SSdata-package: Extracts Fishery Independent and Commercial Landings Data for...

In dempseydanielle/SSdata: Extracts Fishery Independent and Commercial Landings Data for the Scotian Shelf from DFO-Maritimes Databases

Description

SSdata provides functions to extract fishery independent (summer research vessel groundfish survey) and commercial landings data for the Scotian Shelf from DFO-Maritimes databases. Following Bundy, Gomez, and Cook (2017), fishery independent data can be extracted for four different spatial scales: Shelf, ESS/WSS, NAFO divisions,and strata. Commercial landings can be extracted for three spatial scales: Shelf, ESS/WSS, and NAFO divisions. Dataframes can be formatted for use in the marindicators package.

Details

User must define channel = odbcConnect("ptran", uid = ###, pwd = ###) in the global environment using the 'RODBC' package. This channel must have access to tables from several databases (Table 1).

Table 1: Databases and tables for which the user's channel must have access to extract fisheries independent and commercial landings data.

DATABASE	TABLES
Fishery independent data
groundfish	gscat, gsdet, gsinf, gs_lengths
mfd_stomach	nafo_strat
Commercial landings data
comland	nafo_summary, nafo_area_codes
cl	sub_trips_XXXX^1, identified_catches
mfd_obfmi database	marfis_catch_effort
gomezc database	indiseas_marfis2allcodes

^1 _XXXX represents the 4-digit year; e.g., sub_trips_1999

Four RData files are stored in the package to help extract and format the data:

1. strat_weights has two columns: STRAT and the corresponding AREA. Each AREA is converted to tow units in stratifyBiomass() using the conversion TOW UNITS = AREA/((35./6080.2)*1.75) until 1981 and TOW UNITS = AREA/((41./6080.2)*1.75) after 1981.

2. species_codes has three columns: ALLCODES (commercial species code), SPECIES (research vessel species code), and PROPORTION_OF_LANDINGS (for species that have one ALLCODES value but more than one SPECIES value). Used in LANDdataframe() to replace commercial species codes with research vessel species codes.

3. landings_groupings links NAFO sub-unit to area ID for the spatial scales of interest (Shelf, ESS/WSS, NAFO divisions). Applied in LANDdataframe().

4. commercial_groups links species to commercial groups. 11 columns: ALLCODES (commercial species code), ALLNAMES (commercial species name), and a column for each commercial group (GROUNDFISH, CLUPEIDS, INVERTEBRATES, FORAGE, FLATFISH, FINFISH, LARGE_PELAGICS, GADOIDS, SKATES). Species that belong to a commercial group have a 1 in the corresponding column (and NA in all other columns). Applied in extractLAND().

References

Bundy A, Gomez C, Cook AM. 2017. Guidance framework for the selection and evaluation of ecological indicators. Can. Tech. Rep. Fish. Aquat. Sci. 3232: xii + 212 p.

dempseydanielle/SSdata documentation built on May 3, 2020, 5:09 p.m.