-class: SBML type "SBML"
SBMLDocument-class: "SBMLDocument" from libsbml
SBMLProblem-class: SBMLProblem
SBMLProblems-class: SBMLProblems
SimpleSpeciesReference-class: SBML type "SimpleSpeciesReference"
SOSDesign-class: SOSDesign
SOSExperiment-class: SOS Experiment
SOSProtocol-class: SOSProtocol
SOSResult-class: SOSResult
SOSSubject-class: SOSSubject
Species-class: SBML type "Species"
SpeciesConcentrationRule-class: SBML type "SpeciesConcentrationRule"
SpeciesGlyph-class: SBML type "SpeciesGlyph"
SpeciesReference-class: SBML type "SpeciesReference"
SpeciesReferenceGlyph-class: SBML type "SpeciesReferenceGlyph"
SpeciesType-class: SBML Type "SpeciesType"
StoichiometryMath-class: SBML type "StoichiometryMath"
TextGlyph-class: SBML type "TextGlyph"
Trigger-class: SBML Type "Trigger"
Unit-class: SBML type "Unit"
UnitDefinition-class: SBML type "UnitDefinition"

Functions

.condition,SBMLProblem-method Man page
.throw,SBMLError-method Man page
.throw,SBMLFatal-method Man page
.throw,SBMLInfo-method Man page
.throw,SBMLProblems-method Man page
.throw,SBMLWarning-method Man page
AlgebraicRule-class Man page
AssignmentRule-class Man page
BoundingBox-class Man page
CVTerm-class Man page
Compartment-class Man page
CompartmentGlyph-class Man page
CompartmentType-class Man page
CompartmentVolumeRule-class Man page
Constraint-class Man page
CubicBezier-class Man page
Curve-class Man page
Delay-class Man page
Describable-class Man page
Dimensions-class Man page
Event-class Man page
EventAssignment-class Man page
Experiment-class Man page
ExperimentDesign-class Man page
ExperimentProtocol-class Man page
ExperimentResult-class Man page
ExperimentSubject-class Man page
FunctionDefinition-class Man page
GraphicalObject-class Man page
InitialAssignment-class Man page
KineticLaw-class Man page
Layout-class Man page
LineSegment-class Man page
Model-class Man page
ModelCreator-class Man page
ModelHistory-class Man page
ModifierSpeciesReference-class Man page
OptionalCurve-class Man page
OptionalDelay-class Man page
OptionalKineticLaw-class Man page
OptionalModelHistory-class Man page
OptionalStoichiometryMath-class Man page
Parameter-class Man page
ParameterRule-class Man page
Point-class Man page
RateRule-class Man page
Reaction-class Man page
ReactionGlyph-class Man page
Rule-class Man page
SBML-class Man page
SBMLDocument-class Man page
SBMLError-class Man page
SBMLFatal-class Man page
SBMLInfo-class Man page
SBMLProblem-class Man page
SBMLProblems-class Man page
SBMLWarning-class Man page
SBase-class Man page
SOSDesign-class Man page
SOSExperiment-class Man page
SOSProtocol-class Man page
SOSResult-class Man page
SOSSubject-class Man page
SimpleSpeciesReference-class Man page
Species-class Man page
SpeciesConcentrationRule-class Man page
SpeciesGlyph-class Man page
SpeciesReference-class Man page
SpeciesReferenceGlyph-class Man page
SpeciesType-class Man page
StoichiometryMath-class Man page
TextGlyph-class Man page
Trigger-class Man page
Unit-class Man page
UnitDefinition-class Man page
acot Man page Source code
acoth Man page Source code
acsc Man page Source code
acsch Man page Source code
additionalGraphicalObjects Man page
additionalGraphicalObjects,Layout-method Man page
additionalGraphicalObjects<- Man page
additionalGraphicalObjects<-,Layout-method Man page
annotation Man page
annotation,SBase-method Man page
annotation<- Man page
annotation<-,SBase-method Man page
as.character.SBML Man page
as.character.SBMLDocument Man page
as.ts,SOSResult-method Man page
asMath Source code
asec Man page Source code
asech Man page Source code
basePoint1 Man page
basePoint1,CubicBezier-method Man page
basePoint1<- Man page
basePoint1<-,CubicBezier-method Man page
basePoint2 Man page
basePoint2,CubicBezier-method Man page
basePoint2<- Man page
basePoint2<-,CubicBezier-method Man page
biologicalQualifierType Man page
