Package: rsbml 2.65.0
Michael Lawrence
rsbml: R support for SBML, using libsbml
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.
Authors:
rsbml_2.65.0.tar.gz
rsbml_2.65.0.tar.gz(r-4.5-noble)rsbml_2.65.0.tar.gz(r-4.4-noble)
rsbml.pdf |rsbml.html✨
rsbml/json (API)
NEWS
| # Install 'rsbml' in R: |
| install.packages('rsbml', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:rsbml-2.65.0(bioc 3.21)rsbml-2.64.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
graphandnetworkpathwaysnetworklibsbmlcpp
Last updated 2 months agofrom:b523cb66a5. Checks:OK: 1 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 19 2024 |
Exports:acotacothacscacschadditionalGraphicalObjectsadditionalGraphicalObjects<-as.character.SBMLas.character.SBMLDocumentas.tsasecasechasMathbasePoint1basePoint1<-basePoint2basePoint2<-biologicalQualifierTypebiologicalQualifierType<-boundaryConditionboundaryCondition<-boundingBoxboundingBox<-chargecharge<-compartmentcompartment<-compartmentGlyphscompartmentGlyphs<-compartmentscompartments<-compartmentTypescompartmentTypes<-constantconstant<-constraintsconstraints<-cotcothcreatedDatecreatedDate<-creatorscreators<-csccschcurveSegmentscurveSegments<-cvTermscvTerms<-depthdepth<-describedimensionsdimensions<-emailemail<-errorseventAssignmentseventAssignments<-eventDelayeventDelay<-eventsevents<-exponentexponent<-familyNamefamilyName<-fastfast<-fatalsfunctionDefinitionsfunctionDefinitions<-givenNamegivenName<-glyphCurveglyphCurve<-graphicalObjectgraphicalObject<-hasOnlySubstanceUnitshasOnlySubstanceUnits<-heightheight<-idid<-infosinitialAmountinitialAmount<-initialAssignmentsinitialAssignments<-initialConcentrationinitialConcentration<-kindkind<-kineticLawkineticLaw<-layoutslayouts<-levellevel<-mathmath<-metaIdmetaId<-modelmodel<-modelHistorymodelHistory<-modelQualifierTypemodelQualifierType<-modifiedDatemodifiedDate<-modifiersmodifiers<-msgmsg<-multipliermultiplier<-namename<-notesnotes<-offsetoffset<-organizationorganization<-originOfTextoriginOfText<-outsideoutside<-parametersparameters<-positionposition<-productsproducts<-protocolprotocol<-qualifierTypequalifierType<-reactantsreactants<-reactionreaction<-reactionGlyphsreactionGlyphs<-reactionsreactions<-resourcesresources<-resultresult<-reversiblereversible<-rolerole<-rsbml_checkrsbml_docrsbml_domrsbml_graphrsbml_problemsrsbml_readrsbml_writersbml_xmlrulesrules<-sboTermsboTerm<-secsechsimulatesizesize<-spatialDimensionsspatialDimensions<-spatialSizeUnitsspatialSizeUnits<-speciesGlyphspeciesGlyph<-speciesGlyphsspeciesGlyphs<-speciesReferencespeciesReference<-speciesReferenceGlyphsspeciesReferenceGlyphs<-speciesTypesspeciesTypes<-stoichiometrystoichiometry<-stoichiometryMathstoichiometryMath<-stoichiometryMatrixsubjectsubject<-substanceUnitssubstanceUnits<-symbolsymbol<-texttext<-textGlyphstextGlyphs<-timeUnitstimeUnits<-triggertrigger<-unitDefinitionsunitDefinitions<-unitsunits<-unitScaleunitScale<-valuevalue<-variablevariable<-verver<-warnsxx<-yy<-zz<-
Dependencies:BiocGenericsgenericsgraph
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SBML type "AlgebraicRule" | AlgebraicRule-class |
| SBML type "AssignmentRule" | AssignmentRule-class type type,AssignmentRule-method type<- type<-,AssignmentRule-method variable,AssignmentRule-method variable<-,AssignmentRule-method |
| SBML type "BoundingBox" | BoundingBox-class dimensions,BoundingBox-method dimensions<-,BoundingBox-method id,BoundingBox-method id<-,BoundingBox-method position position,BoundingBox-method position<- position<-,BoundingBox-method |
| SBML type "Compartment" | Compartment-class constant,Compartment-method constant<-,Compartment-method id,Compartment-method id<-,Compartment-method name,Compartment-method name<-,Compartment-method outside outside,Compartment-method outside<- outside<-,Compartment-method size size,Compartment-method size<- size<-,Compartment-method spatialDimensions spatialDimensions,Compartment-method spatialDimensions<- spatialDimensions<-,Compartment-method units,Compartment-method units<-,Compartment-method |
