Catchability specification

Holds environmental linkages on survey/index catchability q. The effect of an env_data covariate is written as a formula and can hold priors, bounds, and an estimation phase like any other linkage.

Usage

build_catchability(linkages = NULL)

Arguments

linkages

Optional named list of linkage_spec() objects keyed by catchability parameter. The only parameter is q. Coefficients are per fleet by default (by = ~ fleet), except that fleets sharing a Catchability_index estimate one parameter block and so take ONE coefficient for the whole group. Use the fleet argument of linkage_spec() to restrict a spec to particular fleets.

Value

A list of catchability settings for fit_mod().

Details

Catchability is the one process that accepts link = "exponential", Stock Synthesis's environmental link type 1: q^exp(beta * x), which MULTIPLIES log q where "log" shifts it. It needs an estimated base q and a lognormal or t index likelihood, and cannot share a fleet with a random-effect q linkage; each of those is refused with the reason. See vignette("environmental-linkages-and-priors").

Examples

# \donttest{
# One temperature effect on q per fleet. `by = ~ fleet` is the default, and a
# fleet without an estimated survey catchability is not linkable, so at fit time
# restrict the linkage to the estimated-q fleets (here fleet 7 of BS2017SS).
build_catchability(linkages = list(
  q = linkage_spec(~ temp, fleet = 7)))
#> $linkages
#> $linkages$q
#> <Rceattle linkage spec>
#>   param:   q
#>   formula: ~temp
#>   fleet:   7
#>   link:    log
#> 
#> 

# Restrict it to fleets 1 and 3, with a prior on the slope
build_catchability(linkages = list(
  q = linkage_spec(~ temp, fleet = c(1, 3),
                   priors = list(temp = prior_normal(0, 1)))))
#> $linkages
#> $linkages$q
#> <Rceattle linkage spec>
#>   param:   q
#>   formula: ~temp
#>   prior:    temp ~ normal(0, 1)
#>   fleet:   1, 3
#>   link:    log
#> 
#> 
# }