biologicalQualifierType,CVTerm-method Man page
biologicalQualifierType<- Man page
biologicalQualifierType<-,CVTerm-method Man page
boundaryCondition Man page
boundaryCondition,Species-method Man page
boundaryCondition<- Man page
boundaryCondition<-,Species-method Man page
boundingBox Man page
boundingBox,GraphicalObject-method Man page
boundingBox<- Man page
boundingBox<-,GraphicalObject-method Man page
charge Man page
charge,Species-method Man page
charge<- Man page
charge<-,Species-method Man page
coerce Man page
coerce,SBML,SBMLDocument-method Man page
coerce,SBML,graph-method Man page
coerce,SBMLDocument,SBML-method Man page
coerce,SBMLDocument,graph-method Man page
compartment Man page
compartment,CompartmentGlyph-method Man page
compartment,CompartmentVolumeRule-method Man page
compartment,Species-method Man page
compartment<- Man page
compartment<-,CompartmentGlyph-method Man page
compartment<-,CompartmentVolumeRule-method Man page
compartment<-,Species-method Man page
compartmentGlyphs Man page
compartmentGlyphs,Layout-method Man page
compartmentGlyphs<- Man page
compartmentGlyphs<-,Layout-method Man page
compartmentTypes Man page
compartmentTypes,Model-method Man page
compartmentTypes<- Man page
compartmentTypes<-,Model-method Man page
compartments Man page
compartments,Model-method Man page
compartments,SOSResult-method Man page
compartments<- Man page
compartments<-,Model-method Man page
constant Man page
constant,Compartment-method Man page
constant,Parameter-method Man page
constant,Species-method Man page
constant<- Man page
constant<-,Compartment-method Man page
constant<-,Parameter-method Man page
constant<-,Species-method Man page
constraints Man page
constraints,Model-method Man page
constraints<- Man page
constraints<-,Model-method Man page
cot Man page Source code
coth Man page Source code
createdDate Man page
createdDate,ModelHistory-method Man page Man page
createdDate<- Man page
createdDate<-,ModelHistory,POSIXt-method Man page
createdDate<-,ModelHistory,character-method Man page
creators Man page
creators,ModelHistory-method Man page
creators<- Man page
creators<-,ModelHistory-method Man page
csc Man page Source code
csch Man page Source code
curveSegments Man page
curveSegments,Curve-method Man page
curveSegments<- Man page
curveSegments<-,Curve-method Man page
cvTerms Man page
cvTerms,SBase-method Man page
cvTerms<- Man page
cvTerms<-,SBase-method Man page
depth Man page
depth,Dimensions-method Man page
depth<- Man page
depth<-,Dimensions-method Man page
describe Man page
describe,AlgebraicRule-method Man page
describe,AssignmentRule-method Man page
describe,BoundingBox-method Man page
describe,CVTerm-method Man page
describe,Compartment-method Man page
describe,CompartmentGlyph-method Man page
describe,CompartmentType-method Man page
describe,CompartmentVolumeRule-method Man page
describe,Constraint-method Man page
describe,CubicBezier-method Man page
describe,Curve-method Man page
describe,Delay-method Man page
describe,Dimensions-method Man page
describe,Event-method Man page
describe,EventAssignment-method Man page
describe,FunctionDefinition-method Man page
describe,GraphicalObject-method Man page
describe,InitialAssignment-method Man page
describe,KineticLaw-method Man page
describe,Layout-method Man page
describe,LineSegment-method Man page
describe,Model-method Man page
describe,ModelCreator-method Man page
describe,ModelHistory-method Man page
describe,Parameter-method Man page
describe,ParameterRule-method Man page
describe,Point-method Man page
describe,RateRule-method Man page
describe,Reaction-method Man page
describe,ReactionGlyph-method Man page
describe,SBML-method Man page
describe,SimpleSpeciesReference-method Man page
describe,Species-method Man page
describe,SpeciesConcentrationRule-method Man page
describe,SpeciesGlyph-method Man page
describe,SpeciesReference-method Man page
