Configuration

Runtime configuration schema

The configuration file config_data/config.json provides a number of modelling parameters that are supposedly invariant across experiments. Those values have been extracted from available literature and documented wherever possible. Here we provide an autogenerated list of parameters.

The schema is used for both validation and parsing purposes.

RuntimeConfig

http://slim-project/config.json.schema
type	object
properties
seed	Global seed to use in the simulations
	type	integer
stage_age_evolutions	Stage-age average evolution times (in days)
	type	object
	properties
	L1	type	number
	L2	type	number
	L3	type	number
	L4	type	number
	L5f	type	number
delta_p	Weibull power transformation constant for each development stage
	type	object
	properties
	L0	type	number
	L1	type	number
	L3	type	number
	L4	type	number
delta_s	Weibull shape transformation constant for each development stage
	type	object
	properties
	L1	type	number
	L3	type	number
	L4	type	number
delta_m10	10 °C median development time
	type	object
	properties
	L0	type	number
	L1	type	number
	L3	type	number
	L4	type	number
lice_development_rates	Lice development rates from the ith stage to the next
	properties
	L1	type	number
	L	type	number
	L4	type	number
infection_main_delta	Infection expectation
	type	number
infection_weight_delta	Infection regression coefficient
	type	number
delta_expectation_weight_log	Log-expectation of fish weight
	type	number
fish_mortality_center	Fish mortality sigmoid center
	type	number
fish_mortality_k	Fish mortality sigmoid steepness
	type	number
background_lice_mortality_rates	Background lice mortality rates per stage
	type	object
	properties
	L1	Aldrin et al., 2017
		type	number
	L2	Tucker et al., 2002
		type	number
	L3	Stien et al., 2005
		type	number
	L4	Stien et al., 2005
		type	number
	L5f	Stien et al., 2005
		type	number
reproduction_eggs_first_extruded	Initial number of viable eggs after the first extrusion
	type	number
reproduction_age_dependence	Exponential coefficient on viable eggs depending on age
	type	number
dam_unavailability	Female unavailability time after mating (in days)
	type	integer
smolt_mass_params	Sigmoid parameters that pilot the average smolt-to-adult average weight development
	type	object
	properties
	max_mass	type	number
	skewness	type	number
	x_shift	type	number
initial_genetic_ratios	Genetic ratios of lice population
	type	object
reservoir_offspring_integration_ratio	The ratio of offspring coming being expelled from the external pressure to make available in the reservoir
	type	number
reservoir_offspring_average	The length of the rolling average to consider in the external pressure calculation
geno_mutation_rate	Mutation rate, as in number of individual mutation events that can happen out of the number of offsprings. For example, 1e-5 is one mutation every 10,000 extruded eggs
	type	number
genetic_mechanism	Genetic mechanism to use
male_detachment_rate	Rate at which an adult male detaches from a dying fish and survives
	type	number
treatments	Parameters related to specific treatments
	type	array
	items	type	object
		properties
		treatment_name	The name of the treatment
			type	string
		treatment_type	The type of treatment
			enum	chemical, thermal, mechanical, cleanerfish
		pheno_resistance	Lookup table to translate between genotype.
			type	object
		quadratic_fish_mortality_coeffs	Fitted quadratic regression coefficients from Overton et al.
			type	array
			items	type	number
additionalProperties	False
minProperties	22

Environment-specific configuration schema

Let us consider the Fyne environment located in config_data/Fyne for starters. The organisation-specific configuration is thus inside params.json. Similarly to the runtime configuration, we provide a well-documented schema.

FarmConfig

http://slim-project/config.json.schema
type	object
properties
name	Organisation name
	type	string
start_date	Simulation start date
	type	string
end_date	Simulation end date
	type	string
ext_pressure	Sealice per day per cage/farm arriving from wildlife. Note that this value has been determined experimentally in the original code.
	type	integer
monthly_cost	Fixed infrastructure cost (per 28 activity day)
	type	number
gain_per_kg	Selling rate for fish kg (in GBP)
	type	number
infection_discount	Negative cost of infection, defined as lice / fish kg.
	type	number
genetic_ratios	The initial genotype ratio distribution
	type	object
genetic_learning_rate	Dirichlet learning rate
	type	number
agg_rate_suggested_threshold	The allowed aggregation rate before the organisation asks for a treatment
	type	number
agg_rate_enforcement_threshold	The allowed aggregation rate before the regulator asks for a treatment.
	type	number
agg_rate_enforcement_strikes	The number of times before a regulator’s lice count excess is no longer tolerated.
	type	number
treatment_strategy	Which treatment strategy to apply. Used during standalone simulation
	type	string
farms_per_process	Number of farms per Ray actor during batch updates. Defaults to nfarms (i.e. effectively disables multiprocessing)
	type	number
farms	FarmConfig
	Farm-specific configuration
	type	array
	items	type	object
		properties
		name	Farm name
			type	string
		ncages	Number of cages on the farm
			type	integer
		location	Location of the farm (in northing and easthing)
			type	array
			items	type	number
				maxLength	2
				minLength	2
		num_fish	Starting number of fish. We assume this to be constant across all cages
			type	integer
		start_date	Start date of simulation of the farm
			type	string
		cages_start_dates	Start dates for individual cages. This is discouraged
			type	array
		treatment_types	Available treatments at this site
			type	array
		treatment_dates	Treatment dates for each cage. If not provided the farm will apply treatments only when asked to, or depending on the chosen strategy
			type	array
		max_num_treatments	Maximum number of treatments allowed within one year
			type	integer
		sampling_spacing	Time distance (in days) between fish samplings
			type	integer
		defection_proba	Probability to defect and not apply treatment contemporarily with the other farms
			type	number
		additionalProperties	False
additionalProperties	False