| SBML type "CompartmentGlyph" | compartment,CompartmentGlyph-method compartment<-,CompartmentGlyph-method CompartmentGlyph-class |
| SBML Type "CompartmentType" | CompartmentType-class id,CompartmentType-method id<-,CompartmentType-method name,CompartmentType-method name<-,CompartmentType-method |
| SBML type "CompartmentVolumeRule" | compartment,CompartmentVolumeRule-method compartment<-,CompartmentVolumeRule-method CompartmentVolumeRule-class |
| SBML Type "Constraint" | Constraint-class math,Constraint-method math<-,Constraint-method msg msg,Constraint-method msg<- msg<-,Constraint-method |
| SBML type "CubicBezier" | basePoint1 basePoint1,CubicBezier-method basePoint1<- basePoint1<-,CubicBezier-method basePoint2 basePoint2,CubicBezier-method basePoint2<- basePoint2<-,CubicBezier-method CubicBezier-class |
| SBML type "Curve" | Curve-class curveSegments curveSegments,Curve-method curveSegments<- curveSegments<-,Curve-method OptionalCurve-class |
| SBML Type "CVTerm" | biologicalQualifierType biologicalQualifierType,CVTerm-method biologicalQualifierType<- biologicalQualifierType<-,CVTerm-method CVTerm-class modelQualifierType modelQualifierType,CVTerm-method modelQualifierType<- modelQualifierType<-,CVTerm-method qualifierType qualifierType,CVTerm-method qualifierType<- qualifierType<-,CVTerm-method resources resources,CVTerm-method resources<- resources<-,CVTerm-method |
| SBML Type "Delay" | Delay-class math,Delay-method math<-,Delay-method OptionalDelay-class |
| Describing objects | Describable-class describe describe,AlgebraicRule-method describe,AssignmentRule-method describe,BoundingBox-method describe,Compartment-method describe,CompartmentGlyph-method describe,CompartmentType-method describe,CompartmentVolumeRule-method describe,Constraint-method describe,CubicBezier-method describe,Curve-method describe,CVTerm-method describe,Delay-method describe,Dimensions-method describe,Event-method describe,EventAssignment-method describe,FunctionDefinition-method describe,GraphicalObject-method describe,InitialAssignment-method describe,KineticLaw-method describe,Layout-method describe,LineSegment-method describe,list-method describe,Model-method describe,ModelCreator-method describe,ModelHistory-method describe,Parameter-method describe,ParameterRule-method describe,Point-method describe,RateRule-method describe,Reaction-method describe,ReactionGlyph-method describe,SBML-method describe,SimpleSpeciesReference-method describe,Species-method describe,SpeciesConcentrationRule-method describe,SpeciesGlyph-method describe,SpeciesReference-method describe,SpeciesReferenceGlyph-method describe,SpeciesType-method describe,StoichiometryMath-method describe,TextGlyph-method describe,Trigger-method describe,Unit-method describe,UnitDefinition-method describe-methods show,Describable-method |
| SBML type "Dimensions" | depth depth,Dimensions-method depth<- depth<-,Dimensions-method Dimensions-class height height,Dimensions-method height<- height<-,Dimensions-method width width,Dimensions-method width<- width<-,Dimensions-method |
| SBML type "Event" | Event-class eventAssignments eventAssignments,Event-method eventAssignments<- eventAssignments<-,Event-method eventDelay eventDelay,Event-method eventDelay<- eventDelay<-,Event-method id,Event-method id<-,Event-method name,Event-method name<-,Event-method timeUnits,Event-method timeUnits<-,Event-method trigger trigger,Event-method trigger<- trigger<-,Event-method |
| SBML type "EventAssignment" | EventAssignment-class math,EventAssignment-method math<-,EventAssignment-method variable,EventAssignment-method variable<-,EventAssignment-method |
| Experiment | design design,Experiment-method design<- design<-,Experiment-method Experiment-class ExperimentDesign-class ExperimentProtocol-class ExperimentResult-class ExperimentSubject-class protocol protocol,Experiment-method protocol<- protocol<-,Experiment-method reactions<-,Experiment-method result result,Experiment-method result<- result<-,Experiment-method subject subject,Experiment-method subject<- subject<-,Experiment-method |