describe,SpeciesReferenceGlyph-method Man page
describe,SpeciesType-method Man page
describe,StoichiometryMath-method Man page
describe,TextGlyph-method Man page
describe,Trigger-method Man page
describe,Unit-method Man page
describe,UnitDefinition-method Man page
describe,list-method Man page
describe-methods Man page
design Man page
design,Experiment-method Man page
design<- Man page
design<-,Experiment-method Man page
dimensions Man page
dimensions,BoundingBox-method Man page
dimensions,Layout-method Man page
dimensions<- Man page
dimensions<-,BoundingBox-method Man page
dimensions<-,Layout-method Man page
email Man page
email,ModelCreator-method Man page
email<- Man page
email<-,ModelCreator-method Man page
end Man page
end,LineSegment-method Man page
end<- Man page
end<-,LineSegment-method Man page
errors Man page
errors,SBMLProblems-method Man page
eventAssignments Man page
eventAssignments,Event-method Man page
eventAssignments<- Man page
eventAssignments<-,Event-method Man page
eventDelay Man page
eventDelay,Event-method Man page
eventDelay<- Man page
eventDelay<-,Event-method Man page
events Man page
events,Model-method Man page
events<- Man page
events<-,Model-method Man page
exponent Man page
exponent,Unit-method Man page
exponent<- Man page
exponent<-,Unit-method Man page
familyName Man page
familyName,ModelCreator-method Man page
familyName<- Man page
familyName<-,ModelCreator-method Man page
fast Man page
fast,Reaction-method Man page
fast<- Man page
fast<-,Reaction-method Man page
fatals Man page
fatals,SBMLProblems-method Man page
functionDefinitions Man page
functionDefinitions,Model-method Man page
functionDefinitions<- Man page
functionDefinitions<-,Model-method Man page
givenName Man page
givenName,ModelCreator-method Man page
givenName<- Man page
givenName<-,ModelCreator-method Man page
glyphCurve Man page
glyphCurve,ReactionGlyph-method Man page
glyphCurve,SpeciesReferenceGlyph-method Man page
glyphCurve<- Man page
glyphCurve<-,ReactionGlyph-method Man page
glyphCurve<-,SpeciesReferenceGlyph-method Man page
graphicalObject Man page
graphicalObject,TextGlyph-method Man page
graphicalObject<- Man page
graphicalObject<-,TextGlyph-method Man page
hasOnlySubstanceUnits Man page
hasOnlySubstanceUnits,Species-method Man page
hasOnlySubstanceUnits<- Man page
hasOnlySubstanceUnits<-,Species-method Man page
height Man page
height,Dimensions-method Man page
height<- Man page
height<-,Dimensions-method Man page
id Man page
id,BoundingBox-method Man page
id,Compartment-method Man page
id,CompartmentType-method Man page
id,Event-method Man page
id,FunctionDefinition-method Man page
id,GraphicalObject-method Man page
id,Layout-method Man page
id,Model-method Man page
id,Parameter-method Man page
id,Reaction-method Man page
id,SimpleSpeciesReference-method Man page
id,Species-method Man page
id,SpeciesType-method Man page
id,UnitDefinition-method Man page
id<- Man page
id<-,BoundingBox-method Man page
id<-,Compartment-method Man page
id<-,CompartmentType-method Man page
id<-,Event-method Man page
id<-,FunctionDefinition-method Man page
id<-,GraphicalObject-method Man page
id<-,Layout-method Man page
id<-,Model-method Man page
id<-,Parameter-method Man page
id<-,Reaction-method Man page
id<-,SimpleSpeciesReference-method Man page
id<-,Species-method Man page
id<-,SpeciesType-method Man page
id<-,UnitDefinition-method Man page
infos Man page
infos,SBMLProblems-method Man page
initialAmount Man page
initialAmount,Species-method Man page
initialAmount<- Man page
initialAmount<-,Species-method Man page
initialAssignments Man page
initialAssignments,Model-method Man page
initialAssignments<- Man page
initialAssignments<-,Model-method Man page
initialConcentration Man page
initialConcentration,Species-method Man page
initialConcentration<- Man page
initialConcentration<-,Species-method Man page
