clean.wcann: Clean West Coast Annual Clean data set for the West Coast...

Description Usage Format


Clean West Coast Annual

Clean data set for the West Coast Annual bottom trawl survey




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] 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] 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?

rBatt/trawlData documentation built on May 26, 2019, 7:45 p.m.