clean.sgulf: Clean Southern Gulf of St. Lawrence Clean data set for the...
In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys

Clean Southern Gulf of St. Lawrence

Clean data set for the Southern Gulf of St. Lawrence bottom trawl survey

1	clean.sgulf

A dim = 180583 x 59 data.table data.frame:

[,1]	ref	character	reference taxonomic ID from raw data
[,2]	stratum	character	the statistical stratum of the haul
[,3]	vessel	character	vessel ID
[,4]	cruise	character	cruise ID
[,5]	set	character	insert_description_here
[,6]	year	integer	year of haul
[,7]	species.code	integer	insert_description_here
[,8]	cntcpue	numeric	number of individuals caught per hectare in the haul
[,9]	wtcpue	numeric	weight (mass) of the catch
[,10]	month	integer	insert_description_here
[,11]	day	integer	insert_description_here
[,12]	expt	integer	insert_description_here
[,13]	time	character	starting time of the tow
[,14]	temperature	numeric	insert_description_here
[,15]	depth.start	numeric	insert_description_here
[,16]	depth.end	numeric	insert_description_here
[,17]	dtow	numeric	insert_description_here
[,18]	depth	numeric	the maximum depth of the water at the location of the haul
[,19]	lat	numeric	latitude of the haul
[,20]	lon	numeric	longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360)
[,21]	cnt	numeric	number of individuals in the whole net (may be extrapolated)
[,22]	weight	numeric	the weight (mass) of all items in the net (may be extrapolated)
[,23]	stemp	numeric	water temperature at the surface at the location of the haul
[,24]	bsalin	numeric	bottom salinity
[,25]	btemp	numeric	water temperature at the bottom at the location of the haul
[,26]	trawlableunits	integer	insert_description_here
[,27]	stratumarea	numeric	the area of the statistical stratum (km2)
[,28]	haulid	character	a unique identifier for the haul; vessel ID - cruise ID - haul number
[,29]	datetime	c("POSIXct", "POSIXt")	the day and time of the haul
[,30]	season	character	insert_description_here
[,31]	reg	character	survey region
[,32]	val.src	character	indicates the degree of 'fuzziness' required to find a match to ref in a data.base of taxonomic information; m1 indicates perfect match, m2 indicates that capitalization, whitespace, etc (see `cull`) needed to be adjusted, m3 indicates that `agrep` was used, and m4 means that measures in both m2 and m3 were taken to find the match. See `match.tbl`.
[,33]	tbl.row	integer	the row in the taxonomic data base where a match was found. See `match.tbl`.
[,34]	mtch.src	integer	the database containing the match; 1 is taxInfo, 2 is spp.corr1, 3 is getSppData; if matches are found in multiple sources, a match to 1 takes precedence over 1 & 2, and 2 over 3. See `match.tbl`.
[,35]	tax.src	character	informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet
[,36]	spp	character	species scientific name; Genus species
[,37]	common	character	the common name of the organism sampled
[,38]	taxLvl	character	the most specific level of classification indicated by spp
[,39]	species	character	the species name of the species
[,40]	genus	character	the genus of the species
[,41]	family	character	taxonomic family
[,42]	order	character	taxonomic order
[,43]	class	character	taxonomic class
[,44]	superclass	character	taxonomic superclass
[,45]	subphylum	character	taxonomic subphylum
[,46]	phylum	character	insert_description_here
[,47]	kingdom	character	taxonomic kingdom
[,48]	trophicDiet	character	source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source
[,49]	trophicOrig	character	from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'?
[,50]	Picture	character	Is there a picture of this critter assoicated with the package? Note: this isn't always accurate
[,51]	trophicLevel	numeric	the trophic level from Fish Base or Sea Life Base
[,52]	trophicLevel.se	numeric	the standard error of the trophic level
[,53]	tax.src2	character	informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries)
[,54]	conflict	logical	for a given 'spp' value in spp.key, was there a conflict in the other taxonomic columns? E.g., a single spp corresponding to multiple common names; also TRUE if different ref values were found in different databases (affecting the val.src, tbl.row, mtch.src, tax.src, etc columns), but then the refs converged to same spp -- that would not necessarily be an error, but might deserve checking
[,55]	flag	character	flag related to correcting taxonomic information; relates to automated input, potential errors, and signature of people or methods that have made corrections to spp.key
[,56]	website	character	URL reference for taxonomic information
[,57]	website2	character	secondary URL reference for taxonomic information; often used when website finds the name for a spp name as entered, but website2 points to the most up-to-date scientific name
[,58]	keep.row	logical	Column indicating whether or not the row show likely be excluded
[,59]	row_flag	character	if keep.row is TRUE, why was this row flagged to be dropped?