REA_example_haddock <- function(){
#
# Sample data preparation. Example formatted as RDBES v 1.17
#
# select samples of target species, aphia code for haddock is 126437
SA <- prepRECA::NORportsampling2018$SA[prepRECA::NORportsampling2018$SA$SAsppCode == "126437",]
# extract biological measurements corresponding to these samples
BV <- prepRECA::NORportsampling2018$BV[prepRECA::NORportsampling2018$BV$SAid %in% SA$SAid,]
# merge in needed upper levels.
# SS, SD and DE is not strictly needed,
# but included for checking for stratification and clustering at these levels.
fishdata <- extractBV(BV, c("Age", "Length", "Weight"), c("integer", "numeric", "numeric"))
fishdata <- merge(fishdata, SA, by="SAid")
fishdata <- merge(fishdata, prepRECA::NORportsampling2018$SS, by="SSid")
fishdata <- merge(fishdata, prepRECA::NORportsampling2018$LE, by="LEid", suffixes = c("", ".LE"))
fishdata <- merge(fishdata, prepRECA::NORportsampling2018$VD, by="VDid")
fishdata <- merge(fishdata, prepRECA::NORportsampling2018$OS, by="OSid")
fishdata <- merge(fishdata, prepRECA::NORportsampling2018$SD, by="SDid")
fishdata <- merge(fishdata, prepRECA::NORportsampling2018$DE, by="DEid")
warningsRecaApplicability(fishdata)
# Need to handle Gutted fish. Used for mean-weight estimation in cells, will attempt with removing Gutted fish
# LEstratum: will use gear as covariate, but will use LEmetier5 as it has corresponding entry in landings CL.
# OSstratum: will use as covariate season
#remove Gutted weights
fishdata[fishdata$SApres == "Gutted", "Weight"] <- NA
#check that age, length and covariates (vessel, gear, season, area) are complete
warningsDataCompleteness(fishdata, c("Age", "Length", "VDencrCode", "LEmetier5", "OSstratum", "LEarea"))
#inspect missing measurments
plotSAnas(fishdata, "Age")
plotSAnas(fishdata, "Weight")
#
# Landings data CL
#
landings <- prepRECA::CLCodHadNOR
# select landings of target species, aphia code for haddock is 126437
landings <- landings[landings$Species == "126437",]
month <- landings$Month
landings <- landings[,c("Metier5", "Area", "Quarter")]
warning("Check definition of partcount wrp replicate sampling")
warning("Check effect of nlev not correctly set for random effects not in landings")
#
# Running R-ECA
#
ecadata <- prepRECA(fishdata, landings, c(), c(), NULL, month = month)
warning("Implement prepECA") #gear, season, area
# feed result from prepECA to eca.estimate
# feed result from prepECA to eca.predict
warning("Implement reportECA") #need result from predict, and mapping from prepECA
}
# remove stuff
# prepECA
# run data checks
# run ECA
# plot and report
# convergence check
# for different sampling frames
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