calc_suit_vect: Combines prey preference and prey suitability

In CefasRepRes/LeMaRns: Length-Based Multispecies Analysis by Numerical Simulation

Combines prey preference and prey suitability

Description

Calculates a combined value for prey preference and prey suitability standardised to a value between 0 and 1.

Usage

calc_suit_vect(nsc, nfish, sc_Linf, prefs, tau)

Arguments

nsc	A numeric value representing the number of length classes in the model.
nfish	A numeric value representing the number of species in the model.
sc_Linf	A numeric vector of length nsc representing the length class at which each species reaches its asymptotic length.
prefs	An array of dimensions nsc, nfish, nsc and nfish. The first and second dimensions represent the prey whereas the the third and fourth dimensions represent the predator.
tau	A matrix of dimensions nfish and nfish. Row indices represent predators and column indices represent prey. A value of 1 at location i, j indicates prey j is eaten by predator i.

Details

tau values are assigned to an array of dimensions nsc, nfish, nsc and nfish and multiplied by the array prefs. This creates an array of dimensions nsc, nfish, nsc and nfish indicating prey suitability. Prey suitability is then standardised to sum to 1 for each predator species in each length class.

Value

A list object of length nfish. Each element in the list is an array of dimensions nsc, nsc and nfish containing a value between 0 and 1 that represents prey preference and prey suitability for each species and length class.

References

Hall, S. J., Collie, J. S., Duplisea, D. E., Jennings, S., Bravington, M., & Link, J. (2006). A length-based multispecies model for evaluating community responses to fishing. Canadian Journal of Fisheries and Aquatic Sciences, 63(6):1344-1359.

See Also

calc_M2.

Examples

# Set up the inputs to the function - species-independent parameters
nfish <- nrow(NS_par)
nsc <- 32
maxsize <- max(NS_par$Linf)*1.01 # the biggest size is 1% bigger than the largest Linf
l_bound <- seq(0, maxsize, maxsize/nsc); l_bound <- l_bound[-length(l_bound)]
u_bound <- seq(maxsize/nsc, maxsize, maxsize/nsc)
mid <- l_bound+(u_bound-l_bound)/2

# Set up the inputs to the function - species-specific parameters
Linf <- NS_par$Linf # the von-Bertalanffy asymptotic length of each species (cm).
W_a <- NS_par$W_a # length-weight conversion parameter.
W_b <- NS_par$W_b # length-weight conversion parameter.
k <- NS_par$k # the von-Bertalnaffy growth parameter.
Lmat <- NS_par$Lmat # the length at which 50\% of individuals are mature (cm).

# Get phi_min
tmp <- calc_phi(k, Linf, nsc, nfish, u_bound, l_bound, calc_phi_min=FALSE,
                  phi_min=0.1) # fixed phi_min
phi_min <- tmp$phi_min

# Calculate growth increments
tmp <- calc_ration_growthfac(k, Linf, nsc, nfish, l_bound, u_bound, mid, W_a, W_b, phi_min)
sc_Linf <- tmp$sc_Linf
wgt <- tmp$wgt

# Calculate predator-prey size preferences
prefs <- calc_prefs(pred_mu=-2.25, pred_sigma=0.5, wgt, sc_Linf)

# Calculate prey preference and prey suitability
suit_M2 <- calc_suit_vect(nsc, nfish, sc_Linf, prefs, NS_tau)

CefasRepRes/LeMaRns documentation built on Jan. 27, 2023, 4:01 p.m.