pkgBuild/R/formatTrawl_old.R

In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys

formatTrawlOld <- function(){
	# ==================
	# = Load libraries =
	# ==================
	library(rfishbase)
	library(taxize)
	library(plyr)
	library(reshape)
	library(reshape2)
	library(data.table)


	# ===============================
	# = Guess appropriate directory =
	# ===============================
	if(Sys.info()["sysname"]=="Linux"){
		setwd("~/Documents/School&Work/pinskyPost")
	}else{
		setwd("~/Documents/School&Work/pinskyPost")
	}


	# ==================
	# = Load Functions =
	# ==================
	data.location <- "./trawl/Scripts/DataFunctions"
	invisible(sapply(paste(data.location, list.files(data.location), sep="/"), source, .GlobalEnv))

	stat.location <- "./trawl/Scripts/StatFunctions"
	invisible(sapply(paste(stat.location, list.files(stat.location), sep="/"), source, .GlobalEnv))

	plot.location <- "./trawl/Scripts/PlotFunctions"
	invisible(sapply(paste(plot.location, list.files(plot.location), sep="/"), source, .GlobalEnv))


	# =======================
	# = Load trawl2 Dataset =
	# =======================
	load("./trawl/Data/trawl2.RData")


	# ======================
	# = Remove unknown spp =
	# ======================
	trawl2.veri <- trawl2[(correctSpp)&!is.na(common)&is.species(spp),]


	# ============================
	# = Add missing combinations =
	# ============================
	# Make sure all of a region's strata are present in all years
	# Make sure all of a region's species are present in each stratum in each year
	# If the s.reg-stratum-year was present, but the s.reg-stratum-year-spp was not, fill in w/ 0, NA otherwise
	# Aggregate among "K" replicate hauls (substrata)
	setkey(trawl2.veri, s.reg, year, stratum, K, spp)
	trawl <- expand.data(
		comD = copy(trawl2.veri),
		arr.dim = c("stratum", "year", "spp"), # should uniquely define the keyValue ONLY WHEN combined with fScope (don't accidentally include the gScope value here)
		fillID=c("spp"),
		fillValue=c(0), # values to fill with, for a fillID
		Rule=c("value"), # does fillID use a non-NA fill value, or does it have restricted (more specific than "global") scope?
		keyID=c("s.reg", "stratum","year","spp", "K"), # column names whose values uniquely identify rows in the input
		keyValue="wtcpue", # the column whose values would fill the array
		gScope="s.reg", # global scope
		fScope=list("s.reg"), #
		vScope=list(c("s.reg","stratum", "year")),
		redID=list(
			c("spp"),
			c("s.reg","year","stratum","spp")
		), 
		redValue=list(
			c("correctSpp","taxLvl","phylum","common"),
			c("lat", "lon", "depth", "stemp", "btemp")
		),
		arrayOut=FALSE, aggFun=meanna, maxOut=Inf
	)


	# ========
	# = Save =
	# ========
	setkey(trawl, s.reg, spp, year, stratum)
	# save(trawl, file="/Users/Battrd/Documents/School&Work/pinskyPost/trawl/Data/trawl.RData")
	save(trawl, file="./trawl/Data/trawl.RData")
	# rm(list="trawl")
	
}