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