select_ogive function

Selectivity patterns

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.

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.

Examples

# 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')

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.