PullNominal.PacFIN: Pull the species information table and return nominal code(s)

In nwfsc-assess/PacFIN.Utilities: Generate fishery composition data from PacFIN data for the NWFSC

Pull the species information table and return nominal code(s)

Description

Pull the species information table and attempt to determine which nominal codes pertain to the desired species codes.

Usage

PullNominal.PacFIN(
  pacfin_species_code,
  username = getUserName("PacFIN"),
  password = ask_password()
)

Arguments

pacfin_species_code	A vector of strings specifying the PacFIN species code(s) you are interested in. This has sometimes been referred to as "SPID" in legacy sql scripts. An example for sablefish would be pacfin_species_code = "SABL". Lists of species codes in hierarchical order, by organization, and alphabetically organized can be found on the PacFIN website. Often you will want to include nominal species categories. Where, nominal (i.e., existing in name only) means information for a given species that is "derived" from non-species specific information, e.g., species complexes that are split out by species compositions like "nominal aurora rockfish" which would be ARR1. For some functions, these nominal categories can automatically be added, see the argument addnominal.
username	Most often, this is a string containing your username for the database of interest. You can use getUserName() if you prefer to not enter this argument and assume the default search and/or rules for finding your username will work. This is the default behavior if you leave username as a missing argument, i.e., username <- getUserName(database = database). Sometimes this search will fail because of legacy rules, which are unknown to the development team, that were used to create your username. Please email the maintainer of this package if you need more functionality here.
password	Most often, this is a string containing your password for the database of interest. You can use the function ask_password() if you would prefer to be prompted for your password. Please do not share this password with anyone or push code to a repository that has your password saved in it.

Value

A unique vector of character entries, where entries are valid PACFIN_SPECIES_CODEs. The length of the returned vector may not be the same length as the supplied pacfin_species_code argument because duplicates are removed. NA is returned if no values are found.

nwfsc-assess/PacFIN.Utilities documentation built on March 19, 2024, 11:54 p.m.