fishPiCodes: fishPi project code lists

#' Areas
#'
#' @description Area codes for the fishPi project and the RDB.
#'
#' @usage data(areas)
#'
#' @format A data frame with columns: code: All area codes. area: The FAO area.
#'   subarea: The FAO subarea code. division: The FAO division code.
#'   subdivision: The FAO subdivision code. unit: The FAO unit code.
#'   description: A description of the area to which the code relates.
#'
#' @details The EU master data register uses FAO codes to describe fishing
#'   areas. The FAO codes follow a hierachical structure through areas,
#'   subareas, division, subdivision and unit. For example the IVa subdivision
#'   in the North Sea is "27.4.a". See http://www.fao.org/fishery/area/search/en
#'   and http://ec.europa.eu/fisheries/cfp/control/codes/index_en.htm
#'
#' @md
#' @source Alastair Pout \email{a.pout@marlab.ac.uk} and Work Package 2.2 core
#'   team
#'
#' @examples
#' # loading the data
#' data(areas)
#'
#' # looking at the first 5 rows
#' head(areas)
#'
#' # areas in FAO area 27
#' areas$code[grep("27",areas$code)]
"areas"



#' FAO ASFIS species lists
#'
#' @description Data frame of the ASFIS species lists as used by the FAO.
#'
#' @usage data(ASFIS)
#'
#' @format Data frame consisting of columns:
#'
#'   ISSCAAP: The grouping code e.g. 32 = cod hakes haddocks, 38 = sharks rays,
#'   chimaeras;
#'
#'   TAXOCODE: Taxanomic code
#'
#'   X3A_CODE: 3 alpha code for the species e.g. MAC = mackerel, POK = saithe
#'   etc
#'
#'   Scientific_name: Scientific name of the species
#'
#'   English_name: English names for the species
#'
#'   French_name: French name for the species
#'
#'   Spanish_name: Spanish name for the species
#'
#'   Author: Author for the species type specamine
#'
#'   Family: Family to which the species belongs
#'
#'   Order: Order to which the species belongs
#'
#'   Stats_data: Species for which there is capture data held by FAO
#'
#' @md
#'
#' @source FAO as of Feb 2017
#'
#'   [http://www.fao.org/fishery/collection/asfis/en]{http://www.fao.org/fishery/collection/asfis/en}
#'
#' @seealso [`whatFish`] - function to map names and codes.
#'
#' @examples
#' data(ASFIS)
#' head(ASFIS)
"ASFIS"




#' The FAO ASFIS species lists matched to the WoRMS species lists.
#'
#' @description A look-up table matching the ASFIS species lists with the WoRMS
#'   species lists.
#'
#' @usage data(ASFIS_WoRMS)
#'
#' @format Data frame consisting of columns:
#'
#'   TAXOCODE: ASFIS Taxanomic code
#'
#'   X3A_CODE: ASFIS 3 alpha code for the species e.g. MAC = mackerel, POK =
#'   saithe etc
#'
#'   Scientific_name: ASFIS Scientific name of the species
#'
#'   AphiaID: WoRMS AphiaID number
#'
#'   Match.type: Status of the match between ASFIS and WoRMS
#'
#'   ScientificName: WoRMS Scientific name
#'
#'   AphiaID_accepted: The accepted WoRMS AphiaID
#'
#'   Kingdom: Kingdom to which the species belongs
#'
#'   Phylum: Phylum to which the species belongs
#'
#'   Class: Class to which the species belongs
#'
#'   Order: Order to which the species belongs
#'
#'   Family: Family to which the species belongs
#'
#'   Genus: Genus to which the species belongs
#'
#'   Subgenus: Subgenus to which the species belongs
#'
#'   Species: Species to which the species belongs
#'
#'   Subspecies: Subspecies to which the species belongs
#'
#' @md
#'
#' @source For ASFIS:
#'
#'   [http://www.fao.org/fishery/collection/asfis/en]{http://www.fao.org/fishery/collection/asfis/en}
#'
#'   For WoRMS:
#'
#'   [http://www.marinespecies.org/]{http://www.marinespecies.org/}
#'
#' @seealso [`whatFish`] - function to map names and codes.
#'
#' @examples
#' data(ASFIS_WoRMS)
#' head(ASFIS_WoRMS)
"ASFIS_WoRMS"