| SBML type "FunctionDefinition" | FunctionDefinition-class id,FunctionDefinition-method id<-,FunctionDefinition-method math,FunctionDefinition-method math<-,FunctionDefinition-method name,FunctionDefinition-method name<-,FunctionDefinition-method |
| SBML type "GraphicalObject" | boundingBox boundingBox,GraphicalObject-method boundingBox<- boundingBox<-,GraphicalObject-method GraphicalObject-class id,GraphicalObject-method id<-,GraphicalObject-method |
| SBML Type "InitialAssignment" | InitialAssignment-class math,InitialAssignment-method math<-,InitialAssignment-method symbol symbol,InitialAssignment-method symbol<- symbol<-,InitialAssignment-method |
| SBML type "KineticLaw" | KineticLaw-class math math,KineticLaw-method math<- math<-,KineticLaw-method OptionalKineticLaw-class parameters,KineticLaw-method parameters<-,KineticLaw-method substanceUnits substanceUnits,KineticLaw-method substanceUnits<- substanceUnits<-,KineticLaw-method timeUnits timeUnits,KineticLaw-method timeUnits<- timeUnits<-,KineticLaw-method |
| SBML type "Layout" | additionalGraphicalObjects additionalGraphicalObjects,Layout-method additionalGraphicalObjects<- additionalGraphicalObjects<-,Layout-method compartmentGlyphs compartmentGlyphs,Layout-method compartmentGlyphs<- compartmentGlyphs<-,Layout-method dimensions dimensions,Layout-method dimensions<- dimensions<-,Layout-method id,Layout-method id<-,Layout-method Layout-class reactionGlyphs reactionGlyphs,Layout-method reactionGlyphs<- reactionGlyphs<-,Layout-method speciesGlyphs speciesGlyphs,Layout-method speciesGlyphs<- speciesGlyphs<-,Layout-method textGlyphs textGlyphs,Layout-method textGlyphs<- textGlyphs<-,Layout-method |
| SBML type "LineSegment" | end end,LineSegment-method end<- end<-,LineSegment-method LineSegment-class start start,LineSegment-method start<- start<-,LineSegment-method |
| MathML Utilities | acot acoth acsc acsch asec asech cot coth csc csch sec sech |
| SBML type "Model" | compartments compartments,Model-method compartments<- compartments<-,Model-method compartmentTypes compartmentTypes,Model-method compartmentTypes<- compartmentTypes<-,Model-method constraints constraints,Model-method constraints<- constraints<-,Model-method events events,Model-method events<- events<-,Model-method functionDefinitions functionDefinitions,Model-method functionDefinitions<- functionDefinitions<-,Model-method id,Model-method id<-,Model-method initialAssignments initialAssignments,Model-method initialAssignments<- initialAssignments<-,Model-method layouts layouts,Model-method layouts<- layouts<-,Model-method Model-class modelHistory modelHistory,Model-method modelHistory<- modelHistory<-,Model-method name,Model-method name<-,Model-method parameters parameters,Model-method parameters<- parameters<-,Model-method reactions reactions,Model-method reactions<- reactions<-,Model-method rules rules,Model-method rules<- rules<-,Model-method species,Model-method species<-,Model-method speciesTypes speciesTypes,Model-method speciesTypes<- speciesTypes<-,Model-method stoichiometryMatrix stoichiometryMatrix,Model-method unitDefinitions unitDefinitions,Model-method unitDefinitions<- unitDefinitions<-,Model-method |
| SBML Type "ModelCreator" | email email,ModelCreator-method email<- email<-,ModelCreator-method familyName familyName,ModelCreator-method familyName<- familyName<-,ModelCreator-method givenName givenName,ModelCreator-method givenName<- givenName<-,ModelCreator-method ModelCreator-class organization organization,ModelCreator-method organization<- organization<-,ModelCreator-method |
