spp.key: Species Key Key to taxonomic and ecological information for...
In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys

Species Key

Key to taxonomic and ecological information for all species surveyed

spp.key

A dim = 7146 x 27 data.table data.frame:

[,1]	ref	character	reference taxonomic ID from raw data
[,2]	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`.
[,3]	tbl.row	integer	the row in the taxonomic data base where a match was found. See `match.tbl`.
[,4]	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`.
[,5]	tax.src	character	informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet
[,6]	spp	character	species scientific name; Genus species
[,7]	common	character	the common name of the organism sampled
[,8]	taxLvl	character	the most specific level of classification indicated by spp
[,9]	species	character	the species name of the species
[,10]	genus	character	the genus of the species
[,11]	family	character	taxonomic family
[,12]	order	character	taxonomic order
[,13]	class	character	taxonomic class
[,14]	superclass	character	taxonomic superclass
[,15]	subphylum	character	taxonomic subphylum
[,16]	phylum	character	insert_description_here
[,17]	kingdom	character	taxonomic kingdom
[,18]	trophicDiet	character	source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source
[,19]	trophicOrig	character	from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'?
[,20]	Picture	character	Is there a picture of this critter assoicated with the package? Note: this isn't always accurate
[,21]	trophicLevel	numeric	the trophic level from Fish Base or Sea Life Base
[,22]	trophicLevel.se	numeric	the standard error of the trophic level
[,23]	tax.src2	character	informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries)
[,24]	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
[,25]	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
[,26]	website	character	URL reference for taxonomic information
[,27]	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