pkgBuild/R/formatMsomBasic.R

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

formatMsomBasic <- 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),]


	# ==================================
	# = Example of how to prepare MSOM =
	# ==================================
	setkey(trawl2.veri, s.reg, year, stratum, K, spp)
	basic.dat <- expand.data(
		comD = copy(trawl2.veri),
		arr.dim = c("stratum", "K", "spp"), # should uniquely define the keyValue ONLY WHEN combined with fScope (don't accidentally include the gScope value here)
		fillID=c("spp","K"),
		fillValue=c(0,NA), # values to fill with, for a fillID
		Rule=c("value","scope"), # 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", c("s.reg","year")), #
		vScope=list(c("s.reg","stratum","K","year"), NULL),
		redID=NULL, 
		redValue=NULL,
		arrayOut=TRUE, aggFun=meanna, maxOut=Inf
	)


	# ========
	# = Save =
	# ========
	save(basic.dat, file="./trawl/Data/MSOM/basic.dat.RData")


	
}