kind Man page
kind,Unit-method Man page
kind<- Man page
kind<-,Unit-method Man page
kineticLaw Man page
kineticLaw,Reaction-method Man page
kineticLaw<- Man page
kineticLaw<-,Reaction-method Man page
layouts Man page
layouts,Model-method Man page
layouts<- Man page
layouts<-,Model-method Man page
level Man page
level,SBML-method Man page
level<- Man page
level<-,SBML-method Man page
math Man page
math,Constraint-method Man page
math,Delay-method Man page
math,EventAssignment-method Man page
math,FunctionDefinition-method Man page
math,InitialAssignment-method Man page
math,KineticLaw-method Man page
math,ParameterRule-method Man page
math,Rule-method Man page
math,StoichiometryMath-method Man page
math,Trigger-method Man page
math<- Man page
math<-,Constraint-method Man page
math<-,Delay-method Man page
math<-,EventAssignment-method Man page
math<-,FunctionDefinition-method Man page
math<-,InitialAssignment-method Man page
math<-,KineticLaw-method Man page
math<-,ParameterRule-method Man page
math<-,Rule-method Man page
math<-,StoichiometryMath-method Man page
math<-,Trigger-method Man page
metaId Man page
metaId,SBase-method Man page
metaId<- Man page
metaId<-,SBase-method Man page
model Man page
model,SBML-method Man page
model<- Man page
model<-,SBML-method Man page
modelHistory Man page
modelHistory,Model-method Man page
modelHistory<- Man page
modelHistory<-,Model-method Man page
modelQualifierType Man page
modelQualifierType,CVTerm-method Man page
modelQualifierType<- Man page
modelQualifierType<-,CVTerm-method Man page
modifiedDate Man page
modifiedDate,ModelHistory-method Man page
modifiedDate<- Man page
modifiedDate<-,ModelHistory,POSIXt-method Man page
modifiedDate<-,ModelHistory,character-method Man page
modifiedDate<-,ModelHistory-method Man page
modifiers Man page
modifiers,Reaction-method Man page
modifiers<- Man page
modifiers<-,Reaction-method Man page
msg Man page
msg,Constraint-method Man page
msg<- Man page
msg<-,Constraint-method Man page
multiplier Man page
multiplier,Unit-method Man page
multiplier<- Man page
multiplier<-,Unit-method Man page
name Man page
name,Compartment-method Man page
name,CompartmentType-method Man page
name,Event-method Man page
name,FunctionDefinition-method Man page
name,Model-method Man page
name,Parameter-method Man page
name,ParameterRule-method Man page
name,Reaction-method Man page
name,Species-method Man page
name,SpeciesType-method Man page
name,UnitDefinition-method Man page
name<- Man page
name<-,Compartment-method Man page
name<-,CompartmentType-method Man page
name<-,Event-method Man page
name<-,FunctionDefinition-method Man page
name<-,Model-method Man page
name<-,Parameter-method Man page
name<-,ParameterRule-method Man page
name<-,Reaction-method Man page
name<-,Species-method Man page
name<-,SpeciesType-method Man page
name<-,UnitDefinition-method Man page
notes Man page
notes,SBase-method Man page
notes<- Man page
notes<-,SBase-method Man page
offset Man page
offset,Unit-method Man page
offset<- Man page
offset<-,Unit-method Man page
onLoad Source code
organization Man page
organization,ModelCreator-method Man page
organization<- Man page
organization<-,ModelCreator-method Man page
originOfText Man page
originOfText,TextGlyph-method Man page
originOfText<- Man page
originOfText<-,TextGlyph-method Man page
outside Man page
outside,Compartment-method Man page
outside<- Man page
outside<-,Compartment-method Man page
parameters Man page
parameters,KineticLaw-method Man page
parameters,Model-method Man page
parameters,SOSResult-method Man page
parameters<- Man page
parameters<-,KineticLaw-method Man page
parameters<-,Model-method Man page
position Man page
position,BoundingBox-method Man page
position<- Man page
position<-,BoundingBox-method Man page
products Man page
products,Reaction-method Man page
products<- Man page