#' Metiers
#'
#' @description Allowable metiers for the RDB by region and fishing ground.
#'
#' @details Allowable metiers as circulated between RCM chairs Mar 2015.
#'
#' @usage data(metiers)
#'
#' @format A data frame with columns:
#'
#'   gear: The gear code
#'
#'   target: The intended target assemblage
#'
#'   mesh: The mesh size range in mm.
#'
#'   select: The presence of a selection device, either 0 for not
#'
#'   present, or 1 for present.
#'
#'   meshselect: The mesh size in the selection device, in mm.
#'
#'   level5: The level 5 metier, this is the combination of the gear and the
#'   target assemblage.
#'
#'   level6: The level 6 metier, this is the combination of the gear, target
#'   assemblage, the mesh size, the selection device, and the mesh size in the
#'   selection device.
#'
#' @md
#'
#' @source Alastair Pout \email{a.pout@marlab.ac.uk} and Work Package 2.2 core
#'   team
#'
#' @examples
#' # loading the data
#' data(metiers)
#'
#' # looking at the first 5 rows
#' head(metiers)
#'
#' # metiers allowable in areas 27.4 and 27.7.d
#' metiers$level6[metiers$IV..VIId==1]
"metiers"




#' UK port codes
#'
#' @description The LOCODE of UK ports with additional sub UK level country
#'   codes
#'
#' @details The UN LOCODE data is the United Nations Code for Trade and
#'   Transport Locations. However the GBR code is used for all UK potrs. This
#'   data set resolves the GBR country codes down to Scotland, England, Wales,
#'   Northern Ireland, Channel Iselands and the Isle of Man.
#'
#' @usage data(portCodeUK)
#'
#' @format A data frame with columns:
#'
#'   ctryCode: The country code at sub UK level
#'
#'   loCode: The location code, a 5 letter code the first two of which are
#'   country specific, the following 3 are the unique identifier
#'
#'   of the location
#'
#'   locName: The location name.
#'
#'   lat: Decimal latitude of the location.
#'
#'   lon: Decimal longitude of the location.
#'
#' @md
#'
#' @source Alastair Pout \email{a.pout@marlab.ac.uk} and fishPi core team
#'
#' @examples
#' # loading the data
#' data(portCodeUK)
#'
#' # looking at the first 5 rows
#' head(portCodeUK)
#'
#' # plotting locations
#' plot(portCodeUK$lon,portCodeUK$lat,pch=".")
"portCodeUK"




#' ICES Statistical rectangles.
#'
#' @description Data frame of the ICES statistical rectangles and their area
#'   division and sub division codes.
#'
#' @usage data(rectangles)
#'
#' @format Data frame consisting of columns:
#'
#'   TypeName: mostly ICES there are some FAO areas
#'
#'   AreaCode: The code used for the area; the unique set of all area, subareas
#'   and divisions.
#'
#'   AreaName: The area name
#'
#'   lon: Longitude of the ICES Statistical rectangle.
#'
#'   lat: Longitude of the ICES Statistical rectangle.
#'
#'   statsq: Same as statistical rectangle name
#'
#'   division: The division to which the statistical rectangle belongs.
#'
#'   subarea: The subarea to which the statistical rectangle belongs.
#'
#'   area: The area to which the statistical rectangle belongs.
#'
#' @md
#'
#' @source RDB as of 9 October 2012
#'
#' @examples
#' data(rectangles)
#' head(rectangles)
"rectangles"



#' Species
#'
#' @description Species names and WoRMS codes.
#'
#' @details The species listed here are 782 names and codes that are in the RDB
#'   as of June 2015 and are accepted by the WoRMS list. WoRMS is the World
#'   Register of Marine Species See [http://www.marinespecies.org/]{http://www.marinespecies.org/}
#'
#' @usage data(species)
#'
#' @format A data frame with columns:
#'
#'   spp: The scientific species name
#'
#'   code: The AlphiaID 6 digit code used by WoRMS
#'
#' @md
#'
#' @source Alastair Pout \email{a.pout@marlab.ac.uk} and Work Package 2.2 core
#'   team
#'
#' @examples
#' # loading the data
#' data(species)
#' # looking at the first 5 rows
#' head(species)
"species"




