select_ogive: Selectivity patterns

Description Usage Arguments Details References Examples

View source: R/select_ogive.R

Description

Based on a few parameters, this function estimates the fraction per length group retained in the net. Different selection curves can be used for the estimation.

Usage

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select_ogive(s_list, Lt, Lc = NA)

Arguments

s_list

a list with selectivity parameters dependent on the type of selection curve:

  • selecType type of selection curve used for estimation (options: "knife_edge", "trawl_ogive", "lognormal", "normal_fixed"),

  • Lc length-at-first-capture (also called L50),

  • meshSizes a vector with mesh sizes in increasing order,

  • select_p1 selectivity parameter 1 (see Millar and Holst (1997)),

  • select_p2 selectivity parameter 2 (see Millar and Holst (1997)),

  • L75 length at which individuals are caught with a probability of 75

Lt

a vector with lengths corresponding to age classes

Lc

length-at-first-capture (Default: NA)

Details

This function is embedded within predict_mod. selecType "knife_edge" only requires a Lc value. "trawl_ogive" requires a Lc (L50) and a L75 value. "lognormal" requires two mesh sizes, an estimate of mu and of sigma. "normal_fixed" requires two mesh sizes with an estimate of the selection factor (SF) and an estimate of sigma.

References

Millar, R. B., Holst, R. (1997). Estimation of gillnet and hook selectivity using log-linear models. ICES Journal of Marine Science: Journal du Conseil, 54(3), 471-477.

Sparre, P., Venema, S.C., 1998. Introduction to tropical fish stock assessment. Part 1. Manual. FAO Fisheries Technical Paper, (306.1, Rev. 2). 407 p.

Examples

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# create list with selectivity information
select.list <- list(selecType = 'knife_edge',
   Lc = 34, L75 = 37, tc = 5, meshSizes = c(60,80),
   select_p1 = 2.7977, select_p2 = 0.1175)


# create vector with mid lengths
Lt <- seq(5, 50, 0.01)

# knife edge selectivity
sel_ke <- select_ogive(select.list, Lt)

# trawl ogive selectivity
select.list$selecType = "trawl_ogive"
sel_to <- select_ogive(select.list, Lt)

plot(Lt, sel_ke, type = 'l')
lines(Lt, sel_to, col = 'blue')


# Gillnet selectivity ("lognormal" and "normal_fixed")
select.list$selecType <- "lognormal"
sel_log <- select_ogive(select.list, Lt)

select.list$selecType <- "normal_fixed"
select.list$select_p1 <- 0.2
select.list$select_p2 <- 1.5
sel_nf <- select_ogive(select.list, Lt)

plot(Lt, sel_log, type = 'l')
lines(Lt, sel_nf, col = 'blue')

TropFishR documentation built on Jan. 9, 2018, 1:07 a.m.