products<-,Reaction-method Man page
protocol Man page
protocol,Experiment-method Man page
protocol<- Man page
protocol<-,Experiment-method Man page
qualifierType Man page
qualifierType,CVTerm-method Man page
qualifierType<- Man page
qualifierType<-,CVTerm-method Man page
reactants Man page
reactants,Reaction-method Man page
reactants<- Man page
reactants<-,Reaction-method Man page
reaction Man page
reaction,ReactionGlyph-method Man page
reaction<- Man page
reaction<-,ReactionGlyph-method Man page
reactionGlyphs Man page
reactionGlyphs,Layout-method Man page
reactionGlyphs<- Man page
reactionGlyphs<-,Layout-method Man page
reactions Man page
reactions,Model-method Man page
reactions,SOSDesign-method Man page
reactions,SOSResult-method Man page
reactions<- Man page
reactions<-,Experiment-method Man page
reactions<-,Model-method Man page
reactions<-,SOSDesign-method Man page
resources Man page
resources,CVTerm-method Man page
resources<- Man page
resources<-,CVTerm-method Man page
result Man page
result,Experiment-method Man page
result<- Man page
result<-,Experiment-method Man page
reversible Man page
reversible,Reaction-method Man page
reversible<- Man page
reversible<-,Reaction-method Man page
role Man page
role,SpeciesReferenceGlyph-method Man page
role<- Man page
role<-,SpeciesReferenceGlyph-method Man page
rsbml_check Man page
rsbml_check,SBML-method Man page
rsbml_check,SBMLDocument-method Man page
rsbml_doc Man page
rsbml_doc,SBML-method Man page
rsbml_dom Man page
rsbml_dom,SBMLDocument-method Man page
rsbml_graph Man page
rsbml_graph,Model-method Man page
rsbml_graph,SBML-method Man page
rsbml_graph,SBMLDocument-method Man page
rsbml_problems Man page
rsbml_problems,SBMLDocument-method Man page
rsbml_read Man page Source code
rsbml_write Man page
rsbml_write,SBML-method Man page
rsbml_write,SBMLDocument-method Man page
rsbml_xml Man page
rsbml_xml,SBML-method Man page
rsbml_xml,SBMLDocument-method Man page
rules Man page
rules,Model-method Man page
rules<- Man page
rules<-,Model-method Man page
sboTerm Man page
sboTerm,SBase-method Man page
sboTerm<- Man page
sboTerm<-,SBase-method Man page
sec Man page Source code
sech Man page Source code
show,Describable-method Man page
show,SBMLProblem-method Man page
simulate Man page
simulate,SBML-method Man page
simulate,SBMLDocument-method Man page
simulate,SOSExperiment-method Man page
simulate.SBML Source code
size Man page
size,Compartment-method Man page
size<- Man page
size<-,Compartment-method Man page
spatialDimensions Man page
spatialDimensions,Compartment-method Man page
spatialDimensions<- Man page
spatialDimensions<-,Compartment-method Man page
spatialSizeUnits Man page
spatialSizeUnits,Species-method Man page
spatialSizeUnits<- Man page
spatialSizeUnits<-,Species-method Man page
species Man page
species,Model-method Man page
species,SOSResult-method Man page
species,SimpleSpeciesReference-method Man page
species,SpeciesConcentrationRule-method Man page
species,SpeciesGlyph-method Man page
species<- Man page
species<-,Model-method Man page
species<-,SimpleSpeciesReference-method Man page
species<-,SpeciesConcentrationRule-method Man page
species<-,SpeciesGlyph-method Man page
speciesGlyph Man page
speciesGlyph,SpeciesReferenceGlyph-method Man page
speciesGlyph<- Man page
speciesGlyph<-,SpeciesReferenceGlyph-method Man page
speciesGlyphs Man page
speciesGlyphs,Layout-method Man page
speciesGlyphs<- Man page
speciesGlyphs<-,Layout-method Man page
speciesReference Man page
speciesReference,SpeciesReferenceGlyph-method Man page
speciesReference<- Man page
speciesReference<-,SpeciesReferenceGlyph-method Man page
speciesReferenceGlyphs Man page
speciesReferenceGlyphs,ReactionGlyph-method Man page
speciesReferenceGlyphs<- Man page
speciesReferenceGlyphs<-,ReactionGlyph-method Man page
speciesTypes Man page
speciesTypes,Model-method Man page
