inst/scripts/FileHandlingFormats.R

In REddyProc: Data processing and plotting utilities of (half-)hourly eddy-covariance measurements

# Convenence functions to read standard datasets
# Will reduce support work with people redoing this.

fLoadEuroFlux16 <- function(
	### reads a sequence of annual files in the format of europe-fluxdata 2016
	siteName		##<< scalar string: the name of the site, i.e. start of the filename before _<year>_
	,dirName = ''	##<< scalar string: the directory where the files reside
	,additionalColumnNames=character(0)	##<< character vector: column names to read in addition to c("Month","Day","Hour","NEE_st","qf_NEE_st","ustar","Ta",'Rg')
){
	##author<< TW
	##details<< The filenames should corresppond to the pattern <sitename>_<YYYY>_.*.txt
	## And hold columns c("Month","Day","Hour","NEE_st","qf_NEE_st","ustar","Ta",'Rg').
	## By default only those colums are read and reported only c("DateTime","NEE","Ustar","Tair","Rg","qf_NEE_st" (Note the renaming).
	## NEE is set to NA for all values with "qf_NEE_st != 0.
	## Values  of -9999.0 are replaced by NA
	#	
	filenamePattern <- paste(siteName,".+\\.txt$",sep="")
	fileNames <- dir(dirName,filenamePattern)
	fileName <- fileNames[1]
	colNames <- union(c("Month","Day","Hour","NEE_st","qf_NEE_st","ustar","Ta",'Rh','Rg'),additionalColumnNames)
	# by settting colClasses at a given position to NULL the column is skipped 
	header <- as.character(read.csv(file.path(dirName,fileName), header=FALSE, nrows=1, stringsAsFactors=F))
	iCols <- match( colNames, header )
	if( length(iNACols <- which(is.na(iCols))) ) stop("unknown columns ",colNames[iNACols]," in file ",fileName)
	colClasses <- rep("NULL",length(header))
	colClasses[ iCols ] <- NA
	ds <- do.call( rbind, lapply( fileNames, function(fileName){
					year <- as.integer(sub(".*_(\\d\\d\\d\\d)_.*","\\1",fileName))
					tmp <- read.csv(file.path(dirName,fileName), colClasses=colClasses)
					#doy <- as.POSIXlt(ISOdate(year, tmp$Month, tmp$Day))$yday +1L
					tmp$Year <- year
					nRow <- nrow(tmp)
					if( tmp$Month[nRow] == 1L )
						tmp$Year[nRow] <- year+1L
					tmp
				}))
	dsTime <- fConvertTimeToPosix(ds, 'YMDH', Year.s='Year', Month.s='Month', Day.s='Day', Hour.s='Hour')
	colnames(dsTime)[match(c("NEE_st","ustar","Ta","Rh"),colnames(dsTime))] <-  c("NEE","Ustar","Tair","rH")
	dsTime$NEE[(dsTime$qf_NEE_st != 0)] <- NA
	ans <- dsTime[,c("DateTime","NEE","Ustar","Tair","rH","Rg","qf_NEE_st",additionalColumnNames)]
	ans <- fConvertGapsToNA(ans)
	ans
}