#' Stocks
#'
#' @description Stock definitions.
#'
#' @details A data frame of the ICES Intercatch stock definitions. the species
#'   code is the FAO code, the area field covers Intercatch ICES areas,
#'   divisions and sub-areas, and rectangles, functional units are included for
#'   Nephrops
#'
#' @usage data(stocks)
#'
#' @format A data frame with columns:
#'
#'   stock: the ICES stock definition
#'
#'   sppFAO: The species FAO name
#'
#'   area: The ICES area or rectangle.
#'
#'   desc: The stock description
#'
#'   areaType: the area type
#'
#' @md
#'
#' @source Lucia Zarauz and fishPi 2 Work Package 2 core team
#'
#' @examples
#' # loading the data
#' data(stocks)
#' # looking at the first 5 rows
#' head(stocks)
"stocks"




#' UN Location Codes
#'
#' @description UN Location Codes v 1.7.
#'
#' @details The UN LOCODE data is the United Nations Code for Trade and
#'   Transport Locations. Full details of the data can be obtained at
#'   [http://www.unece.org/cefact/locode/welcome.html]{http://www.unece.org/cefact/locode/welcome.html}.
#'
#' @usage data(UNLOCODE)
#'
#' @format A data frame with columns: ctryCode: The country code
#'
#'   loCode: The location code, a 5 letter code the first two of which are
#'   country specific, the following 3 are the unique identifier of the location
#'
#'   locName: The location name.
#'
#'   lat: Decimal latitude of the location.
#'
#'   lon: Decimal longitude of the location.
#'
#'   fishPort: Logical variable Y and N as to whether the location is a fish
#'   port.
#'
#'   funcCode: 8 character string relating to the location function and the
#'   following 8 columns: port, rail, road, airport, post, multi, fixed, border.
#'
#'   port: Logical variable Y and N as to whether the location is a port.
#'
#'   rail: Logical variable Y and N as to whether the location is a rail
#'   terminal.
#'
#'   road: Logical variable Y and N as to whether the location is a road
#'   terminal.
#'
#'   airport: Logical variable Y and N as to whether the location is a airport.
#'
#'   post: Logical variable Y and N as to whether the location is a postal
#'   exchange office.
#'
#'   multi: Logical variable Y and N as to whether the location is a multi
#'   functional.
#'
#'   fixed: Logical variable Y and N as to whether the location is a fixed
#'   transport function e.g. oil platform.
#'
#'   boarder: Logical variable Y and N as to whether the location is a boarder
#'   crossing.
#'
#' @md
#'
#' @source Alastair Pout \email{a.pout@marlab.ac.uk} and Work Package 2.2 core
#'   team
#'
#' @examples
#' # loading the data
#' data(UNLOCODE)
#' # looking at the first 5 rows
#' head(UNLOCODE)
#' # metiers allowable in areas 27.4 and 27.7.d
#' # plotting locations
#' plot(UNLOCODE$lon,UNLOCODE$lat,pch=".")
"UNLOCODE"




#' Vessel Types and DCF gear codes
#'
#' @description Vessel Types used for the DCF fleet segmentation and their
#'   repective DCF gear codes.
#'
#' @details The DCF fleet segmantations are based on a vessel Type
#'   classification, these vessel types are in turn based on aggregations of DCF
#'   defined gear types. This data set enables vessel Types to be mapped from
#'   gear types. Full details of the data can be obtained at
#'   [http://datacollection.jrc.ec.europa.eu/web/dcf/wordef/fleet-segment-dcf]{http://datacollection.jrc.ec.europa.eu/web/dcf/wordef/fleet-segment-dcf}.
#'
#' @usage data(vslType)
#'
#' @format A data frame with columns:
#'
#'   DCFGear: The DCF gear code i.e. the first 3 characters of the metier code
#'
#'   NominalGearType: The DCF gear type description.
#'
#'   vslType: the DCF vessel type appropriate to the gear type.
#'
#'   GearType: Active or passive gear type classification.
#'
#' @md
#'
#' @source Alastair Pout \email{a.pout@marlab.ac.uk} and Work Package 2.2 core
#'   team
#'
#' @examples
#' # loading the data
#' data(vslType)
#' # looking at the first 5 rows
#' head(vslType)
"vslType"