speciesTypes<- Man page
speciesTypes<-,Model-method Man page
start Man page
start,LineSegment-method Man page
start<- Man page
start<-,LineSegment-method Man page
stoichiometry Man page
stoichiometry,SpeciesReference-method Man page
stoichiometry<- Man page
stoichiometry<-,SpeciesReference-method Man page
stoichiometryMath Man page
stoichiometryMath,SpeciesReference-method Man page
stoichiometryMath<- Man page
stoichiometryMath<-,SpeciesReference-method Man page
stoichiometryMatrix Man page
stoichiometryMatrix,Model-method Man page
subject Man page
subject,Experiment-method Man page
subject<- Man page
subject<-,Experiment-method Man page
substanceUnits Man page
substanceUnits,KineticLaw-method Man page
substanceUnits,Species-method Man page
substanceUnits<- Man page
substanceUnits<-,KineticLaw-method Man page
substanceUnits<-,Species-method Man page
symbol Man page
symbol,InitialAssignment-method Man page
symbol<- Man page
symbol<-,InitialAssignment-method Man page
text Man page
text,TextGlyph-method Man page
text<- Man page
text<-,TextGlyph-method Man page
textGlyphs Man page
textGlyphs,Layout-method Man page
textGlyphs<- Man page
textGlyphs<-,Layout-method Man page
timeUnits Man page
timeUnits,Event-method Man page
timeUnits,KineticLaw-method Man page
timeUnits<- Man page
timeUnits<-,Event-method Man page
timeUnits<-,KineticLaw-method Man page
trigger Man page
trigger,Event-method Man page
trigger<- Man page
trigger<-,Event-method Man page
type Man page
type,AssignmentRule-method Man page
type,ParameterRule-method Man page
type<- Man page
type<-,AssignmentRule-method Man page
type<-,ParameterRule-method Man page
unitDefinitions Man page
unitDefinitions,Model-method Man page
unitDefinitions<- Man page
unitDefinitions<-,Model-method Man page
unitScale Man page
unitScale,Unit-method Man page
unitScale<- Man page
unitScale<-,Unit-method Man page
units Man page
units,Compartment-method Man page
units,Parameter-method Man page
units,ParameterRule-method Man page
units,Species-method Man page
units,UnitDefinition-method Man page
units<- Man page
units<-,Compartment-method Man page
units<-,Parameter-method Man page
units<-,ParameterRule-method Man page
units<-,Species-method Man page
units<-,UnitDefinition-method Man page
value Man page
value,Parameter-method Man page
value<- Man page
value<-,Parameter-method Man page
variable Man page
variable,AssignmentRule-method Man page
variable,EventAssignment-method Man page
variable,ParameterRule-method Man page
variable,RateRule-method Man page
variable<- Man page
variable<-,AssignmentRule-method Man page
variable<-,EventAssignment-method Man page
variable<-,ParameterRule-method Man page
variable<-,RateRule-method Man page
ver Man page
ver,SBML-method Man page
ver<- Man page
ver<-,SBML-method Man page
warns Man page
warns,SBMLProblems-method Man page
width Man page
width,Dimensions-method Man page
width<- Man page
width<-,Dimensions-method Man page
x Man page
x,Point-method Man page
x<- Man page
x<-,Point-method Man page
y Man page
y,Point-method Man page
y<- Man page
y<-,Point-method Man page
z Man page
z,Point-method Man page
z<- Man page
z<-,Point-method Man page

Files

DESCRIPTION
INSTALL
NAMESPACE
NEWS
R
R/AAADescribable.R
R/AAASBase.R
R/AADimensions.R
R/AAPoint.R
R/AARule.R
R/AAStoichiometryMath.R
R/ABoundingBox.R
R/ACompartmentType.R
R/ACurve.R
R/AEventAssignment.R
R/AGraphicalObject.R
R/ALineSegment.R
R/AModelCreator.R
R/AModelHistory.R
R/ASimpleSpeciesReference.R
R/ASpeciesReference.R
R/ASpeciesReferenceGlyph.R
R/ASpeciesType.R
R/ATrigger.R
R/AlgebraicRule.R
R/AssignmentRule.R
R/CVTerm.R
R/Compartment.R
R/CompartmentGlyph.R
R/CompartmentVolumeRule.R
R/Constraint.R
R/CubicBezier.R
R/Delay.R
R/Event.R
R/FunctionDefinition.R
R/InitialAssignment.R
R/KineticLaw.R
R/Layout.R
R/Model.R
R/ModifierSpeciesReference.R
R/Parameter.R
R/ParameterRule.R
R/RateRule.R
