ftmb: Fits Stock Recruitment Relationships (SRR) in TBM

In laurieKell/FLCandy: Candidate methods for FLR

Fits Stock Recruitment Relationships (SRR) in TBM

Description

Fits Stock Recruitment Relationships (SRR) in TBM

Usage

ftmb(
  object,
  spr0 = spr0,
  s = 0.7,
  s.est = TRUE,
  s.logitsd = 1.3,
  inits = function(object = object, s = s) c(median(c(log(rec(object)))), log(0.4),
    to_logits(s)),
  lower = function(object = object, s = -20) c(quantile(c(log(rec(object))), probs =
    0.1), log(0.05), -20),
  upper = function(object = object, s = 20) c(quantile(c(log(rec(object))), probs = 0.9),
    log(1.5), 20),
  SDreport = TRUE
)

Arguments

object	Input FLSR object.
spr0	unfished spawning biomass per recruit from FLCore::spr0(FLStock) or FLCore:::spr0Yr
s	steepness parameter of SRR (fixed or prior mean)
s.est	option to estimate steepness
s.logitsd	prior sd for logit(s), default is 1.3 (flat) if s.est = TRUE
inits	option to specify initial values of log(r0), log(SigR) and logit(s)
lower	option to specify lower bounds of log(r0), log(SigR) and logit(s)
upper	option to specify upper bounds of log(r0), log(SigR) and logit(s)
SDreport	option to converge hessian and get vcov

Value

A list containing elements 'FLSR', of class FLSR

## Not run: load(neamac) spr0=spr0Yr(neamac) object=as.FLSR(neamac,model="bevholtSV") sr=ftmb(object,s.est=T,s=0.7,s.logitsd=0.3,spr0) ## End(Not run)

laurieKell/FLCandy documentation built on April 17, 2025, 5:23 p.m.