srrTMB {FLSRTMB}

R Documentation

Fits Stock Recruitment Relationships (SRR) in TBM

Description

Fits Stock Recruitment Relationships (SRR) in TBM

Usage

srrTMB(
  object,
  spr0 = "missing",
  s = NULL,
  s.est = TRUE,
  s.logitsd = 20,
  r0.pr = "missing",
  lplim = 0.001,
  uplim = 0.3,
  plim = lplim,
  pmax = uplim,
  nyears = NULL,
  report.sR0 = FALSE,
  inits = NULL,
  lower = NULL,
  upper = NULL,
  SDreport = TRUE,
  verbose = FALSE
)

Arguments

object	Input FLSR = as.FLSR(stock,model) object with current model options bevholtSV rickerSV segreg geomean
spr0	unfished spawning biomass per recruit from FLCore::spr0(FLStock)
s	steepness parameter of SRR (fixed or prior mean)
s.est	option to estimate steepness
s.logitsd	prior sd for logit(s), default is 1.4 (flat) if s.est = TRUE
r0.pr	option to condition models on r0 priors (NULL = geomean)
lplim	lower bound of spawning ratio potential SRP, default 0.0001
uplim	upper bound of plausible spawning ratio potential SRP , default 0.3
plim	depreciated plim = usrp
pmax	depreciated pmax = lsrp
nyears	yearMeans from the tail used to compute a,b from the reference spr0 (default all years)
report.sR0	option to report s and R0 instead of a,b
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
verbose	if TRUE, it shows tracing

Value

A list containing elements 'FLSR', of class FLSR

Examples

data(ple4)
gm <- srrTMB(as.FLSR(ple4,model=geomean),spr0=mean(spr0y(ple4)))
bh <- srrTMB(as.FLSR(ple4,model=bevholtSV),spr0=spr0y(ple4))
ri <- srrTMB(as.FLSR(ple4,model=rickerSV),spr0=spr0y(ple4))
hs <- srrTMB(as.FLSR(ple4,model=segreg),spr0=spr0y(ple4),lplim=0.05,uplim=0.2)
srs = FLSRs(gm=gm,bh=bh,ri=ri,hs=hs) # combine
plotsrs(srs) 
plotsrts(srs)  # relative
plotsrs(srs[2:4],b0=TRUE) # through to B0
plotsrs(srs[2:4],b0=TRUE,rel=TRUE)  # relative
gm@SV # estimates
do.call(rbind,lapply(srs,AIC))

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