API for the animal_traits module

The models.animal.animal_traits module contains classes that organizes animal traits into enumerations for use by the Functional Group class in the functional_group module.

Classes:

DevelopmentStatus(*values)	Enumeration for development status.
DevelopmentType(*values)	Enumeration for development types.
DietType(*values)	Enumeration for diet resource types.
ExcretionType(*values)	Enumeration for excretion type.
MetabolicType(*values)	Enumeration for metabolic types.
MigrationType(*values)	Enumeration for external migration trait.
ReproductiveEnvironment(*values)	Where and how reproduction happens: aquatic vs terrestrial.
ReproductiveType(*values)	Enumeration for reproductive types.
TaxaType(*values)	Enumeration for taxa types.
VerticalOccupancy(*values)	Enumeration for vertical occupancy trait.

class virtual_ecosystem.models.animal.animal_traits.DevelopmentStatus(*values)

Enumeration for development status.

class virtual_ecosystem.models.animal.animal_traits.DevelopmentType(*values)

Enumeration for development types.

class virtual_ecosystem.models.animal.animal_traits.DietType(*values)

Enumeration for diet resource types.

TODO: refine categorizations

Methods:

coarse_category()	Classify the detailed diet into a broad trophic category.
count_dietary_categories()	Count the number of distinct dietary categories in this flag set.
parse(diet_string)	Parse a string of underscore-separated diet terms into a DietType flag.

coarse_category() → DietType

Classify the detailed diet into a broad trophic category.

This method examines the components of the current DietType flag and returns one of the three broad trophic categories: HERBIVORE, CARNIVORE, or OMNIVORE. These categories are defined as composite flags within the DietType enumeration.

• Returns OMNIVORE if the diet includes both plant/fungal and animal-derived

  resources.

• Returns CARNIVORE if the diet includes only animal-derived resources.

• Returns HERBIVORE for all other combinations, including plant-only or empty

  diets.

Returns:

A diet type flag representing the coarse category.

Return type:

DietType

count_dietary_categories() → int

Count the number of distinct dietary categories in this flag set.

Returns:

An integer of the number of different type types possessed by the functional group.

classmethod parse(diet_string: str) → DietType

Parse a string of underscore-separated diet terms into a DietType flag.

This method takes a lowercase string such as ‘fruit_foliage_fish’ and converts it into a combined DietType flag using bitwise OR logic. This allows diet traits to be specified flexibly in configuration files or CSV inputs.

Parameters:

diet_string – A lowercase underscore-separated string representing one or more diet components (e.g., ‘foliage’, ‘fruit_fish’, ‘nectar_fungus’).

Returns:

A DietType flag representing the combined diet traits.

class virtual_ecosystem.models.animal.animal_traits.ExcretionType(*values)

Enumeration for excretion type.

class virtual_ecosystem.models.animal.animal_traits.MetabolicType(*values)

Enumeration for metabolic types.

class virtual_ecosystem.models.animal.animal_traits.MigrationType(*values)

Enumeration for external migration trait.

class virtual_ecosystem.models.animal.animal_traits.ReproductiveEnvironment(*values)

Where and how reproduction happens: aquatic vs terrestrial.

class virtual_ecosystem.models.animal.animal_traits.ReproductiveType(*values)

Enumeration for reproductive types.

class virtual_ecosystem.models.animal.animal_traits.TaxaType(*values)

Enumeration for taxa types.

class virtual_ecosystem.models.animal.animal_traits.VerticalOccupancy(*values)

Enumeration for vertical occupancy trait.

Methods:

parse(occupancy)

Convert a string like 'soil_ground' into a VerticalOccupancy flag.

classmethod parse(occupancy: str) → VerticalOccupancy

Convert a string like ‘soil_ground’ into a VerticalOccupancy flag.

This method parses a lowercase underscore-separated string into a combined VerticalOccupancy flag using bitwise OR logic. It enables easy construction of multi-layer occupancy traits from a single string field, such as those found in CSV imports or config files.

Parameters:

occupancy – A string representing one or more vertical layers, such as ‘soil’, ‘ground_canopy’, or ‘soil_ground_canopy’.

Returns:

A VerticalOccupancy flag representing the combined vertical occupancy.