diet_data.hpp File Reference

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Functions
template<class Type>
void	organize_diet_obs (const int &nspp, const int &nyrs, const int &nyrs_hind, const int &styr, const vector< int > &minage, const vector< int > &nsex, matrix< Type > &diet_obs, matrix< int > &diet_ctl, array< Type > &diet_prop)
	Parses empirical diet observations and maps them into a 5D proportion array.
template<class Type>
void	calculate_other_food_diet_prop (const int &nspp, const int &nyrs, const vector< int > &nsex, const vector< int > &nages, const vector< Type > &other_food, array< Type > &diet_prop, array< Type > &other_food_diet_prop)
	Residual stomach content: the "other food" not explicitly modeled.
template<class Type>
void	predict_stomach_content (const int &nspp, const int &nyrs_hind, const int &styr, const vector< int > &suit_styr, const vector< int > &suit_endyr, const vector< int > &minage, const vector< int > &nsex, const vector< int > &nages, matrix< Type > &diet_obs, matrix< int > &diet_ctl, array< Type > &avgN_at_age, array< Type > &diet_prop_hat, matrix< Type > &diet_hat)
	Expected stomach content proportions given the modeled population state.

Function Documentation

calculate_other_food_diet_prop()

template<class Type>

void calculate_other_food_diet_prop	(	const int &	nspp,
		const int &	nyrs,
		const vector< int > &	nsex,
		const vector< int > &	nages,
		const vector< Type > &	other_food,
		array< Type > &	diet_prop,
		array< Type > &	other_food_diet_prop )

Residual stomach content: the "other food" not explicitly modeled.

The unattributed diet share divided by other_food (mt) is on the same per-biomass scale as stom_div_bio, which calculate_msvpa_suitability() sums over prey and adds it to.

Definition at line 97 of file diet_data.hpp.

organize_diet_obs()

template<class Type>

void organize_diet_obs	(	const int &	nspp,
		const int &	nyrs,
		const int &	nyrs_hind,
		const int &	styr,
		const vector< int > &	minage,
		const vector< int > &	nsex,
		matrix< Type > &	diet_obs,
		matrix< int > &	diet_ctl,
		array< Type > &	diet_prop )

Parses empirical diet observations and maps them into a 5D proportion array.

Maps diet_obs proportions onto the 5D diet_prop array used for MSVPA based suitability, handling 1-sex and 2-sex indexing. A row with flt_yr == 0 is written to every modeled year. Rows aggregated over predator or prey ages are skipped: only diet-data type 1 (a prey age in a predator age) can be used for MSVPA suitability.

Parameters

nspp	Number of species.
nyrs	Years, hindcast plus projection.
nyrs_hind	Years in the hindcast.
styr	First year of the model.
minage	Minimum modeled age per species.
nsex	Sexes modelled per species: 1 = combined, 2 = both.
diet_obs	Diet observations; column 0 sample size, column 1 the proportion.
diet_ctl	Maps each observation row to predator, prey, sexes, ages, and year.
diet_prop	[Output] Observed diet proportions (pred_idx, prey_idx, pred_age, prey_age, yr). Modified by reference.

Definition at line 24 of file diet_data.hpp.

predict_stomach_content()

template<class Type>

void predict_stomach_content	(	const int &	nspp,
		const int &	nyrs_hind,
		const int &	styr,
		const vector< int > &	suit_styr,
		const vector< int > &	suit_endyr,
		const vector< int > &	minage,
		const vector< int > &	nsex,
		const vector< int > &	nages,
		matrix< Type > &	diet_obs,
		matrix< int > &	diet_ctl,
		array< Type > &	avgN_at_age,
		array< Type > &	diet_prop_hat,
		matrix< Type > &	diet_hat )

Expected stomach content proportions given the modeled population state.

Maps diet_prop_hat back onto the rows of the empirical diet_obs, which are often aggregated over ages or sexes. The four diet-data types, as the ages encode them:

• Type 1: Specific predator age and prey age (weighted across sexes if combined).
• Type 2: Specific predator age, summed across all prey ages.
• Type 3: Unweighted mean over predator ages, summed over prey ages (r_age > -500).
• Type 4: As Type 3, but weighted by predator numbers-at-age (r_age < -500).

Parameters

nspp	Number of species.
nyrs_hind	Years in the hindcast.
styr	First year of the model.
suit_styr	Start year index of the suitability window, per predator.
suit_endyr	End year index of the suitability window, per predator.
minage	Minimum modeled age per species.
nsex	Sexes modelled per species: 1 = combined, 2 = both.
nages	Age bins per species.
diet_obs	Empirical diet observations, used here for row-matching.
diet_ctl	Maps each observation row to its aggregation levels.
avgN_at_age	Average numbers-at-age (thousands of fish), used for weighting.
diet_prop_hat	Predicted diet proportions for specific ages/sexes.
diet_hat	[Output] Predicted diet proportions matching diet_obs.

Definition at line 161 of file diet_data.hpp.