clean.neus: Clean Northeast US Clean data set for the Northeast US bottom...
In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys
Description
Clean Northeast US
Clean data set for the Northeast US bottom trawl survey
Usage
1
Format
A dim = 2523907 x 56 data.table data.frame:
[,1] ref character reference taxonomic ID from raw data
[,2] cruise character cruise ID
[,3] station character the station ID for the haul
[,4] stratum character the statistical stratum of the haul
[,5] SID integer species identification number
[,6] sex integer the gender of the catch
[,7] vessel character vessel ID
[,8] year integer year of haul
[,9] season character insert_description_here
[,10] lat numeric latitude of the haul
[,11] lon numeric longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360)
[,12] datetime c("POSIXct", "POSIXt") the day and time of the haul
[,13] depth numeric the maximum depth of the water at the location of the haul
[,14] stemp numeric water temperature at the surface at the location of the haul
[,15] ssalin numeric surface salinity
[,16] btemp numeric water temperature at the bottom at the location of the haul
[,17] bsalin numeric bottom salinity
[,18] cnt numeric number of individuals in the whole net (may be extrapolated)
[,19] weight numeric the weight (mass) of all items in the net (may be extrapolated)
[,20] length numeric length of catch (typically of an individual, but may be average for some regions)
[,21] NUMLEN integer number of individuals used to ascertain catch length
[,22] ITISSPP integer insert_description_here
[,23] AUTHOR character insert_description_here
[,24] stratumarea numeric the area of the statistical stratum (km2)
[,25] haulid character a unique identifier for the haul; vessel ID - cruise ID - haul number
[,26] cntcpue numeric number of individuals caught per hectare in the haul
[,27] wtcpue numeric weight (mass) of the catch
[,28] reg character survey region
[,29] 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.
[,30] tbl.row integer the row in the taxonomic data base where a match was found. See match.tbl.
[,31] 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.
[,32] tax.src character informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet
[,33] spp character species scientific name; Genus species
[,34] common character the common name of the organism sampled
[,35] taxLvl character the most specific level of classification indicated by spp
[,36] species character the species name of the species
[,37] genus character the genus of the species
[,38] family character taxonomic family
[,39] order character taxonomic order
[,40] class character taxonomic class
[,41] superclass character taxonomic superclass
[,42] subphylum character taxonomic subphylum
[,43] phylum character insert_description_here
[,44] kingdom character taxonomic kingdom
[,45] trophicDiet character source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source
[,46] trophicOrig character from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'?
[,47] Picture character Is there a picture of this critter assoicated with the package? Note: this isn't always accurate
[,48] trophicLevel numeric the trophic level from Fish Base or Sea Life Base
[,49] trophicLevel.se numeric the standard error of the trophic level
[,50] tax.src2 character informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries)
[,51] 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
[,52] 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
[,53] website character URL reference for taxonomic information
[,54] 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
[,55] keep.row logical Column indicating whether or not the row show likely be excluded
[,56] 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.
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Description
Clean Northeast US
Clean data set for the Northeast US bottom trawl survey
Usage
1 |
Format
A dim = 2523907 x 56 data.table data.frame:
| [,1] | ref | character | reference taxonomic ID from raw data |
| [,2] | cruise | character | cruise ID |
| [,3] | station | character | the station ID for the haul |
| [,4] | stratum | character | the statistical stratum of the haul |
| [,5] | SID | integer | species identification number |
| [,6] | sex | integer | the gender of the catch |
| [,7] | vessel | character | vessel ID |
| [,8] | year | integer | year of haul |
| [,9] | season | character | insert_description_here |
| [,10] | lat | numeric | latitude of the haul |
| [,11] | lon | numeric | longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360) |
| [,12] | datetime | c("POSIXct", "POSIXt") | the day and time of the haul |
| [,13] | depth | numeric | the maximum depth of the water at the location of the haul |
| [,14] | stemp | numeric | water temperature at the surface at the location of the haul |
| [,15] | ssalin | numeric | surface salinity |
| [,16] | btemp | numeric | water temperature at the bottom at the location of the haul |
| [,17] | bsalin | numeric | bottom salinity |
| [,18] | cnt | numeric | number of individuals in the whole net (may be extrapolated) |
| [,19] | weight | numeric | the weight (mass) of all items in the net (may be extrapolated) |
| [,20] | length | numeric | length of catch (typically of an individual, but may be average for some regions) |
| [,21] | NUMLEN | integer | number of individuals used to ascertain catch length |
| [,22] | ITISSPP | integer | insert_description_here |
| [,23] | AUTHOR | character | insert_description_here |
| [,24] | stratumarea | numeric | the area of the statistical stratum (km2) |
| [,25] | haulid | character | a unique identifier for the haul; vessel ID - cruise ID - haul number |
| [,26] | cntcpue | numeric | number of individuals caught per hectare in the haul |
| [,27] | wtcpue | numeric | weight (mass) of the catch |
| [,28] | reg | character | survey region |
| [,29] | 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. |
| [,30] | tbl.row | integer | the row in the taxonomic data base where a match was found. See match.tbl. |
| [,31] | 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. |
| [,32] | tax.src | character | informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet |
| [,33] | spp | character | species scientific name; Genus species |
| [,34] | common | character | the common name of the organism sampled |
| [,35] | taxLvl | character | the most specific level of classification indicated by spp |
| [,36] | species | character | the species name of the species |
| [,37] | genus | character | the genus of the species |
| [,38] | family | character | taxonomic family |
| [,39] | order | character | taxonomic order |
| [,40] | class | character | taxonomic class |
| [,41] | superclass | character | taxonomic superclass |
| [,42] | subphylum | character | taxonomic subphylum |
| [,43] | phylum | character | insert_description_here |
| [,44] | kingdom | character | taxonomic kingdom |
| [,45] | trophicDiet | character | source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source |
| [,46] | trophicOrig | character | from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'? |
| [,47] | Picture | character | Is there a picture of this critter assoicated with the package? Note: this isn't always accurate |
| [,48] | trophicLevel | numeric | the trophic level from Fish Base or Sea Life Base |
| [,49] | trophicLevel.se | numeric | the standard error of the trophic level |
| [,50] | tax.src2 | character | informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries) |
| [,51] | 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 |
| [,52] | 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 |
| [,53] | website | character | URL reference for taxonomic information |
| [,54] | 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 |
| [,55] | keep.row | logical | Column indicating whether or not the row show likely be excluded |
| [,56] | row_flag | character | if keep.row is TRUE, why was this row flagged to be dropped? |
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