R/selectivity_funcs_therMizer.R

In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included

# Selectivity functions for size based model
# First argument to the function has to be w

# Copyright 2012 Finlay Scott, Julia Blanchard and Ken Andersen.
# Distributed under the GPL 2 or later
# Maintainer of mizer package: Finlay Scott, CEFAS

# Modified for therMizer by Phoebe.Woodworth-Jefcoats@noaa.gov
# Largely unchanged for therMizer, except for adding:
# mig_window function
# knife_edge_phased function

#' Length based sigmoid selectivity function
#'
#' A sigmoid shaped selectivity function. Based on two parameters \code{l25} and
#' \code{l50} which determine the length at which 25\% and 50\% of the stock is
#' selected respectively. As the size-based model is weight based, and this
#' selectivity function is length based, it is also necessary to supply the
#' length-weight parameters \code{a} and \code{b}.
#'
#' @param w the size of the individual.
#' @param l25 the length which gives a selectivity of 25\%.
#' @param l50 the length which gives a selectivity of 50\%.
#' @param a the multiplier of the length-weight function.
#' @param b the exponent of the length-weight function.
#' @export
sigmoid_length <- function(w,l25,l50,a,b) {
	l <- (w/a)^(1/b)
	sr <- l50 - l25
	s1 <- l50*log(3)/sr
	s2 <- s1 / l50
	return(1 / (1 + exp(s1 - s2*l)))
}

#' Size based knife-edge selectivity function
#'
#' A knife-edge selectivity function where only sizes greater or equal to
#' \code{knife_edge_size} are selected.
#'
#' @param w The size of the individual.
#' @param knife_edge_size The size at which the knife-edge operates.
#' @export
knife_edge <- function(w, knife_edge_size) {
	sel <- rep(0, length(w))
	sel[w >= knife_edge_size] <- 1
	return(sel)
} 

#' Size based knife-edge selectivity function that is phased in 
#'
#' A knife-edge selectivity function where only sizes greater or equal to
#' \code{knife_edge_size1} are selected.  Selectivity is then phased in through
#' size \code{knife_edge_size2}.  This simulates the reduced effectiveness of 
#' longline gear for smaller fish
#'
#' @param w The size of the individual.
#' @param knife_edge_size1 The size at which the knife-edge is initiated.
#' @param knife_edge_size2 The size at which selectivity is fully realized.
#' @export
knife_edge_phased <- function(w, knife_edge_size1, knife_edge_size2) { 
	sel <- rep(0, length(w)) 
	
	# Phased in linearly
	F0 <- which(w < knife_edge_size1) # to find one size smaller than that fished, for the 0 value 
	F1 <- which(w < knife_edge_size2) # to find end of escalation size range 
	lo_sel <- max(F0):max(F1) 
	sel[lo_sel] <- seq(0, 1, length = length(lo_sel)) # linear increase from 0 to F 
	sel[w >= knife_edge_size2] <- 1 
	return(sel) 
	
} 

#' Size based window selectivity function 
#' 
#' Essentiall a double-knife-edge selectivity function where only sizes 
#' within a range given by \code{mig_min_size} and \code{mig_max_size}
#' are selected. 
#'
#' @param w The size of the individual. 
#' @param mig_min_size The minimum window size. 
#' @param mig_max_size The maximum window size. 
#' @export
mig_window <- function(w, mig_min_size, mig_max_size) { 
	mig <- rep(0, length(w)) 
	mig[w >= mig_min_size] <- 1 
	mig[w > mig_max_size] <- 0 
	return(mig) 
}