Welcome to the pyRBM documentation!

pyRBM is a Python library to enable the construction and simulation of rules based models.

Check out the Usage section for further information, including how to Installation the project.

Note

This project is under active development.

Contents

• pyRBM package
  • Subpackages
    • pyRBM.Analysis package
      • Module contents
    • pyRBM.Build package
      • Submodules
      • pyRBM.Build.Classes module
        • Classes
          • Classes.addClass()
          • Classes.returnBuiltInClasses()
          • Classes.returnClassDict()
      • pyRBM.Build.Compartment module
      • pyRBM.Build.ProcessDescriptionFiles module
        • LoadedCompartments
          • LoadedCompartments.loadCompartmentsFromJSONFile()
      • pyRBM.Build.RuleMatching module
        • isSubtypeOf()
        • obtainPropensity()
        • obtainStochiometry()
        • returnMatchedRulesDict()
        • returnRuleMatchingIndices()
      • pyRBM.Build.RuleTemplates module
        • ExitEntranceRule
        • SingleLocationProductionRule
        • SingleLocationRule
        • TransportRule
      • pyRBM.Build.Rules module
        • Rule
          • Rule.addLinearStoichiomety()
          • Rule.addSimplePropensityFunction()
          • Rule.addWaitTimeDistribution()
          • Rule.checkRuleDefinition()
          • Rule.returnRuleDict()
          • Rule.validateFormula()
        • Rules
          • Rules.addRule()
          • Rules.addRules()
          • Rules.removeTypeRequirement()
          • Rules.returnMetaRuleDict()
        • isNonDefaultTargetArray()
        • returnSympyClassVarsDict()
      • pyRBM.Build.Utils module
        • createArgsDict()
        • createEuclideanDistanceMatrix()
        • haversine()
      • Module contents
    • pyRBM.Core package
      • Submodules
      • pyRBM.Core.Cache module
        • ModelPaths
          • ModelPaths.compartment_path
          • ModelPaths.classes_path
          • ModelPaths.matched_rules_path
          • ModelPaths.metarule_path
          • ModelPaths.save_model_folder
          • ModelPaths.classes_path
          • ModelPaths.compartments_path
          • ModelPaths.matched_rules_path
          • ModelPaths.metarules_path
        • loadClasses()
        • loadCompartments()
        • loadMatchedRules()
        • processFilenameOrDict()
        • readDictFromJSON()
        • writeDictToJSON()
      • pyRBM.Core.Interfaces module
        • ICompartment
          • ICompartment.checkConditionDict()
          • ICompartment.setConstants()
          • ICompartment.setInitialConditions()
      • pyRBM.Core.Model module
      • pyRBM.Core.Plotting module
        • FrequencyBarChart
          • FrequencyBarChart.animate()
        • SolverDataPlotting
      • pyRBM.Core.StringUtilities module
        • parseVarName()
        • replaceVarName()
      • Module contents
    • pyRBM.Examples package
      • Submodules
      • pyRBM.Examples.Epidemology module
      • Module contents
    • pyRBM.Simulation package
      • Submodules
      • pyRBM.Simulation.Compartment module
        • Compartment
          • Compartment.reset()
          • Compartment.updateCompartmentValues()
      • pyRBM.Simulation.EventQueue module
      • pyRBM.Simulation.Rule module
        • Rule
          • Rule.partial_evaluation()
          • Rule.returnEventRate()
          • Rule.returnPropensity()
          • Rule.triggerAttemptedRuleChange()
      • pyRBM.Simulation.RuleChain module
        • returnOneStepRuleUpdates()
      • pyRBM.Simulation.Solvers module
      • pyRBM.Simulation.State module
        • ModelState
          • ModelState.changeDate()
          • ModelState.changeModelClassValue()
          • ModelState.changeMonth()
          • ModelState.processUpdate()
          • ModelState.reset()
          • ModelState.resetClassVars()
          • ModelState.returnChangedVars()
          • ModelState.returnModelClasses()
          • ModelState.returnModelClassesValues()
      • pyRBM.Simulation.StaticSeries module
      • pyRBM.Simulation.Trajectory module
        • Trajectory
          • Trajectory.addEntry()
          • Trajectory.plotAllClassesOverTime()
      • pyRBM.Simulation.WaitTimeDistributions module
        • Distribution
          • Distribution.checkParams()
          • Distribution.checkParamsLaplace()
          • Distribution.isLaplaceGillespieCompatible()
          • Distribution.isNMGACompatible()
          • Distribution.returnLaplaceRate()
          • Distribution.returnRandomLaplaceFunc()
          • Distribution.returnRandomNMGAFunc()
          • Distribution.returnRate()
          • Distribution.returnStringRepr()
        • DistributionFactory
          • DistributionFactory.createDistribution()
        • DoublePowerLawDistribution
          • DoublePowerLawDistribution.checkParamsLaplace()
          • DoublePowerLawDistribution.returnRandomLaplaceFunc()
        • ExponentialDistribution
          • ExponentialDistribution.checkParamsLaplace()
          • ExponentialDistribution.returnRandomLaplaceFunc()
        • GammaDistribution
          • GammaDistribution.checkParamsLaplace()
          • GammaDistribution.returnRandomLaplaceFunc()
        • GammaPowerLawDistribution
          • GammaPowerLawDistribution.checkParamsLaplace()
          • GammaPowerLawDistribution.returnRandomLaplaceFunc()
        • MittagLefflerDistribution
          • MittagLefflerDistribution.tba()
        • ShiftedGammaPowerLawDistribution
          • ShiftedGammaPowerLawDistribution.checkParamsLaplace()
          • ShiftedGammaPowerLawDistribution.returnRandomLaplaceFunc()
        • UniformPowerLawDistribution
          • UniformPowerLawDistribution.checkParamsLaplace()
          • UniformPowerLawDistribution.returnRandomLaplaceFunc()
        • processDistributionString()
      • Module contents
  • Module contents