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Pull biological data (age, length, weight) from the NWFSC data warehouse

pull_bio.Rd

The website is: https://www.webapps.nwfsc.noaa.gov/data This function can be used to pull a single species or all observed species In order to pull all species leave common_name or sci_name as NULL

Usage

pull_bio(
  survey,
  common_name = NULL,
  sci_name = NULL,
  years = c(1970, 2050),
  dir = NULL,
  convert = TRUE,
  verbose = TRUE,
  standard_filtering = TRUE
)

Arguments

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.

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.

dir

Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.

convert

TRUE/FALSE to convert column names to first letter uppercase which aligns with the expected names in data processing functions.

verbose

A logical that specifies if you want to print messages and warnings to the console. The default is TRUE.

standard_filtering

A logical TRUE/FALSE that specifies whether data should be filtered using the standard filtering which removes tows with bad performance (water haul or poor net performance), or stations that have been removed from the survey sampling protocol.

Author

Chantel Wetzel

Examples

if (FALSE) { # \dontrun{
# SurveyName is only arg that has to be specified
bio_dat <- PullBio.fn(SurveyName = "NWFSC.Combo")

# Example with specified common name
bio_dat <- PullBio.fn(
  Name = "vermilion rockfish",
  SurveyName = "NWFSC.Combo"
)

# Example with specified scientific name
bio_dat <- PullBio.fn(
  SciName = "Eopsetta jordani",
  SurveyName = "NWFSC.Combo"
)

# Example with multiple names
bio_dat <- PullBio.fn(
  SciName = c("Sebastes aurora", "Eopsetta jordani"),
  SurveyName = "NWFSC.Combo"
)
} # }