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

Clean West Coast Annual

Clean data set for the West Coast Annual bottom trawl survey

1	clean.wcann

A dim = 217514 x 54 data.table data.frame:

[,1]	ref	character	reference taxonomic ID from raw data
[,2]	haulid	character	a unique identifier for the haul; vessel ID - cruise ID - haul number
[,3]	weight	numeric	the weight (mass) of all items in the net (may be extrapolated)
[,4]	Individual.Average.Weight..kg.	numeric	insert_description_here
[,5]	Survey	character	insert_description_here
[,6]	year	integer	year of haul
[,7]	vessel	character	vessel ID
[,8]	Cruise.Leg	integer	insert_description_here
[,9]	Trawl.Performance	character	insert_description_here
[,10]	date	character	date of the tow
[,11]	datetime	c("POSIXct", "POSIXt")	the day and time of the haul
[,12]	lat	numeric	latitude of the haul
[,13]	lon	numeric	longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360)
[,14]	Best.Position.Type	character	insert_description_here
[,15]	depth	numeric	the maximum depth of the water at the location of the haul
[,16]	Best.Depth.Type	character	insert_description_here
[,17]	towduration	numeric	the duration (time) for the tow
[,18]	towarea	numeric	insert_description_here
[,19]	btemp	numeric	water temperature at the bottom at the location of the haul
[,20]	stratum	character	the statistical stratum of the haul
[,21]	stratumarea	numeric	the area of the statistical stratum (km2)
[,22]	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
[,23]	wtcpue	numeric	weight (mass) of the catch
[,24]	cnt	numeric	number of individuals in the whole net (may be extrapolated)
[,25]	cntcpue	numeric	number of individuals caught per hectare in the haul
[,26]	reg	character	survey region
[,27]	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`.
[,28]	tbl.row	integer	the row in the taxonomic data base where a match was found. See `match.tbl`.
[,29]	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`.
[,30]	tax.src	character	informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet
[,31]	spp	character	species scientific name; Genus species
[,32]	common	character	the common name of the organism sampled
[,33]	taxLvl	character	the most specific level of classification indicated by spp
[,34]	species	character	the species name of the species
[,35]	genus	character	the genus of the species
[,36]	family	character	taxonomic family
[,37]	order	character	taxonomic order
[,38]	class	character	taxonomic class
[,39]	superclass	character	taxonomic superclass
[,40]	subphylum	character	taxonomic subphylum
[,41]	phylum	character	insert_description_here
[,42]	kingdom	character	taxonomic kingdom
[,43]	trophicDiet	character	source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source
[,44]	trophicOrig	character	from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'?
[,45]	Picture	character	Is there a picture of this critter assoicated with the package? Note: this isn't always accurate
[,46]	trophicLevel	numeric	the trophic level from Fish Base or Sea Life Base
[,47]	trophicLevel.se	numeric	the standard error of the trophic level
[,48]	tax.src2	character	informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries)
[,49]	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
[,50]	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
[,51]	website	character	URL reference for taxonomic information
[,52]	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
[,53]	keep.row	logical	Column indicating whether or not the row show likely be excluded
[,54]	row_flag	character	if keep.row is TRUE, why was this row flagged to be dropped?