R/FSRSclf.r

In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes

#' @export
FSRSclf<-function(lfa= c("27", "28", "29", "30", "31.1", "31.2", "32", "33"), yrs=2004:2015, bins=seq(0,140,10),fn="FSRS",sex=1:2,maxsoak=10,...){

	loadfunctions("lobster")


	#LATEST DATA EXPORT FROM FSRS DATABASE:
	#lobster.db("fsrs.redo")
	lobster.db("fsrs")
	#recruitment.trap.db('raw.redo',p=p)

	fsrs$SYEAR<-fsrs$HAUL_YEAR
	fsrs$SYEAR[fsrs$LFA%in%c("33","34")]<-as.numeric(substr(fsrs$S_LABEL[fsrs$LFA%in%c("33","34")],6,9))

	fsrs<-subset(fsrs,SOAK_DAYS<=maxsoak&SEX%in%sex&SYEAR%in%yrs&LFA%in%lfa)	# Remove soak days greater than 5,  do not iclude berried females
	fsrs$HAUL_DATE<-as.Date(fsrs$HAUL_DATE)

	if(DS=="fsrs"){

		names.keep<-names(LFdat)

		scd<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","inputs","FSRS_SIZE_CODES.csv"))
		scd$pseudoCL<-rowMeans(scd[c("MIN_S","MAX_S")])

		LFdat<-merge(LFdat,scd[c("LENGTH","pseudoCL")])
		LFdat$LENGTH<-LFdat$pseudoCL
		LFdat<-LFdat[names.keep]

	}

	#MLS
	mls<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","inputs","MinLegalSize.csv"))
	mlslfas<-as.numeric(substr(names(mls[-1]),4,5))
	mlslfas[which(mlslfas==31)]<-c(31.1,31.2)

	#browser()
	CLF<-list()
	for(i in 1:length(lfa)){
		print(lfa[i])
		CLF[[i]]<-t(sapply(yrs,function(y){with(subset(fsrs,LFA==lfa[i]&SYEAR==y),hist(pseudoCL,breaks=bins,plot=F)$counts)}))

	}
	names(CLF)<-paste("LFA",lfa)		
	BarPlotCLF(CLF,yrs=yrs,bins=bins,col='grey',filen=fn,rel=T,LS=cbind(mls[mls$Year%in%yrs,which(mlslfas%in%lfa)+1]),wd=9,...)
	return(list(CLF=CLF,yrs=yrs))
}