| SBML Type "ModelHistory" | createdDate createdDate,ModelHistory-method createdDate<- createdDate<-,ModelHistory,character-method createdDate<-,ModelHistory,POSIXt-method creators creators,ModelHistory-method creators<- creators<-,ModelHistory-method ModelHistory-class modifiedDate modifiedDate,ModelHistory-method modifiedDate<- modifiedDate<-,ModelHistory,character-method modifiedDate<-,ModelHistory,POSIXt-method modifiedDate<-,ModelHistory-method OptionalModelHistory-class |
| SBML type "ModifierSpeciesReference" | ModifierSpeciesReference-class |
| SBML type "Parameter" | constant,Parameter-method constant<-,Parameter-method id,Parameter-method id<-,Parameter-method name,Parameter-method name<-,Parameter-method Parameter-class units,Parameter-method units<-,Parameter-method value value,Parameter-method value<- value<-,Parameter-method |
| SBML type "ParameterRule" | math,ParameterRule-method math<-,ParameterRule-method name,ParameterRule-method name<-,ParameterRule-method ParameterRule-class type,ParameterRule-method type<-,ParameterRule-method units,ParameterRule-method units<-,ParameterRule-method variable,ParameterRule-method variable<-,ParameterRule-method |
| SBML type "Point" | Point-class x x,Point-method x<- x<-,Point-method y y,Point-method y<- y<-,Point-method z z,Point-method z<- z<-,Point-method |
| SBML type "RateRule" | RateRule-class variable variable,RateRule-method variable<- variable<-,RateRule-method |
| SBML type "Reaction" | fast fast,Reaction-method fast<- fast<-,Reaction-method id,Reaction-method id<-,Reaction-method kineticLaw kineticLaw,Reaction-method kineticLaw<- kineticLaw<-,Reaction-method modifiers modifiers,Reaction-method modifiers<- modifiers<-,Reaction-method name,Reaction-method name<-,Reaction-method products products,Reaction-method products<- products<-,Reaction-method reactants reactants,Reaction-method reactants<- reactants<-,Reaction-method Reaction-class reversible reversible,Reaction-method reversible<- reversible<-,Reaction-method |
| SBML type "ReactionGlyph" | glyphCurve glyphCurve,ReactionGlyph-method glyphCurve<- glyphCurve<-,ReactionGlyph-method reaction reaction,ReactionGlyph-method reaction<- reaction<-,ReactionGlyph-method ReactionGlyph-class speciesReferenceGlyphs speciesReferenceGlyphs,ReactionGlyph-method speciesReferenceGlyphs<- speciesReferenceGlyphs<-,ReactionGlyph-method |
| SBML type "Rule" | math,Rule-method math<-,Rule-method Rule-class |
| SBML type "SBase" | annotation annotation,SBase-method annotation<- annotation<-,SBase-method cvTerms cvTerms,SBase-method cvTerms<- cvTerms<-,SBase-method metaId metaId,SBase-method metaId<- metaId<-,SBase-method notes notes,SBase-method notes<- notes<-,SBase-method SBase-class sboTerm sboTerm,SBase-method sboTerm<- sboTerm<-,SBase-method |
| Read in an SBML file (start here) | rsbml_read |
| SBML type "SBML" | as.character.SBML coerce coerce,SBML,graph-method coerce,SBML,SBMLDocument-method level level,SBML-method level<- level<-,SBML-method model model,SBML-method model<- model<-,SBML-method rsbml_check,SBML-method rsbml_doc rsbml_doc,SBML-method rsbml_graph,SBML-method rsbml_write rsbml_write,SBML-method rsbml_xml rsbml_xml,SBML-method SBML-class simulate,SBML-method ver ver,SBML-method ver<- ver<-,SBML-method |
| "SBMLDocument" from libsbml | as.character.SBMLDocument coerce,SBMLDocument,graph-method coerce,SBMLDocument,SBML-method rsbml_check rsbml_check,SBMLDocument-method rsbml_dom rsbml_dom,SBMLDocument-method rsbml_graph rsbml_graph,Model-method rsbml_graph,SBMLDocument-method rsbml_problems rsbml_problems,SBMLDocument-method rsbml_write,SBMLDocument-method rsbml_xml,SBMLDocument-method SBMLDocument-class simulate,SBMLDocument-method |
| SBMLProblem | .condition,SBMLProblem-method .throw,SBMLError-method .throw,SBMLFatal-method .throw,SBMLInfo-method .throw,SBMLWarning-method SBMLError-class SBMLFatal-class SBMLInfo-class SBMLProblem-class SBMLWarning-class show,SBMLProblem-method |
| SBMLProblems | .throw,SBMLProblems-method errors errors,SBMLProblems-method fatals fatals,SBMLProblems-method infos infos,SBMLProblems-method SBMLProblems-class warns warns,SBMLProblems-method |
