2.2. Entities, state variables, and scales

2.2.1. Entities

• The EnergyBudget entity describes the parameters and the bioenergetic processes of BIOEN-OSMOSE.

• The TempFunction entity describes the parameters and the temperature-related processes of BIOEN-OSMOSE.

• The OxygenFunction entity describes the parameters and the oxygen-related processes of BIOEN-OSMOSE.

2.2.2. State variables

2.2.2.1. EnergyBudget

The EnergyBudget entity contains the following state variables:

Table 2.1 EnergyBudget state variables in BIOEN-OSMOSE

Variable	Description	Type	Units
c_m	Array of mass-specific maintenance rate (one for each species)	float[]	\(g.year^{-1}\)
m0	Array of intercept of a deterministic linear maturation reaction norm (one for each species)	float[]	\(cm\)
m1	Array of slope of a deterministic linear maturation reaction norm (one for each species)	float[]	\(cm.year^{-1}\)
eta	Array of energy density ratio between somatic and gonadic tissue	float[]
temp_function	Temperature function entity	TemperatureFunction
oxygen_function	Oxygen function entity	OxygenFunction
r	Array of gonado-somatic index of school
larvaePredationRateBioen	Array of multiplication factor for ingestion of larva individuals	float[]
assimilation	Array of assimilation efficiency	float[]

2.2.2.2. TempFunction

The TempFunction entity contains the following state variables:

Table 2.2 TempFunction state variables in BIOEN-OSMOSE

Variable	Description	Type	Units
e_M	Array of increasing activation energy of the energy mobilization temperature function	float[]	J
e_D	Array of declining activation energy of the energy mobilization temperature function	float[]	J
Tp	Array of temperature of peak value in energy mobilization	float[]	C
e_m	Activation energy of the maintenance temperature function	float[]	J
temperature_input	Temperature input dataset	PhysicalData
isPhiTActivated	True if the mobilized energy should depend on temperature	bool, default is true

2.2.2.3. OxygenFunction

The OxygenFunction entity contains the following state variables:

Table 2.3 OxygenFunction state variables in BIOEN-OSMOSE

Variable	Description	Type	Units
c1	Array of asymptote of energy mobilization dose-response function to dissolved oxygen saturation	float[]
c2	Array of slope of energy mobilization dose-response function to dissolved oxygen saturation	float[]
o2_input	Oxygen dataset	PhysicalData
isFO2Activated	True if the oxygen function should be used in the ingestion formula	bool, default is true

2.2.2.4. School

The Species entity contains the following state variables:

Table 2.4 Species state variables in BIOEN-OSMOSE

Variable	Description	Type	Units
zlayer	Index of the temperature/oxygen layer to read	int
sizeMaturity	Size at maturity	float, set to \(\infty\)	cm
ageMaturity	Age at maturity	float, set to \(\infty\)	year
eggSize	Size of eggs	float, set to \(\infty\)	cm
beta_bioen	Scaling exponent of maximum ingestion rate and maintenance rate with body mass	float

2.2.2.5. School

The School entity contains the following state variables:

Table 2.5 School state variables in BIOEN-OSMOSE

Variable	Description	Type	Units
e_gross	Mobilized energy rate of individuals of school at time step	float	g / timestep
e_maint	Maintenance cost rate of individuals of school at time step	float	g / timestep
e_net	Net energy available for new tissue production	float	g / timestep
ingestion	Ingestion rate of individuals in school at time step	float	g / timestep
ingestionTot	Sum of all the food ingested during life of the school	float	g
kappa	Proportion of new tissues allocated to the gonadic compartment	float
e_net_faced	Mean net energy faced during lifespan of the school	float	g
mort_starv_rate
mort_oxy_rate