R/Reaction.R
R/ReactionGlyph.R
R/SBML.R
R/Species.R
R/SpeciesConcentrationRule.R
R/SpeciesGlyph.R
R/TextGlyph.R
R/Unit.R
R/UnitDefinition.R
R/aaa.R
R/graph.R
R/math.R
R/problems.R
R/rsbml.R
R/simulate.R
R/utils.R
R/zzz.R
build
build/vignette.rds
configure
configure.in
inst
inst/SBML_odeSolver-1.7.0beta
inst/SBML_odeSolver-1.7.0beta/AUTHORS
inst/SBML_odeSolver-1.7.0beta/COPYING
inst/SBML_odeSolver-1.7.0beta/ChangeLog
inst/SBML_odeSolver-1.7.0beta/INSTALL
inst/SBML_odeSolver-1.7.0beta/Makefile.am
inst/SBML_odeSolver-1.7.0beta/Makefile.in
inst/SBML_odeSolver-1.7.0beta/NEWS
inst/SBML_odeSolver-1.7.0beta/OUTLOOK
inst/SBML_odeSolver-1.7.0beta/README
inst/SBML_odeSolver-1.7.0beta/SOSlib.doxy
inst/SBML_odeSolver-1.7.0beta/TODO
inst/SBML_odeSolver-1.7.0beta/VERSION.txt
inst/SBML_odeSolver-1.7.0beta/aclocal.m4
inst/SBML_odeSolver-1.7.0beta/config
inst/SBML_odeSolver-1.7.0beta/config.log
inst/SBML_odeSolver-1.7.0beta/config/ax_compare_version.m4
inst/SBML_odeSolver-1.7.0beta/config/config.guess
inst/SBML_odeSolver-1.7.0beta/config/config.sub
inst/SBML_odeSolver-1.7.0beta/config/cvode.m4
inst/SBML_odeSolver-1.7.0beta/config/depcomp
inst/SBML_odeSolver-1.7.0beta/config/fpic.m4
inst/SBML_odeSolver-1.7.0beta/config/grace.m4
inst/SBML_odeSolver-1.7.0beta/config/graphviz.m4
inst/SBML_odeSolver-1.7.0beta/config/install-sh
inst/SBML_odeSolver-1.7.0beta/config/missing
inst/SBML_odeSolver-1.7.0beta/config/sbml.m4
inst/SBML_odeSolver-1.7.0beta/config/sundials.m4
inst/SBML_odeSolver-1.7.0beta/config/tcc.m4
inst/SBML_odeSolver-1.7.0beta/configure
inst/SBML_odeSolver-1.7.0beta/configure.in
inst/SBML_odeSolver-1.7.0beta/configure.lineno
inst/SBML_odeSolver-1.7.0beta/doc
inst/SBML_odeSolver-1.7.0beta/doc/README
inst/SBML_odeSolver-1.7.0beta/odeSolver.doxy
inst/SBML_odeSolver-1.7.0beta/scripts
inst/SBML_odeSolver-1.7.0beta/scripts/gnuplotscript.awk
inst/SBML_odeSolver-1.7.0beta/scripts/xmgracefile.pl
inst/SBML_odeSolver-1.7.0beta/src
inst/SBML_odeSolver-1.7.0beta/src/ASTIndexNameNode.cpp
inst/SBML_odeSolver-1.7.0beta/src/Makefile.am
inst/SBML_odeSolver-1.7.0beta/src/Makefile.in
inst/SBML_odeSolver-1.7.0beta/src/arithmeticCompiler.c
inst/SBML_odeSolver-1.7.0beta/src/charBuffer.cpp
inst/SBML_odeSolver-1.7.0beta/src/compiler.c
inst/SBML_odeSolver-1.7.0beta/src/cvodeData.c
inst/SBML_odeSolver-1.7.0beta/src/cvodeSolver.c
inst/SBML_odeSolver-1.7.0beta/src/daeSolver.c
inst/SBML_odeSolver-1.7.0beta/src/drawGraph.c
inst/SBML_odeSolver-1.7.0beta/src/integratorInstance.c
inst/SBML_odeSolver-1.7.0beta/src/integratorSettings.c
inst/SBML_odeSolver-1.7.0beta/src/interpol.c
inst/SBML_odeSolver-1.7.0beta/src/libODES.pc
inst/SBML_odeSolver-1.7.0beta/src/libODES.pc.in
inst/SBML_odeSolver-1.7.0beta/src/modelSimplify.c
inst/SBML_odeSolver-1.7.0beta/src/nullSolver.c
inst/SBML_odeSolver-1.7.0beta/src/odeConstruct.c
inst/SBML_odeSolver-1.7.0beta/src/odeModel.c
inst/SBML_odeSolver-1.7.0beta/src/odeSolver.c
inst/SBML_odeSolver-1.7.0beta/src/processAST.c
inst/SBML_odeSolver-1.7.0beta/src/sbml.c
inst/SBML_odeSolver-1.7.0beta/src/sbmlResults.c
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/Makefile
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/arithmeticCompiler.c
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/arithmeticCompilerTest.c
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/interfaceSimulation.c
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTIndexNameNode.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/arithmeticCompiler.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/charBuffer.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/compiler.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/config.h.in
