In laurieKell/FLCandy: Candidate methods for FLR

knitr::opts_chunk$set(echo = FALSE)
# getwd()
library(knitr)

opts_chunk$set(cache     =TRUE, 
               comment   =NA, 
               warning   =FALSE, 
               message   =FALSE, 
               error     =FALSE, 
               echo      =!FALSE, 
               eval      =TRUE,cache   =TRUE,
               cache.path="cache/m12/",
               fig.path  ="../outputs/tex/m12",
               fig.width =8,
               fig.height=6,
               dev       ="png")

iFig=0
iTab=0

library(FLCore)    # install.packages("FLCore",   repos="http://flr-project.org/R")
library(FLBRP)     # install.packages("FLBRP",    repos="http://flr-project.org/R")
library(FLasher)   # install.packages("FLasher",  repos="http://flr-project.org/R")
library(FLife)     # install.packages("FLife",    repos="http://flr-project.org/R")
library(ggplotFL)  # install.packages("ggplotFL", repos="http://flr-project.org/R")

theme_set(theme_bw(16))

setGeneric("m1", function(object, ...)
  standardGeneric("m1"))
setGeneric("m2", function(object, ...)
  standardGeneric("m2"))
setGeneric("forage", function(object, ...)
  standardGeneric("forage"))
setGeneric("predNeed", function(object, ...)
  standardGeneric("predNeed"))

setMethod("z", "FLBRP", function(object, ...) {
  f <- harvest(object)
  if(units(f) != 'f')
    stop("Your exploitation rate is not defined as F, cannot be added to M")
  else 
    return(m(object) %+% f)
  })

setMethod("m1", "FLComp", function(object, ...) {
  if(units(harvest(object)) != 'f') 
    stop("Exploitation not defined as 'f', cannot be combined with  'm'")
  if (!"m1"%in%names(attributes(stk)))
    stop("m1 is not an attribute")

  return(attributes(object)$m1)})

setMethod("m2", "FLComp", function(object, ...) {
  if(units(harvest(object)) != 'f') 
    stop("Exploitation not defined as 'f', cannot be combined with  'm'")
  if (!"m1"%in%names(attributes(stk)))
    stop("m1 is not an attribute")

  return(m(object) - m1(object))})

setMethod("forage", "FLComp", function(object, ...) {
  if(units(harvest(object)) != 'f') 
    stop("Exploitation not defined as 'f', cannot be combined with  'm'")
  if (!"m1"%in%names(attributes(stk)))
    stop("m1 is not an attribute")

  #zFn<-function(object) m(object)%+%harvest(object)

  return(FLCore:::apply((stock.wt(object)%*%stock.n(object)%*%(m2(object))%/%(z(object))%*%(1-exp(-z(object))))[-1],c(2,6),sum))})

setMethod("predNeed", "FLBRP", function(object, ...) {

  # reference points
  rfs=refpts(object)[,"harvest"]

  # F reference points
  hvt=aperm(rfs,c(2,1,3:length(dim(rfs))))

  # Change to FLQuant  
  dimnames(hvt)[1:2]=list(age="all","year"=seq(dim(hvt)[2]))
  names(dimnames(hvt))[2]="year"
  fbar(object)=FLQuant(hvt)

  # Calc forage
  dimnames(rfs)[[2]]="forage"
  rfs[]=c(forage(object))

  rfs})

lh=FLPar(linf=25)
lh=lhPar(lh)

eq=lhEql(lh)

plot(eq,refpts="msy")

Figure r iFig=iFig+1; iFig Equilibrium dynamics

stk=as(eq,"FLStock")
stk=qapply(stk, function(object) {dimnames(object)$year=an(dimnames(object)$year)+1960; object})
stk=fwd(stk,f=fbar(stk)[,-1],sr=eq)

attributes(eq)$m1 =FLQuant(0.025,dimnames=dimnames(m(eq)))
attributes(stk)$m1=FLQuant(0.025,dimnames=dimnames(m(stk)))

ggplot(model.frame(FLQuants(eq,ssb=ssb,yield=catch,forage=forage),drop=T))+
  geom_line(aes(ssb,forage),col="red")+
  geom_line(aes(ssb,yield),col="blue")+
  xlab("SSB")+ylab("Production")

Figure r iFig=iFig+1; iFig Yiele verses Forage

plot(stk, metrics=list(F=fbar,SSB=ssb,Yield=catch,Forage=forage))+
  geom_vline(aes(xintercept=1995),col="red")+
  xlab("Year")

Figure r iFig=iFig+1; iFig Simulated time series.

predNeed(eq)

Software Versions

• r version$version.string
• FLCore: r packageVersion('FLCore')
• FLBRP: r packageVersion('FLCore')
• FLasher: r packageVersion('FLCore')
• FLife: r packageVersion('FLCore')

• ggplotFL: r packageVersion('FLCore')

• FLPKG: r # packageVersion('FLPKG')

• Compiled: r date()

• Git Hash: r system("git log --pretty=format:'%h' -n 1", intern=TRUE)

Author information

Laurence KELL. laurie.kell.es

Acknowledgements

References {#References}

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