RVdataframe: Formats fishery independent survey data for use in the...

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

Description

This function imports data exported by stratifyBiomass(), adds column YEAR, and binds all years together.

Usage

RVdataframe(path, s.year, e.year, areas = c("shelf", "esswss", "nafo",
  "strat"), lengthbased, qadjusted, update_RV = FALSE, csv = TRUE,
  rdata = TRUE)

Arguments

path	The filepath to the /data folder.
s.year	Year for which to begin data extraction.
e.year	Year for which to end data extraction.
areas	Areas (spatial scales) for which to format data. A separate dataframe will be exported for each area. Options are "shelf", "esswss", "nafo", "strat", or any combination of the four. Default is areas = c("shelf", "esswss", "nafo", "strat").
lengthbased	Logical parameter indicating whether to return stratified length-based data (lengthBased = TRUE) or not length-based data (lengthBased = FALSE).
qadjusted	Logical parameter indicating whether to return q-adjusted biomass and abundance data (qadjusted = TRUE) or not q-adjusted biomass and abundance data (qadjusted = FALSE). q-adjustments are applied at the set level.
update_RV	Logical parameter indicating whether to run extractRV(). Extracting the abundance and biomass data for all years and areas is time consuming, so if data is already extracted, use the default update_biomass = FALSE. If update_RV = TRUE, user must define channel in the global environment (see Details).
csv	Logical value indicating whether to export dataframe as a .csv file. Default is csv = TRUE.
rdata	Logical value indicating whether to export dataframe as a .RData file. Default is rdata = TRUE.

Details

If update_RV = TRUE, user must define channel = odbcConnect("ptran", uid = ###, pwd = ###) in the global environment. This channel must have access to the gscat, gsdet, gsinf, and gs_lengths tables from the groundfish database and the nafo_strat table from the mfd_stomach database.

Value

This function creates a directory path/output/RV/area for each entry in area. In each area folder is a csv and/or RData file for the specified combination of lengthbased and qadjusted (object name RVdata). These files are formatted for the marindicators package.

If lengthbased = TRUE, then RVdata has 6 columns: YEAR, SPECIES, ID, LENGTH (cm), BIOMASS (kg), and ABUNDANCE (numbers).

If lengthbased = FALSE, then RVdata has 5 columns: YEAR, SPECIES, ID, BIOMASS (kg), and ABUNDANCE (numbers).

References

Original code by DD.

See Also

Other RV functions: biomassData, extractRV, qBiomass, stratifyBiomass, vesselCorr

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