R/CPUEModelData2.r

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

#' @export
CPUEModelData2 = function(p,redo=T){

	if(redo){
	  fn.root =  file.path( project.datadirectory('bio.lobster'), "data")
	  fnODBC  =  file.path(fn.root, "ODBCDump")
	  logs = lobster.db("process.logs")
		vlog = lobster.db("process.vlog.redo")
	  #get.vlog=load(file.path( fnODBC, "processed.vlog.rdata"),.GlobalEnv)
		#vlog=load(file.path( fnODBC, "processed.vlog.rdata"))
		
		tmp1 = subset(logs,select=c("DATE_FISHED","SYEAR","WEIGHT_KG","LFA","NUM_OF_TRAPS","subarea","GRID_NUM"))
		tmp1$type = 'mandatory'
		tmp2 = subset(vlog,select=c("FDATE","SYEAR","W_KG","N_TRP","LFA","X","Y"))
		names(tmp2) = c("DATE_FISHED","SYEAR","WEIGHT_KG","NUM_OF_TRAPS","subarea","X","Y")
		tmp2$LFA = tmp2$subarea
		tmp2 = assignArea(tmp2,coords=c("X","Y"))
		tmp2 = subset(tmp2,select=c("DATE_FISHED","SYEAR","WEIGHT_KG","LFA","NUM_OF_TRAPS","subarea","LFA_GRID"))
		tmp2$type = 'voluntary'
	    names(tmp2) = names(tmp1)

	    tmp = rbind(tmp2,tmp1)

	    if('subareas'%in%names(p)){
	       tmp = subset(tmp,subarea %in% p$subareas)
	    } else { tmp = subset(tmp,LFA %in% p$lfas)}

	    tmp$LFA = tmp$subarea
	    tmp$LFA[tmp$subarea%in%c("27N","27S")] = "27"
	    tmp$LFA[tmp$subarea%in%c("33W","33E")] = "33"

	    depths = getGridVar2(grids=sort(unique(tmp$GRID_NUM)))
	    names(depths)[1] = "GRID_NUM"

	    cpue.data = merge(tmp,depths,all=T)
		cpue.data$y =	decimal_date(cpue.data$DATE_FISHED)
		cpue.data$DATE_FISHED = as.Date(cpue.data$DATE_FISHED)


		# Create column for week and day of season (WOS, DOS)
		subareas<-unique(cpue.data$subarea[!is.na(cpue.data$subarea)])
		cpue.data$WOS<-NA
		cpue.data$DOS<-NA
		for(a in 1:length(subareas)){
			season<-sort(unique(cpue.data$SYEAR[cpue.data$subarea==subareas[a]]))
			for(i in 1:length(season)){
				cpue.data$WOS[cpue.data$SYEAR==season[i]&cpue.data$subarea==subareas[a]]<-floor((cpue.data$DATE_FISHED[cpue.data$SYEAR==season[i]&cpue.data$subarea==subareas[a]]-min(cpue.data$DATE_FISHED[cpue.data$SYEAR==season[i]&cpue.data$subarea==subareas[a]]))/7)+1
				cpue.data$DOS[cpue.data$SYEAR==season[i]&cpue.data$subarea==subareas[a]]<-cpue.data$DATE_FISHED[cpue.data$SYEAR==season[i]&cpue.data$subarea==subareas[a]]-min(cpue.data$DATE_FISHED[cpue.data$SYEAR==season[i]&cpue.data$subarea==subareas[a]])+1
			}
		}
	   
		write.csv(cpue.data,file.path( project.datadirectory("bio.lobster"), "data","products","CPUEModelData.csv"),row.names=F) 

	cpue.data = read.csv(file.path( project.datadirectory("bio.lobster"), "data","products","CPUEModelData.csv"))


	return(cpue.data)
}
}