clean.gmex: Clean Gulf of Mexico Clean data set for the Gulf of Mexico...
In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys
Description
Clean Gulf of Mexico
Clean data set for the Gulf of Mexico bottom trawl survey
Usage
1
Format
A dim = 716550 x 76 data.table data.frame:
[,1] ref character reference taxonomic ID from raw data
[,2] cruise character cruise ID
[,3] vessel character vessel ID
[,4] SID character species identification number
[,5] station character the station ID for the haul
[,6] CRUISE_NO numeric cruise ID as number
[,7] P_STA_NO numeric insert_description_here
[,8] BGSID integer record ID number
[,9] unknown integer insert_description_here
[,10] BGSCODE character flags information about the biological sample
[,11] cnt numeric number of individuals in the whole net (may be extrapolated)
[,12] weight numeric the weight (mass) of all items in the net (may be extrapolated)
[,13] towID character insert_description_here
[,14] gearsize integer the dimension of the gear; for trawl net, the width of the mouth in ft
[,15] geartype character code for the type of gear used
[,16] meshsize numeric the size of the net mesh (inches of stretch)
[,17] OP character insert_description_here
[,18] towduration numeric the duration (time) for the tow
[,19] timezone character time zone
[,20] time character starting time of the tow
[,21] lat.deg.start numeric insert_description_here
[,22] lat.min.start numeric insert_description_here
[,23] lon.deg.start numeric insert_description_here
[,24] lon.min.start numeric insert_description_here
[,25] depth numeric the maximum depth of the water at the location of the haul
[,26] date character date of the tow
[,27] lat.deg.end numeric insert_description_here
[,28] lat.min.end numeric insert_description_here
[,29] lon.deg.end numeric insert_description_here
[,30] lon.min.end numeric insert_description_here
[,31] stemp numeric water temperature at the surface at the location of the haul
[,32] btemp numeric water temperature at the bottom at the location of the haul
[,33] towspeed numeric the speed of the vessel
[,34] station.comment character insert_description_here
[,35] survey.name character insert_description_here
[,36] haulid character a unique identifier for the haul; vessel ID - cruise ID - haul number
[,37] datetime c("POSIXct", "POSIXt") the day and time of the haul
[,38] year integer year of haul
[,39] season character insert_description_here
[,40] lat numeric latitude of the haul
[,41] lon numeric longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360)
[,42] stratum character the statistical stratum of the haul
[,43] stratumarea numeric the area of the statistical stratum (km2)
[,44] towarea numeric insert_description_here
[,45] 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
[,46] wtcpue numeric weight (mass) of the catch
[,47] cntcpue numeric number of individuals caught per hectare in the haul
[,48] reg character survey region
[,49] 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.
[,50] tbl.row integer the row in the taxonomic data base where a match was found. See match.tbl.
[,51] 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.
[,52] tax.src character informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet
[,53] spp character species scientific name; Genus species
[,54] common character the common name of the organism sampled
[,55] taxLvl character the most specific level of classification indicated by spp
[,56] species character the species name of the species
[,57] genus character the genus of the species
[,58] family character taxonomic family
[,59] order character taxonomic order
[,60] class character taxonomic class
[,61] superclass character taxonomic superclass
[,62] subphylum character taxonomic subphylum
[,63] phylum character insert_description_here
[,64] kingdom character taxonomic kingdom
[,65] trophicDiet character source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source
[,66] trophicOrig character from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'?
