Genetics Module

It defines the genetic architecture of each species, specifying the number of loci and alleles per trait, the recombination parameters, and the configuration of modules and traits that determine how genetic variation influences phenotypic traits in the simulation.

Main Properties

Properties:

Name	Type	Description
numberOfLociPerTrait	integer	Number of loci defining each trait. Minimum value: 0.
numberOfAllelesPerLocus	integer	Number of alleles per locus. Minimum value: 0.
numberOfChiasmasPerChromosome	integer	Number of chiasmas per chromosome. Minimum value: 0.
modules	object	Defines the modular genetic organization.
modifyAlleles	array[object]	Describes allele modification events applied to certain loci or traits.
traits	object	Describes the genetic definition of traits and their temperature dependence.

Object modules

Properties:

Name	Type	Description
traitsPerModule	integer	Number of traits per genetic module. Minimum value: 0.
correlationCoefficientRhoPerModule	array[number]	Correlation coefficients (ρ) describing genetic linkage among traits within a module.

Object modifyAlleles

Properties of each element:

Name	Type	Description
affectedAlleles	number	Identifier of the affected allele.
timesAlleles	number	Multiplicative factor applied to the alleles. Minimum: 0.0.
affectedLocus	array[number]	List of locus indices (between 0 and 1) affected by the modification.
affectedTraits	array[object]	List of trait elements influenced by the modification.

Object affectedTraits

Properties:

Name	Type	Description
trait	string	Name of the trait affected.
element	string (enum)	Component of the trait affected. Possible values: - value - activationEnergy - energyDecay - temperatureOptimal - temperatureRef

Object traits

Properties:

Name	Type	Description
individualLevelTraitsOrder	array[object]	Defines the order and structure of individual-level traits.
definition	object	Contains the complete definitions of each trait type.

Object individualLevelTraitsOrder

Properties of each element:

Name	Type	Description
trait	string	Name of the individual-level trait.
element	string (enum)	Component of the trait. Possible values: - value - activationEnergy - energyDecay - temperatureOptimal - temperatureRef

Object definition

Contains the definition of the different types of traits.

Properties:

Name	Type	Description
base	object	A diverse set of traits with different functionalities.
decisions	object	Traits of weights that influence decisions.
probabilityDensityFunction	object	Traits of the coefficients of probability density functions.
cellValue	object	Weights that influence the value of cells.

Object base

Within this section, three types of traits are defined depending on the definition of their temperature subsection.

The traits without temperature definition are as follows:

• energy_tank

The traits with temperature size rule as their temperature definition are as follows:

• lengthAtMaturation

The traits with dells as the temperature definition are as follows:

• growth

• eggDevTime

• factorEggMass

• assim

• voracityProportion

• met_rate

• shock_resistance

• actE_met

• memoryDepth

• coeffMassForScopeRadius

• scaleMassForScopeRadius

• coeffMassForInteractionRadius

• scaleMassForInteractionRadius

• coeffMassForSearchRadius

• scaleMassForSearchRadius

• coeffMassForSpeed

• scaleMassForSpeed

• devTime

• pupaPeriodTime

• longevitySinceMaturation

• dummy

• eggFertility

Object decisions

Properties:

Name	Type	Description
escapeProbabilityWeight	object	Factors influencing the probability of escape.
predationProbabilityWeight	object	Factors influencing the probability of predation.
edibilityValueWeight	object	Factors that influence edibility value.
preferences	object	Factors influencing preferences.

Object escapeProbabilityWeight

The weights defined in this section use traits with dells as the temperature definition.

The weights are as follows:

• Pvelocity

• PattackDistance

Object predationProbabilityWeight

The weights defined in this section use traits with dells as the temperature definition.

The weights are as follows:

• Preach

• Ppdf

• PvorPred

Object edibilityValueWeight

The weights defined in this section use traits with dells as the temperature definition.

The weights are as follows:

• Pp

Object preferences

The weights defined in this section use traits with dells as the temperature definition.

The weights are as follows:

• experienceInfluenceWithEdibles

Object probabilityDensityFunction

The coefficients defined in this section use traits with dells as the temperature definition.

The coefficients are as follows:

• muForPDF

• sigmaForPDF

Object cellValue

The weights defined in this section use traits with dells as the temperature definition.

The weights are as follows:

• cellEvaluationBiomass

• cellEvaluationProConspecific

• conspecificWeight

Object <trait-non-temperature-section>

Properties:

Name	Type	Description
definitionType	string (enum)	Type of definition. Possible values: - SpeciesLevel - IndividualLevel
speciesLevelParams	object	Species-level parameters.
individualLevelParams	object	Individual-level parameters.

Object speciesLevelParams

Properties:

Name	Type	Description
value	number	Fixed species-level trait value.

Object individualLevelParams

Properties:

Name	Type	Description
limits	object	Limits for individual-level trait values.
ranges	object	Ranges for individual-level trait values.
restrictValue	number	Restriction factor for individual-level trait values (between 0.0 and 1.0).

Object limits

Properties:

Name	Type	Description
min	number	Minimum limit for individual-level trait values. Minimum value: 0.0.
max	number	Maximum limit for individual-level trait values. Minimum value: 0.0.

Object ranges

Properties:

Name	Type	Description
min	number	Minimum range for individual-level trait values.
max	number	Maximum range for individual-level trait values.