| SBML type "SimpleSpeciesReference" | id,SimpleSpeciesReference-method id<-,SimpleSpeciesReference-method SimpleSpeciesReference-class species,SimpleSpeciesReference-method species<-,SimpleSpeciesReference-method |
| SOSDesign | reactions,SOSDesign-method reactions<-,SOSDesign-method SOSDesign-class |
| SOS Experiment | simulate simulate,SOSExperiment-method SOSExperiment-class |
| SOSProtocol | SOSProtocol-class |
| SOSResult | as.ts,SOSResult-method compartments,SOSResult-method parameters,SOSResult-method reactions,SOSResult-method SOSResult-class species,SOSResult-method |
| SOSSubject | SOSSubject-class |
| SBML type "Species" | boundaryCondition boundaryCondition,Species-method boundaryCondition<- boundaryCondition<-,Species-method charge charge,Species-method charge<- charge<-,Species-method compartment compartment,Species-method compartment<- compartment<-,Species-method constant constant,Species-method constant<- constant<-,Species-method hasOnlySubstanceUnits hasOnlySubstanceUnits,Species-method hasOnlySubstanceUnits<- hasOnlySubstanceUnits<-,Species-method id,Species-method id<-,Species-method initialAmount initialAmount,Species-method initialAmount<- initialAmount<-,Species-method initialConcentration initialConcentration,Species-method initialConcentration<- initialConcentration<-,Species-method name,Species-method name<-,Species-method spatialSizeUnits spatialSizeUnits,Species-method spatialSizeUnits<- spatialSizeUnits<-,Species-method Species-class substanceUnits,Species-method substanceUnits<-,Species-method units,Species-method units<-,Species-method |
| SBML type "SpeciesConcentrationRule" | species,SpeciesConcentrationRule-method species<-,SpeciesConcentrationRule-method SpeciesConcentrationRule-class |
| SBML type "SpeciesGlyph" | species species,SpeciesGlyph-method species<- species<-,SpeciesGlyph-method SpeciesGlyph-class |
| SBML type "SpeciesReference" | SpeciesReference-class stoichiometry stoichiometry,SpeciesReference-method stoichiometry<- stoichiometry<-,SpeciesReference-method stoichiometryMath stoichiometryMath,SpeciesReference-method stoichiometryMath<- stoichiometryMath<-,SpeciesReference-method |
| SBML type "SpeciesReferenceGlyph" | glyphCurve,SpeciesReferenceGlyph-method glyphCurve<-,SpeciesReferenceGlyph-method role role,SpeciesReferenceGlyph-method role<- role<-,SpeciesReferenceGlyph-method speciesGlyph speciesGlyph,SpeciesReferenceGlyph-method speciesGlyph<- speciesGlyph<-,SpeciesReferenceGlyph-method speciesReference speciesReference,SpeciesReferenceGlyph-method speciesReference<- speciesReference<-,SpeciesReferenceGlyph-method SpeciesReferenceGlyph-class |
| SBML Type "SpeciesType" | id,SpeciesType-method id<-,SpeciesType-method name,SpeciesType-method name<-,SpeciesType-method SpeciesType-class |
| SBML type "StoichiometryMath" | math,StoichiometryMath-method math<-,StoichiometryMath-method OptionalStoichiometryMath-class StoichiometryMath-class |
| SBML type "TextGlyph" | graphicalObject graphicalObject,TextGlyph-method graphicalObject<- graphicalObject<-,TextGlyph-method originOfText originOfText,TextGlyph-method originOfText<- originOfText<-,TextGlyph-method text text,TextGlyph-method text<- text<-,TextGlyph-method TextGlyph-class |
| SBML Type "Trigger" | math,Trigger-method math<-,Trigger-method Trigger-class |
| SBML type "Unit" | exponent exponent,Unit-method exponent<- exponent<-,Unit-method kind kind,Unit-method kind<- kind<-,Unit-method multiplier multiplier,Unit-method multiplier<- multiplier<-,Unit-method offset offset,Unit-method offset<- offset<-,Unit-method Unit-class unitScale unitScale,Unit-method unitScale<- unitScale<-,Unit-method |
| SBML type "UnitDefinition" | id id,UnitDefinition-method id<- id<-,UnitDefinition-method name name,UnitDefinition-method name<- name<-,UnitDefinition-method UnitDefinition-class units units,UnitDefinition-method units<- units<-,UnitDefinition-method |
