In HaikunXu/BSE: IATTC's BSE code

knitr::opts_chunk$set(results = FALSE)

This example code demonstrates how to extract the purse-seine catch and length composition data for the stock assessment of yellowfin tuna in the eastern Pacific Ocean. Data are extracted for yellowfin between 1975 and 1999 based on the R package BSE (version r packageVersion("BSE")). The package can be installed using devtools::install_github('HaikunXu/BSE',ref='main'). Fishery definition for this data extraction is based on the benchmark assessment conducted in 2020.

Step 1: set up some directories and parameters for the extraction

# devtools::install_github('HaikunXu/BSE',ref='main') 
library(BSE)

# Load the base files (please ask Haikun to get those data)
load("D:/OneDrive - IATTC/IATTC/2022/BSE stuff from Cleridy/single spp programs_PS_1975-1999/Raw data extractions/base files_1975-1999_for SAC 2020.RData")
# the directory where output will be saved
save_dir <- "D:/OneDrive - IATTC/IATTC/2022/BSE stuff from Cleridy/YFT/"
yr.start <- 1975
yr.end <- 1999
Species <- "YFT"
grow.increments <- grow.increments.betyftskj # the growth increment matrix

Step 2: compile the OBJ catch and composition data for YFT

PS <- "OBJ"
cae.stratflg <- create.strat.flg.f(cae$latc5,cae$lonc5,is.lwrght=F,cae$month,cae$setype,cae$class,PS=PS,Species=Species)

Check the strata definition for OBJ to make sure that it is correct

check.strat.flg.f(cae$latc5,cae$lonc5,cae.stratflg)

Loop through every year between yr.start and yr.end to get catch and composition data for YFT in the OBJ fishery

for(year in yr.start:yr.end) {
  # print(paste0("Year: ",year))

  # print("Step 1: get well estimates")
  well.estimates <- well.estimates.7599.f(year)

  # print("Step 2: get catch estimates")
  catch.estimates <- get.catch.estimates.7599.f(cae,cae.stratflg,corrected.unlds,lfgrpd,lfmm,year,2,well.estimates,PS,Species)

  # print("Step 3: get fishery estimates")
  # str(catch.estimates$stratum.estimates.withsamps)
  fishery.estimates <- call.fishery.estimates.f(catch.estimates$stratum.estimates.withsamps,catch.estimates$totunlds.bystrat,year,PS,Species)

  fishery.estimates.yft <- fishery.estimates$yft

  assign(paste0("fishery.estimates.yft.", year), fishery.estimates.yft, pos=1)
}
save(list=objects(pat="fishery.estimates.yft."),file=paste0(save_dir,"YFT_",PS,"_1975-1999.RData"))

Get final OBJ catch and comp output for the stock assessment

YFT.OBJ.Catch.19751999<-compile.catch.output.7599.f(yr.start,yr.end,PS=PS,Species=Species,c("A1","A2","A3","A4","A5"))
YFT.OBJ.Comp.19751999<-compile.sizecomps.output.7599.f(yr.start,yr.end,PS=PS,Species=Species)

Step 3: compile the NOA catch and composition data for YFT

PS <- "NOA"
cae.stratflg <- create.strat.flg.f(cae$latc5,cae$lonc5,is.lwrght=F,cae$month,cae$setype,cae$class,PS=PS,Species=Species)

Check the strata definition for NOA make sure that it is correct

check.strat.flg.f(cae$latc5,cae$lonc5,cae.stratflg)

Loop through every year between yr.start and yr.end to get catch and composition data for YFT in the NOA fishery

for(year in yr.start:yr.end) {
  # print(paste0("Year: ",year))

  # print("Step 1: get well estimates")
  well.estimates <- well.estimates.7599.f(year)

  # print("Step 2: get catch estimates")
  catch.estimates <- get.catch.estimates.7599.f(cae,cae.stratflg,corrected.unlds,lfgrpd,lfmm,year,2,well.estimates,PS,Species)

