bioenergetics.hpp File Reference

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Functions
template<class Type>
void	calculate_temperature_function (matrix< Type > &fT, int nspp, int nyrs, const vector< int > &Ceq, const vector< int > &Cindex, const vector< Type > &Qc, const vector< Type > &Tcm, const vector< Type > &Tco, const vector< Type > &Tcl, const vector< Type > &CK1, const vector< Type > &CK4, const matrix< Type > &env_index)
	Temperature-dependent function of consumption (fT) for bioenergetics.
template<class Type>
void	calculate_ration (array< Type > &consumption_at_age, int nspp, int nyrs, int nyrs_hind, const vector< int > &nsex, const vector< int > &nages, const vector< int > &Ceq, const vector< Type > &CA, const vector< Type > &CB, const vector< Type > &fday, const vector< Type > &Pvalue, matrix< Type > &fT, array< Type > &ration_data, array< Type > &weight_hat)
	Annual ration of a predator at age, in kg per predator per year.

Function Documentation

calculate_ration()

template<class Type>

void calculate_ration	(	array< Type > &	consumption_at_age,
		int	nspp,
		int	nyrs,
		int	nyrs_hind,
		const vector< int > &	nsex,
		const vector< int > &	nages,
		const vector< int > &	Ceq,
		const vector< Type > &	CA,
		const vector< Type > &	CB,
		const vector< Type > &	fday,
		const vector< Type > &	Pvalue,
		matrix< Type > &	fT,
		array< Type > &	ration_data,
		array< Type > &	weight_hat )

Annual ration of a predator at age, in kg per predator per year.

Updates consumption_at_age in place, from the bioenergetics equations (Ceq 1-3) or from input consumption (Ceq 4).

Parameters

consumption_at_age	Individual consumption, kg/yr [nspp, max_sex, max_age, nyrs].
nspp	Number of species.
nyrs	Years, hindcast plus projection.
nyrs_hind	Years in the hindcast.
nsex	Sexes modelled per species: 1 = combined, 2 = both.
nages	Age bins per species.
Ceq	Consumption equation per species.
CA	Allometric mass function intercept (Cmax = CA * W^(1+CB)).
CB	Allometric mass function slope.
fday	Foraging days per year, per species.
Pvalue	Proportion of maximum consumption (scales Cmax).
fT	Temperature-dependence function [nspp, nyrs].
ration_data	Relative foraging rates (Ceq 1-3), input consumption (Ceq 4).
weight_hat	Weight-at-age [n_wt_indices, max_sex, max_age, nyrs].

Definition at line 125 of file bioenergetics.hpp.

calculate_temperature_function()

template<class Type>

void calculate_temperature_function	(	matrix< Type > &	fT,
		int	nspp,
		int	nyrs,
		const vector< int > &	Ceq,
		const vector< int > &	Cindex,
		const vector< Type > &	Qc,
		const vector< Type > &	Tcm,
		const vector< Type > &	Tco,
		const vector< Type > &	Tcl,
		const vector< Type > &	CK1,
		const vector< Type > &	CK4,
		const matrix< Type > &	env_index )

Temperature-dependent function of consumption (fT) for bioenergetics.

Updates the fT matrix in place. Supports multiple bioenergetics models: 1 = Exponential function (Stewart et al. 1983) 2 = Warm-water species temperature dependence (Kitchell et al. 1977) 3 = Cool/cold-water species temperature dependence (Thornton and Lessem 1979) 4 = Constant (fT = 1.0)

Parameters

fT	Temperature functions [nspp, nyrs], updated.
nspp	Number of species.
nyrs	Years, hindcast plus projection.
Ceq	Consumption equation per species.
Cindex	Environmental index driving each species.
Qc	Q coefficient in equations 1-2, a temperature in equation 3.
Tcm	Thermal max.
Tco	Thermal optimum.
Tcl	Thermal limit for Thornton/Lessem.
CK1	Ascending limit for Thornton/Lessem.
CK4	Descending limit for Thornton/Lessem.
env_index	Environmental predictors, e.g. bottom temperature [nyrs, n_indices].

Definition at line 27 of file bioenergetics.hpp.