download_catch_rates: Compile and harmonize fish survey data

View source: R/download_catch_rates.R

download_catch_ratesR Documentation

Compile and harmonize fish survey data

Description

download_catch_rates queries and harmonizes fish survey data from public databases

Usage

download_catch_rates(survey = "Eastern_Bering_Sea", add_zeros = TRUE,
  species_set = 10, error_tol = 1e-12, localdir = NULL)

Arguments

survey

name of survey to be queried

add_zeros

Boolean, whether to add zeros for species in samples that were conducted but where the species was not encountered (recommended: TRUE)

species_set

either a character vector (giving scientific names of species) or a integer (giving number of most-frequently sighted species) to be queried

error_tol

tolerance for errors when error-checking the algorithm for adding zeros

localdir

local directory to save and load data from regional databases (to potentially avoid download times or problems without internet access)

Value

A data frame of survey data with the following columns

Sci

Scientific name

Year

Calendar year

TowID

UniqueID associated with each sampling occasion

Lat

Latitude

Long

Longitude

Wt

Catch in KG (may be standardized by effort, check survey for details)

Num

Catch in numbers (may be standardized by effort, check survey for details)

...

Potentially other column labels


James-Thorson/FishData documentation built on March 21, 2023, 3:54 a.m.