clean.wctri: Clean West Coast Triennial Clean data set for the West Coast...
In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys

Clean West Coast Triennial

Clean data set for the West Coast Triennial bottom trawl survey

1	clean.wctri

A dim = 108138 x 80 data.table data.frame:

[,1]	ref	character	reference taxonomic ID from raw data
[,2]	SID	integer	species identification number
[,3]	CRUISEJOIN	integer	insert_description_here
[,4]	HAULJOIN	integer	insert_description_here
[,5]	REGION	character	insert_description_here
[,6]	vessel	character	vessel ID
[,7]	cruise	character	cruise ID
[,8]	haul	character	the integer haul number within a cruise
[,9]	CATCHJOIN	integer	insert_description_here
[,10]	weight	numeric	the weight (mass) of all items in the net (may be extrapolated)
[,11]	cnt	numeric	number of individuals in the whole net (may be extrapolated)
[,12]	SUBSAMPLE_CODE	logical	insert_description_here
[,13]	VOUCHER	integer	insert_description_here
[,14]	AUDITJOIN	integer	insert_description_here
[,15]	HAUL_TYPE	integer	insert_description_here
[,16]	PERFORMANCE	numeric	insert_description_here
[,17]	datetime	c("POSIXct", "POSIXt")	the day and time of the haul
[,18]	towduration	numeric	the duration (time) for the tow
[,19]	towdistance	numeric	insert_description_here
[,20]	gearsize	numeric	the dimension of the gear; for trawl net, the width of the mouth in ft
[,21]	NET_MEASURED	character	insert_description_here
[,22]	NET_HEIGHT	numeric	insert_description_here
[,23]	stratum	character	the statistical stratum of the haul
[,24]	lat.start	numeric	insert_description_here
[,25]	lat.end	numeric	insert_description_here
[,26]	lon.start	numeric	insert_description_here
[,27]	lon.end	numeric	insert_description_here
[,28]	station	character	the station ID for the haul
[,29]	GEAR_DEPTH	integer	insert_description_here
[,30]	depth	numeric	the maximum depth of the water at the location of the haul
[,31]	BOTTOM_TYPE	character	insert_description_here
[,32]	stemp	numeric	water temperature at the surface at the location of the haul
[,33]	btemp	numeric	water temperature at the bottom at the location of the haul
[,34]	WIRE_LENGTH	integer	insert_description_here
[,35]	geartype	character	code for the type of gear used
[,36]	ACCESSORIES	character	insert_description_here
[,37]	SUBSAMPLE	character	insert_description_here
[,38]	REVISION	character	insert_description_here
[,39]	BS	character	insert_description_here
[,40]	GOA	character	insert_description_here
[,41]	WC	character	insert_description_here
[,42]	haulid	character	a unique identifier for the haul; vessel ID - cruise ID - haul number
[,43]	year	numeric	year of haul
[,44]	season	character	insert_description_here
[,45]	lat	numeric	latitude of the haul
[,46]	lon	numeric	longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360)
[,47]	stratumarea	numeric	the area of the statistical stratum (km2)
[,48]	towarea	numeric	insert_description_here
[,49]	effort	numeric	some measure of the effort for this catch; could be area, time, speed, net size, or some combination. When possible, was converted to area swept by net during the entire tow
[,50]	wtcpue	numeric	weight (mass) of the catch
[,51]	cntcpue	numeric	number of individuals caught per hectare in the haul
[,52]	reg	character	survey region
[,53]	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`.
[,54]	tbl.row	integer	the row in the taxonomic data base where a match was found. See `match.tbl`.
[,55]	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`.
[,56]	tax.src	character	informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet
[,57]	spp	character	species scientific name; Genus species
[,58]	common	character	the common name of the organism sampled
[,59]	taxLvl	character	the most specific level of classification indicated by spp
[,60]	species	character	the species name of the species
[,61]	genus	character	the genus of the species
[,62]	family	character	taxonomic family
[,63]	order	character	taxonomic order
[,64]	class	character	taxonomic class
[,65]	superclass	character	taxonomic superclass
[,66]	subphylum	character	taxonomic subphylum
[,67]	phylum	character	insert_description_here
[,68]	kingdom	character	taxonomic kingdom
[,69]	trophicDiet	character	source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source
[,70]	trophicOrig	character	from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'?
[,71]	Picture	character	Is there a picture of this critter assoicated with the package? Note: this isn't always accurate
[,72]	trophicLevel	numeric	the trophic level from Fish Base or Sea Life Base
[,73]	trophicLevel.se	numeric	the standard error of the trophic level
[,74]	tax.src2	character	informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries)
[,75]	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
[,76]	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
[,77]	website	character	URL reference for taxonomic information
[,78]	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
[,79]	keep.row	logical	Column indicating whether or not the row show likely be excluded
[,80]	row_flag	character	if keep.row is TRUE, why was this row flagged to be dropped?