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/cvodeData.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/cvodeSolver.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/daeSolver.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/drawGraph.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/exportdefs.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/integratorInstance.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/integratorSettings.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/interpol.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/modelSimplify.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/nullSolver.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/odeConstruct.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/odeModel.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/odeSolver.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/processAST.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/sbml.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/sbmlResults.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/sensSolver.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/solverError.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/stamp-h1
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/util.h
inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/variableIndex.h
inst/SBML_odeSolver-1.7.0beta/src/sensSolver.c
inst/SBML_odeSolver-1.7.0beta/src/solverError.c
inst/SBML_odeSolver-1.7.0beta/src/util.c
inst/doc
inst/doc/quick-start.R
inst/doc/quick-start.Rnw
inst/doc/quick-start.pdf
inst/gen
inst/gen/gen.R
inst/sbml
inst/sbml/GlycolysisLayout.xml
inst/sbml/biotin-fa.xml
inst/sbml/cell-cycle.xml
inst/sbml/curto.xml
inst/sbml/squid-axon.xml
inst/tests
inst/tests/l1v1-branch-schema-error.xml
inst/tests/l1v1-branch.xml
inst/tests/l1v1-minimal.xml
inst/tests/l1v1-rules.xml
inst/tests/l1v1-units.xml
inst/tests/l1v2-branch.xml
inst/tests/l2v1-2D-compartments.xml
inst/tests/l2v1-algebraic.xml
inst/tests/l2v1-assignment.xml
inst/tests/l2v1-boundary.xml
inst/tests/l2v1-branch.xml
inst/tests/l2v1-delay.xml
inst/tests/l2v1-events.xml
inst/tests/l2v1-functions.xml
inst/tests/l2v1-mc-ode.xml
inst/tests/l2v1-units.xml
man
man/AlgebraicRule-class.Rd
man/AssignmentRule-class.Rd
man/BoundingBox-class.Rd
man/CVTerm-class.Rd
man/Compartment-class.Rd
man/CompartmentGlyph-class.Rd
man/CompartmentType-class.Rd
man/CompartmentVolumeRule-class.Rd
man/Constraint-class.Rd
man/CubicBezier-class.Rd
man/Curve-class.Rd
man/Delay-class.Rd
man/Describable-class.Rd
man/Dimensions-class.Rd
man/Event-class.Rd
man/EventAssignment-class.Rd
man/Experiment-class.Rd
man/FunctionDefinition-class.Rd
man/GraphicalObject-class.Rd
man/InitialAssignment-class.Rd
man/KineticLaw-class.Rd
man/Layout-class.Rd
man/LineSegment-class.Rd
man/Model-class.Rd
man/ModelCreator-class.Rd
man/ModelHistory-class.Rd
man/ModifierSpeciesReference-class.Rd
man/Parameter-class.Rd
man/ParameterRule-class.Rd
man/Point-class.Rd
man/RateRule-class.Rd
man/Reaction-class.Rd
man/ReactionGlyph-class.Rd
man/Rule-class.Rd
man/SBML-class.Rd
man/SBMLDocument-class.Rd
man/SBMLProblem-class.Rd
man/SBMLProblems-class.Rd
man/SBase-class.Rd
man/SOSDesign-class.Rd
man/SOSExperiment-class.Rd
man/SOSProtocol-class.Rd
man/SOSResult-class.Rd
man/SOSSubject-class.Rd
man/SimpleSpeciesReference-class.Rd
man/Species-class.Rd
man/SpeciesConcentrationRule-class.Rd
man/SpeciesGlyph-class.Rd
man/SpeciesReference-class.Rd
man/SpeciesReferenceGlyph-class.Rd
man/SpeciesType-class.Rd
man/StoichiometryMath-class.Rd
man/TextGlyph-class.Rd
man/Trigger-class.Rd
man/Unit-class.Rd
man/UnitDefinition-class.Rd
man/math.Rd
man/read.Rd
src
src/Makevars
src/Makevars.in
src/Makevars.win
src/StringMap.c
src/StringMap.h
src/check.c
src/doc.c
src/dom.c
src/graph.c
src/init.c
src/io.c
src/layoutWrappers.cpp
src/mathml.c
src/rsbml.h
src/simulate.c
start.R
vignettes
vignettes/quick-start.Rnw
vignettes/rsbml.bib
rsbml documentation built on May 20, 2017, 10:44 p.m.

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