  # print("Step 3: get fishery estimates")
  # str(catch.estimates$stratum.estimates.withsamps)
  fishery.estimates <- call.fishery.estimates.f(catch.estimates$stratum.estimates.withsamps,catch.estimates$totunlds.bystrat,year,PS,Species)

  fishery.estimates.yft <- fishery.estimates$yft

  assign(paste0("fishery.estimates.yft.", year), fishery.estimates.yft, pos=1)
}
save(list=objects(pat="fishery.estimates.yft."),file=paste0(save_dir,"YFT_",PS,"_1975-1999.RData"))

Get final NOA catch and comp output for the stock assessment

YFT.NOA.Catch.19751999<-compile.catch.output.7599.f(yr.start,yr.end,PS=PS,Species=Species,c("A1","A2","A3","A4"))
YFT.NOA.Comp.19751999<-compile.sizecomps.output.7599.f(yr.start,yr.end,PS=PS,Species=Species)

Step 4: compile the DEL catch and composition data for YFT

PS <- "DEL"
cae.stratflg <- create.strat.flg.f(cae$latc5,cae$lonc5,is.lwrght=F,cae$month,cae$setype,cae$class,PS=PS,Species=Species)

Check the strata definition for DEL to make sure that it is correct

check.strat.flg.f(cae$latc5,cae$lonc5,cae.stratflg)

Loop through every year between yr.start and yr.end to get catch and composition data for YFT in the DEL fishery

for(year in yr.start:yr.end) {
  # print(paste0("Year: ",year))

  # print("Step 1: get well estimates")
  well.estimates <- well.estimates.7599.f(year)

  # print("Step 2: get catch estimates")
  catch.estimates <- get.catch.estimates.7599.f(cae,cae.stratflg,corrected.unlds,lfgrpd,lfmm,year,2,well.estimates,PS,Species)

  # print("Step 3: get fishery estimates")
  # str(catch.estimates$stratum.estimates.withsamps)
  fishery.estimates <- call.fishery.estimates.f(catch.estimates$stratum.estimates.withsamps,catch.estimates$totunlds.bystrat,year,PS,Species)

  fishery.estimates.yft <- fishery.estimates$yft

  assign(paste0("fishery.estimates.yft.", year), fishery.estimates.yft, pos=1)
}
save(list=objects(pat="fishery.estimates.yft."),file=paste0(save_dir,"YFT_",PS,"_1975-1999.RData"))

Get final DEL catch and comp output for the stock assessment

YFT.DEL.Catch.19751999<-compile.catch.output.7599.f(yr.start,yr.end,PS=PS,Species=Species,c("A1","A2","A3","A4","A5","A6","A7"))
YFT.DEL.Comp.19751999<-compile.sizecomps.output.7599.f(yr.start,yr.end,PS=PS,Species=Species)

Step 6: save all results for YFT as csv files

write.csv(YFT.OBJ.Catch.19751999,file=paste0(save_dir,"YFT.OBJ.Catch.19751999.csv"),row.names = FALSE)
write.csv(YFT.OBJ.Comp.19751999,file=paste0(save_dir,"YFT.OBJ.Comp.19751999.csv"),row.names = FALSE)
write.csv(YFT.NOA.Catch.19751999,file=paste0(save_dir,"YFT.NOA.Catch.19751999.csv"),row.names = FALSE)
write.csv(YFT.NOA.Comp.19751999,file=paste0(save_dir,"YFT.NOA.Comp.19751999.csv"),row.names = FALSE)
write.csv(YFT.DEL.Catch.19751999,file=paste0(save_dir,"YFT.DEL.Catch.19751999.csv"),row.names = FALSE)
write.csv(YFT.DEL.Comp.19751999,file=paste0(save_dir,"YFT.DEL.Comp.19751999.csv"),row.names = FALSE)