R/LAFSS.r

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

#' @export
LAFSS<-function(size.range=c(0,250),SPA,Years){
	
	require(lubridate)

	# import bycatch data from scallop survey
	lobster.db('scallop')
	scallop.tows$YEAR<-year(scallop.tows$TOW_DATE)

	# calculate area swept for bycatch
	scallop.tows$GEAR_WIDTH_BYCATCH<-with(scallop.tows,DRAG_WIDTH*(NUM_LINED+NUM_UNLINED)*0.3048)
	scallop.tows$GEAR_WIDTH_BYCATCH[scallop.tows$MGT_AREA_ID=='29']<-18*0.3048
	scallop.tows$AREA_SWEPT<-with(scallop.tows,GEAR_WIDTH_BYCATCH*TOW_LEN)

	# select for lobsters
	lobster.catch<-subset(scallop.catch,SPECCD_ID==2550,c(2,5:8))
	
	# merge with tow data
	ScalSurvLob.dat<-merge(scallop.tows,lobster.catch,all=T)
	
	# subset for area and years
	if(!missing(SPA))	ScalSurvLob.dat<-subset(ScalSurvLob.dat,MGT_AREA_ID%in%SPA)
	if(!missing(Years))	ScalSurvLob.dat<-subset(ScalSurvLob.dat,YEAR%in%Years)

	# 
	ScalSurvLob.dat$NLobs<-0
	ScalSurvLob.dat$NLobs[ScalSurvLob.dat$MEAS_VAL>size.range[1]&ScalSurvLob.dat$MEAS_VAL<size.range[2]]<-1
	ScalSurvLob.dat$lon<-convert.dd.dddd(ScalSurvLob.dat$START_LONG)
	ScalSurvLob.dat$lat<-convert.dd.dddd(ScalSurvLob.dat$START_LAT)

	tmp<-with(ScalSurvLob.dat,tapply(NLobs,TOW_SEQ,sum))
	d1<-subset(ScalSurvLob.dat,!duplicated(TOW_SEQ),c('TOW_SEQ','YEAR','TOW_DATE','MGT_AREA_ID','AREA_SWEPT','lon','lat'))
	d2<-data.frame(TOW_SEQ=as.numeric(names(tmp)),NLobs=as.vector(tmp))
	ScalSurvLob<-merge(d1,d2,all.x=T)

	# standardized to 4000 m^2
	ScalSurvLob$NLobsStd<-ScalSurvLob$NLobs/ScalSurvLob$AREA_SWEPT*4000

	print("Lobster Abundance From Scallop Survey")
	print(sort(unique(ScalSurvLob$YEAR)))
	print(sort(unique(ScalSurvLob$MGT_AREA_ID)))

	return(ScalSurvLob)

}