[,67] Picture character Is there a picture of this critter assoicated with the package? Note: this isn't always accurate
[,68] trophicLevel numeric the trophic level from Fish Base or Sea Life Base
[,69] trophicLevel.se numeric the standard error of the trophic level
[,70] tax.src2 character informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries)
[,71] 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
[,72] 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
[,73] website character URL reference for taxonomic information
[,74] 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
[,75] keep.row logical Column indicating whether or not the row show likely be excluded
[,76] 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 Gulf of Mexico
Clean data set for the Gulf of Mexico bottom trawl survey
Usage
1 |
Format
A dim = 716550 x 76 data.table data.frame:
| [,1] | ref | character | reference taxonomic ID from raw data |
| [,2] | cruise | character | cruise ID |
| [,3] | vessel | character | vessel ID |
| [,4] | SID | character | species identification number |
| [,5] | station | character | the station ID for the haul |
| [,6] | CRUISE_NO | numeric | cruise ID as number |
| [,7] | P_STA_NO | numeric | insert_description_here |
| [,8] | BGSID | integer | record ID number |
| [,9] | unknown | integer | insert_description_here |
| [,10] | BGSCODE | character | flags information about the biological sample |
| [,11] | cnt | numeric | number of individuals in the whole net (may be extrapolated) |
| [,12] | weight | numeric | the weight (mass) of all items in the net (may be extrapolated) |
| [,13] | towID | character | insert_description_here |
| [,14] | gearsize | integer | the dimension of the gear; for trawl net, the width of the mouth in ft |
| [,15] | geartype | character | code for the type of gear used |
| [,16] | meshsize | numeric | the size of the net mesh (inches of stretch) |
| [,17] | OP | character | insert_description_here |
| [,18] | towduration | numeric | the duration (time) for the tow |
| [,19] | timezone | character | time zone |
| [,20] | time | character | starting time of the tow |
| [,21] | lat.deg.start | numeric | insert_description_here |
| [,22] | lat.min.start | numeric | insert_description_here |
| [,23] | lon.deg.start | numeric | insert_description_here |
| [,24] | lon.min.start | numeric | insert_description_here |
| [,25] | depth | numeric | the maximum depth of the water at the location of the haul |
| [,26] | date | character | date of the tow |
| [,27] | lat.deg.end | numeric | insert_description_here |
| [,28] | lat.min.end | numeric | insert_description_here |
| [,29] | lon.deg.end | numeric | insert_description_here |
| [,30] | lon.min.end | numeric | insert_description_here |
| [,31] | stemp | numeric | water temperature at the surface at the location of the haul |
| [,32] | btemp | numeric | water temperature at the bottom at the location of the haul |
| [,33] | towspeed | numeric | the speed of the vessel |
| [,34] | station.comment | character | insert_description_here |
| [,35] | survey.name | character | insert_description_here |
| [,36] | haulid | character | a unique identifier for the haul; vessel ID - cruise ID - haul number |
| [,37] | datetime | c("POSIXct", "POSIXt") | the day and time of the haul |
| [,38] | year | integer | year of haul |
| [,39] | season | character | insert_description_here |
| [,40] | lat | numeric | latitude of the haul |
| [,41] | lon | numeric | longitude of the haul, in western hemisphere degrees (for lon > 0, do lon-360) |
| [,42] | stratum | character | the statistical stratum of the haul |
| [,43] | stratumarea | numeric | the area of the statistical stratum (km2) |
| [,44] | towarea | numeric | insert_description_here |
| [,45] | 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 |
| [,46] | wtcpue | numeric | weight (mass) of the catch |
| [,47] | cntcpue | numeric | number of individuals caught per hectare in the haul |
| [,48] | reg | character | survey region |
| [,49] | 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. |
| [,50] | tbl.row | integer | the row in the taxonomic data base where a match was found. See match.tbl. |
| [,51] | 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. |
| [,52] | tax.src | character | informs source of taxonomic correction of ref to spp and other tax info; is taxInfo if found from manually checked spreadsheet |
| [,53] | spp | character | species scientific name; Genus species |
| [,54] | common | character | the common name of the organism sampled |
| [,55] | taxLvl | character | the most specific level of classification indicated by spp |
| [,56] | species | character | the species name of the species |
| [,57] | genus | character | the genus of the species |
| [,58] | family | character | taxonomic family |
| [,59] | order | character | taxonomic order |
| [,60] | class | character | taxonomic class |
| [,61] | superclass | character | taxonomic superclass |
| [,62] | subphylum | character | taxonomic subphylum |
| [,63] | phylum | character | insert_description_here |
| [,64] | kingdom | character | taxonomic kingdom |
| [,65] | trophicDiet | character | source of trophic level from Fish Base or Sea Life Base; 'y' means it was from this source |
| [,66] | trophicOrig | character | from Fish Base or Sea Life Base; was the trophic level estimated from an 'Original sample'? |
| [,67] | Picture | character | Is there a picture of this critter assoicated with the package? Note: this isn't always accurate |
| [,68] | trophicLevel | numeric | the trophic level from Fish Base or Sea Life Base |
| [,69] | trophicLevel.se | numeric | the standard error of the trophic level |
| [,70] | tax.src2 | character | informs source of taxonomic correct; the name of a source of taxonomic information other than taxInfo (other than manual entries) |
| [,71] | 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 |
| [,72] | 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 |
| [,73] | website | character | URL reference for taxonomic information |
| [,74] | 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 |
| [,75] | keep.row | logical | Column indicating whether or not the row show likely be excluded |
| [,76] | row_flag | character | if keep.row is TRUE, why was this row flagged to be dropped? |
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