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Changing serialized demographics parameters

Not every parameter can be changed after the creation of serialized files. The following overview is intended as high-level guidance for what changes can and cannot be made.

See also: Serializing populations, Serialized population file format, Working with serialized data.

Population-level parameters

Cannot be changed

  • Age_Initialization_Distribution_Type
  • Birth_Rate_Boxcar_Forcing
  • Birth_Rate_Dependence
  • Birth_Rate_Time_Dependence
  • Birth_Rate_Sinusoidal
  • Death_Rate_Dependence
  • Enable_Birth
  • Enable_Demographics_Risk
  • Enable_Initial_Prevalence
  • Enable_Natural_Mortality
  • Enable_Vital_Dynamics
  • Population_Scale_Type
  • x_Base_Population
  • x_Birth
  • x_Other_Mortality

Can be changed

  • Enable_Disease_Mortality

NodeAttributes

Cannot be changed

  • InitialPopulation
  • InitialVectorsPerSpecies
  • LarvalHabitatMultiplier

Note

We discourage use of LarvalHabitatMultiplier due to its deserialization issues.

LarvalHabitatMultiplier is read but not used at deserialization time. Both LarvalHabitatMultiplier and x_Temporary_Larval_Habitat are applied when a habitat is created at the beginning of a simulation. When the habitat is serialized, it is stored with the results of these multipliers already applied.

  • If Serialization_Mask_Node_Read = 0, both LarvalHabitatMultiplier and x_Temporary_Larval_Habitat are ignored and the values from the serialized file are used as-is.
  • If Serialization_Mask_Node_Read = 16, new habitats are created from configuration parameters and the serialized habitat data is ignored. The x_Temporary_Larval_Habitat setting is used to adjust the new habitat, but it is a known issue that LarvalHabitatMultiplier is not also applied in this case.

Can be changed

  • Altitude
  • BirthRate
  • Latitude
  • Longitude
  • NodePropertyValues
  • Airport
  • Region
  • Seaport

IndividualAttributes

Cannot be changed

  • AgeDistributionFlag, AgeDistribution1, AgeDistribution2
  • SusceptibilityDistributionFlag, SusceptibilityDistribution1, SusceptibilityDistribution2
  • PrevalenceDistributionFlag, PrevalenceDistribution1, PrevalenceDistribution2

Can be changed (with dependencies)

  • FertilityDistribution: If Birth_Rate_Dependence was serialized with the value INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR, then you can change this distribution.
  • MigrationHeterogeneityDistributionFlag, MigrationHeterogeneityDistribution1, MigrationHeterogeneityDistribution2: These values can be changed if Enable_Migration_Heterogeneity is set to 1 in config.json.
  • MortalityDistributionFlag, MortalityDistribution1, MortalityDistribution2: These can be changed if Enable_Natural_Mortality was serialized as true/on. Which distribution is used depends on the serialized value of Death_Rate_Dependence.
  • RiskDistributionFlag, RiskDistribution1, RiskDistribution2: These can be changed if Enable_Demographics_Risk was serialized as true/on, however the new parameters will only be applied to newborns. Existing individuals will retain their risk values from the serialized file.
  • InnateImmuneDistributionFlag, InnateImmuneDistribution1, InnateImmuneDistribution2: These can be changed if Innate_Immune_Variation_Type was serialized as a value other than NONE, however the new parameters will only be applied to newborns. Existing individuals will retain their innate immune values from the serialized file.

IndividualProperties

Cannot be changed

  • Remove value from existing key: You cannot remove an existing value from a key if the serialized population contains individuals with this value.

Can be changed

  • Add new value to existing key
  • Change Initial_Distribution: You can change the Initial_Distribution to change the likelihood that a newborn will have a specific IndividualProperties value. It will not change how IndividualProperties values are distributed in the serialized population.
  • Add/Remove IP/Key: It is best practice to not add or remove IndividualProperties keys unless you also update the serialized file. However, if you remove a value and do not reference it in the simulation running from the serialized file, the simulation may run without errors. If you add values and don't add them to individuals in the serialized file, you should not reference them until all individuals from the serialized file have died.