pull_biological_samples: Pull biological sample information from the NWFSC data...

In nwfsc-assess/nwfscSurvey: Northwest Fisheries Science Center Survey

Pull biological sample information from the NWFSC data warehouse for biological collections taken at sea. Generally these are samples that require lab processing. Generally, these types of biological sample are maturity, stomach, fin clips, and tissue samples. This function returns collection information for these samples include the sample numbers which allows the lab analysis to be linked back to the sampled fish. The website is: https://www.webapps.nwfsc.noaa.gov/data.

Description

Pull biological sample information from the NWFSC data warehouse for biological collections taken at sea. Generally these are samples that require lab processing. Generally, these types of biological sample are maturity, stomach, fin clips, and tissue samples. This function returns collection information for these samples include the sample numbers which allows the lab analysis to be linked back to the sampled fish. The website is: https://www.webapps.nwfsc.noaa.gov/data.

Usage

pull_biological_samples(
  common_name = NULL,
  sci_name = NULL,
  years = c(1980, 2050),
  survey = "NWFSC.Combo",
  dir = NULL,
  verbose = TRUE
)

Arguments

common_name	A character entry with the desired common name of the species you want to pull data for from the data warehouse. Use a vector of names if you want information for more than one species or if the desired species is included in the database using more than one name, e.g., vermilion rockfish (see the example below). Use the sci_name argument if you know the latin name.
sci_name	A character entry with the desired scientific name of the species you want to pull data for from the data warehouse. Use a vector of names if you want information for more than one species or if the desired species is included in the database using more than one name, e.g., vermilion rockfish (see the example below). Use the common_name argument if you know the common name.
years	An integer vector of length two with the range of years to pull data for (e.g., c(2003, 2024)). Vector can not contain -Inf or Inf.
survey	A character entry from one of the following options that specifies which survey to pull the data for. The input options are: Triennial, AFSC.Slope, NWFSC.Combo, NWFSC.Slope, NWFSC.Shelf, NWFSC.Hypoxia, NWFSC.Santa.Barb.Basin, NWFSC.Shelf.Rockfish (not yet working), NWFSC.Hook.Line (not yet working), NWFSC.Video, Triennial.Canada The National Marine Fishery Service Alaska Fisheries Science Center (AFSC) Triennial survey was conducted between 1977 - 2004 occurring every 3rd year. The initial year, 1977, survey is not traditionally used in calculating indices of abundance. The Triennial survey sampled areas within the Canadian EEZ on the West Coast of Vancouver Island in 1980 - 2001 but these data are associated with a different survey name "Triennial.Canada". The AFSC Slope Survey (AFSC.Slope) along the west coast of the U.S. began in 1984 and occurred annually from 1988-2001, with the exception of 1994 and 1998, when surveys were not conducted. Prior to 1997, only a limited portion of the coast was covered in each year. U.S. West Coast groundfish stock assessments only use the four years of consistent and complete survey coverage (1997, 1999-2001). The Northwest Fisheries Science Center (NWFSC) Slope survey (NWFSC.Slope) was conducted between 1998 - 2001. The NWFSC West Coast Groundfish Bottom Trawl survey (NWFSC.Combo) is conducted annualy starting in 2003 (excluding 2020) and samples both the U.S. west coast shelf and slope between 55 - 1,280 meters. Data can only be pulled from one survey at a time, though we are working on allowing for a vector of survey names. Currently, NWFSC.Shelf.Rockfish and NWFSC.Hook.Line are not supported.
dir	directory where ouptut will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
verbose	A logical that specifies if you want to print messages and warnings to the console. The default is TRUE.

Value

Returns a data frame of special biological samples with sample number

Author(s)

Chantel Wetzel

nwfsc-assess/nwfscSurvey documentation built on April 29, 2024, 9:51 p.m.