seasonalise: Adds ICES PA & MSY reference points to refpts and fits a SRR
In laurieKell/FLCandy: Candidate methods for FLR

addRefs

R Documentation

Adds ICES PA & MSY reference points to refpts and fits a SRR

Description

Adds ICES PA & MSY reference points to an FLStock

Takes an FLStock that was annual and adjusts numbers-at-age to take accoubt of seasons

Takes an FLStock with seasons and collapses into years

Age at which a cohort achieves it;s maximum biomass, i.e. where losses due to M are greater than gains die to increase in size/mass

Runs ICES rountine to calculate MSY and PA reference points

Fits an SRR to an FLStock and estimates reference points

Sets M, wt, sel & mat to vary by iter based on annual values to look at non-stationarity

While 'expand' adds seasons to an annually structured 'FLStock' it does not change the 'FLQuants' such as m, stock.wt, mat, stock.n, catch.n and harvest to take account of seasonal effects, such as growth and spawning. It also does not account for changes in the population due to seasonal fishing. Therefore 'seasonalise', divides M into seasons, interpolates wts, and projects a cohort across ages to estimate numbers and catch-at-age.

Calculates the spawner per recruit down a cohort

Calculates the spawner per recruit in each year

Usage

addRefs(x, refs)

adjust(object)

annualise(x)

aopt(object, nyears = 3)

eqsim1(
  object,
  Blim = unlist(c(object@benchmark["Blim"])),
  Bpa = unlist(c(object@benchmark["Bpa"])),
  Btrigger = unlist(c(object@benchmark["Btrigger"])),
  Fmsy = unlist(c(object@benchmark["Fmsy"])),
  Fscan = "missing",
  Fcv = 0.212,
  Fphi = 0.423,
  bio.years = 3,
  bio.const = FALSE,
  sel.years = 3,
  sel.const = FALSE,
  verbose = FALSE,
  process.error = TRUE,
  Nrun = 200,
  nsamp = 1000,
  rhologRec = TRUE,
  SSBcv = 0,
  extreme.trim = c(0.05, 0.95)
)

getBlim(object, model = "Segreg", nsamp = 1000)

icesRefpts(x, refs = NULL, model = "bevholtSV", steepness = 0.7, nyears = 3)

nonStationarity(
  object,
  sr,
  slots = c("m", "mat", "stock.wt", "catch.wt", "catch.sel"),
  abi = FALSE
)

seasonalise(object, season = 1:4)

spr0Cohort(object)

spr0Yr(object)

Arguments

`object`	an `FLStock` object
`seasons`	a numeric with seasons

Value

FLStock object

Examples

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data(ple4brp)
aopt(ple4brp)

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load(neamac)

spr0=spr0Yr(neamac)

sr=as.FLSR(neamac,model="bevholtSV")
sr=ftmb(sr,s.est=T,s=0.7,s.logitsd=0.3,spr0)

refs=nonStationarity(neamac,sr)

refs=subset(refs,data>0&!is.na(data))
dat=subset(refs,(refpt=="spr.100"&quant%in%c("ssb"))|
                (refpt=="msy"&quant%in%c("ssb","harvest","rec","yield"))|
                (refpt=="virgin"&quant%in%c("ssb")))

ggplot(dat)+
  geom_line(aes(year,data,col=refpt))+facet_grid(quant~.,scale="free")

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data(ple4)
ple4seasonal=seasonalise(ple4)
plot(FLStocks("Annual"=ple4,"Seasonal"=ple4seasonal)

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