slim.types.treatments module

class slim.types.treatments.ChemicalTreatment(payload)

Bases: slim.types.treatments.TreatmentParams

Trait for all chemical treatments

class slim.types.treatments.CleanerFish(payload)

Bases: slim.types.treatments.TreatmentParams

Cleaner Fish (lump/wrasse) treatment.

delay(_)

Delay before treatment should have a noticeable effect

get_lice_treatment_mortality_rate(_temperature, cage: Cage) → GenoTreatmentDistrib

Calculate the mortality rates of this treatment

Parameters

• temperature – the water temperature

• cage – the calling cage

Returns

the mortality rates, arranged by geno.

name = 'Cleaner Fish'

susceptible_stages: List[str] = ['L4', 'L5m', 'L5f']

class slim.types.treatments.EMB(payload)

Bases: slim.types.treatments.ChemicalTreatment

Emamectin Benzoate

delay(average_temperature: float)

Delay before treatment should have a noticeable effect

get_lice_treatment_mortality_rate(_temperature=None, _cage=None)

Calculate the mortality rates of this treatment

Parameters

• temperature – the water temperature

• cage – the calling cage

Returns

the mortality rates, arranged by geno.

name = 'EMB'

susceptible_stages: List[str] = ['L3', 'L4', 'L5m', 'L5f']

class slim.types.treatments.GeneticMechanism(value)

Bases: enum.Enum

Genetic mechanism to be used when generating egg genotypes

DISCRETE = 1

MATERNAL = 2

class slim.types.treatments.HeterozygousResistance(value)

Bases: enum.Enum

Resistance in a monogenic, heterozygous setting.

DOMINANT = 1

INCOMPLETELY_DOMINANT = 2

RECESSIVE = 3

class slim.types.treatments.ThermalTreatment(payload)

Bases: slim.types.treatments.TreatmentParams

Trait for all thermal-based treatments

class slim.types.treatments.Thermolicer(payload)

Bases: slim.types.treatments.ThermalTreatment

delay(_)

Delay before treatment should have a noticeable effect

get_lice_treatment_mortality_rate(temperature: float, _cage=None) → Dict[str, GenoTreatmentValue]

Calculate the mortality rates of this treatment

Parameters

• temperature – the water temperature

• cage – the calling cage

Returns

the mortality rates, arranged by geno.

name = 'Thermolicer'

susceptible_stages: List[str] = ['L3', 'L4', 'L5m', 'L5f']

class slim.types.treatments.Treatment(value)

Bases: enum.Enum

A stub for treatment types

CLEANERFISH = 2

EMB = 0

THERMOLICER = 1

class slim.types.treatments.TreatmentParams(payload)

Bases: abc.ABC

Abstract class for all the treatments

abstract delay(average_temperature: float)

Delay before treatment should have a noticeable effect

static get_allele_heterozygous_trait(gene: str, alleles: str)

Get the allele heterozygous type

get_fish_mortality_occurrences(temperature: float, fish_mass: float, num_fish: float, efficacy_window: float, mortality_events: int)

Get the number of fish that die due to treatment

Parameters

• temperature – the temperature of the cage

• num_fish – the number of fish

• fish_mass – the average fish mass (in grams)

• efficacy_window – the length of the efficacy window

• mortality_events – the number of fish mortality events to subtract from

abstract get_lice_treatment_mortality_rate(temperature: float, cage: Cage) → GenoTreatmentDistrib

Calculate the mortality rates of this treatment

Parameters

• temperature – the water temperature

• cage – the calling cage

Returns

the mortality rates, arranged by geno.

name = ''

static parse_pheno_resistance(pheno_resistance_dict: dict) → Dict[HeterozygousResistance, float]

susceptible_stages: List[str] = []

slim.types.treatments.treatment_to_class(treatment: Treatment)

Get the right treatment class

Parameters

treatment – a treatment tag

Returns

the correct treatment class