Object <trait-temperature-size-rule-section>

Properties:

Name	Type	Description
definitionType	string (enum)	Type of definition. Possible values: - SpeciesLevel - IndividualLevel
speciesLevelParams	object	Species-level parameters.
individualLevelParams	object	Individual-level parameters.
temperature	object	Temperature dependence parameters.

Object temperature of <trait-temperature-size-rule-section>

Properties:

Name	Type	Description
dependent	boolean	Indicates if the trait is temperature-dependent.
tempSizeRuleVector	array[object]	Array defining the temperature-size rule.

Object tempSizeRuleVector

Properties of each element:

Name	Type	Description
temperature	number	Temperature value (greater than 0.0).
dryMass	number	Dry mass value (greater than 0.0).

Object <trait-dells-section>

Properties:

Name	Type	Description
definitionType	string (enum)	Type of definition. Possible values: - SpeciesLevel - IndividualLevel
speciesLevelParams	object	Species-level parameters.
individualLevelParams	object	Individual-level parameters.
temperature	object	Temperature dependence parameters.

Object temperature of <trait-dells-section>

Properties:

Name	Type	Description
dependent	boolean	Indicates if the trait is temperature-dependent.
activationEnergy	<trait-non-temperature-section>	Temperature activation energy parameters.
energyDecay	<trait-non-temperature-section>	Temperature energy decay parameters.
temperatureOptimal	<trait-non-temperature-section>	Temperature optimal parameters.
temperatureRef	<trait-non-temperature-section>	Reference temperature parameters.

Hierarchical Summary

genetics
├── numberOfLociPerTrait: integer ≥ 0
├── numberOfAllelesPerLocus: integer ≥ 0
├── numberOfChiasmasPerChromosome: integer ≥ 0
├── modules:
│   ├── traitsPerModule: integer ≥ 0
│   └── correlationCoefficientRhoPerModule: array[number]
├── modifyAlleles:
│   ├── affectedAlleles: number
│   ├── timesAlleles: number ≥ 0.0
│   ├── affectedLocus: array[number 0.0–1.0]
│   └── affectedTraits:
│       ├── trait: string
│       └── element: enum [value, activationEnergy, energyDecay, temperatureOptimal, temperatureRef]
└── traits:
    ├── individualLevelTraitsOrder:
    │   ├── trait: string
    │   └── element: enum [value, activationEnergy, energyDecay, temperatureOptimal, temperatureRef]
    └── definition:
        ├── base
        │   ├── <enum-base-nonTemperatureTraits>
        │   │   └── <trait-non-temperature-section>
        │   ├── <enum-base-temperatureSizeRuleTraits>
        │   │   └── <trait-temperature-size-rule-section>
        │   └── <enum-base-dellsTraits>
        │       └── <trait-dells-section>
        ├── decisions
        │   ├── escapeProbabilityWeight
        │   │   └── <enum-escapeProbabilityWeight-dellsTraits>
        │   │       └── <trait-dells-section>
        │   ├── predationProbabilityWeight
        │   │   └── <enum-predationProbabilityWeight-dellsTraits>
        │   │       └── <trait-dells-section>
        │   ├── edibilityValueWeight
        │   │   └── <enum-edibilityValueWeight-dellsTraits>
        │   │       └── <trait-dells-section>
        │   └── preferences
        │       └── <enum-preferences-dellsTraits>
        │           └── <trait-dells-section>
        ├── probabilityDensityFunction
        │   └── <enum-probabilityDensityFunction-dellsTraits>
        │       └── <trait-dells-section>
        └── cellValue
            └── <enum-cellValue-dellsTraits>
                └── <trait-dells-section>

<trait-non-temperature-section>
├── definitionType: enum [SpeciesLevel, IndividualLevel]
├── speciesLevelParams
│   └── value: number
└── individualLevelParams
    ├── limits
    │   ├── min: number  ≥ 0.0
    │   └── max: number  ≥ 0.0
    ├── ranges
    │   ├── min: number
    │   └── max: number
    └── restrictValue: number [0.0 - 1.0]

<trait-temperature-size-rule-section>
├── definitionType: enum [SpeciesLevel, IndividualLevel]
├── speciesLevelParams
│   └── value: number
├── individualLevelParams
│   ├── limits
│   │   ├── min: number  ≥ 0.0
│   │   └── max: number  ≥ 0.0
│   ├── ranges
│   │   ├── min: number
│   │   └── max: number
│   └── restrictValue: number [0.0 - 1.0]
└── temperature
    ├── dependent: boolean
    └── tempSizeRuleVector: array[object]
        ├── temperature: number > 0.0
        └── dryMass: number > 0.0

<trait-dells-section>
├── definitionType: enum [SpeciesLevel, IndividualLevel]
├── speciesLevelParams
│   └── value: number
├── individualLevelParams
│   ├── limits
│   │   ├── min: number  ≥ 0.0
│   │   └── max: number  ≥ 0.0
│   ├── ranges
│   │   ├── min: number
│   │   └── max: number
│   └── restrictValue: number [0.0 - 1.0]
└── temperature
    ├── dependent: boolean
    ├── activationEnergy
    │   └── <trait-non-temperature-section>
    ├── energyDecay
    │   └── <trait-non-temperature-section>
    ├── temperatureOptimal
    │   └── <trait-non-temperature-section>
    └── temperatureRef
        └── <trait-non-temperature-section>