Welcome
This R package generates the standard design-based indices of biomass, abundance, size composition, and age composition from NOAA-NMFS-AFSC-RACE-GAP bottom trawl survey data. Survey regions include: Gulf of Alaska (from 1990), Aleutian Islands (from 1991), Eastern Bering Sea Shelf (from 1982), Eastern Bering Sea Slope (from 2002), and Northern Bering Sea Shelf (from 2010).
Installation Instructions
In addition to the default packages in R (base, stats), the functions in gapindex use functions from five additional packages:
- RODBC: Enables ODBC (Open Database Connectivity) interface the AFSC Oracle database where the survey data are housed
- getPass: Allows for masking of Oracle user credentials (usernames, passwords) when accessing RODBC
- keyring: Allows the option for users to store their passwords
- lifecycle: Aids developers and users with shared conventions, documentation badges, deprecation warnings as the package develops over time
- data.table: Speeds up data.frame manipulations like reading, writing, aggregations, joins, ordering, sorting.
Please make sure these five packages are installed before installing gapindex
devtools::install_github("afsc-gap-products/gapindex")Collaborators
The gapindex R package is a product of two AFSC-RACE-GAP working groups regarding GAP data processes and index computation. Many thanks to those who participated in those working groups:
| Data Processes Working Group | Index Computation Working Group | Supervisors |
|---|---|---|
| Alexandra Dowlin (AlexandraDowlin-NOAA) | Zack Oyafuso (zoyafuso-NOAA)* | Stan Kotwicki (StanKotwicki-NOAA) |
| Emily Markowitz (EmilyMarkowitz-NOAA) | Margaret Siple (MargaretSiple-NOAA) | Duane Stevenson (Duane-Stevenson-NOAA) |
| Liz Dawson (liz-dawson-NOAA) | Rebecca Haehn (RebeccaHaehn-NOAA) | Ned Laman (Ned-Laman-NOAA) |
| Sarah Friedman (SarahFriedman-NOAA) | Lukas DeFilippo (Lukas-DeFilippo-NOAA) | Susanne McDermott (smcdermo) |
| Christopher Anderson (ChrisAnderson-NOAA) | Paul von Szalay (vszalay) | |
| Nancy Roberson (NancyRoberson) | Thaddaeus Buser (ThaddaeusBuser-NOAA) | |
| *package maintainer |
Legacy
Here is an non-exhaustive list of people who provided the foundation for many of the functions in this package:
AI-GOA: Michael Martin, Peter Munro, Ned Laman
Bering Sea: REM, Jason Conner, Jerry Hoff, Rebecca Haehn
Many of the index calculations are from Wakabayashi et al. (1985):
Wakabayashi, K., R. G. Bakkala, and M. S. Alton. 1985. Methods of the U.S.-Japan demersal trawl surveys, p. 7-29. In R. G. Bakkala and K. Wakabayashi (editors), Results of cooperative U.S.-Japan groundfish investigations in the Bering Sea during May-August 1979. Int. North Pac. Fish. Comm. Bull. 44.
Organization Acronymns
NOAA: National Oceanic and Atmospheric Administration
NMFS: National Marine Fisheries Service
AFSC: Alaska Fisheries Science Center
RACE: Resource Assessment and Conservation Engineering Division
GAP: Groundfish Assessment Program
Legal disclaimer
This repository is a software product and is not official communication of the National Oceanic and Atmospheric Administration (NOAA), or the United States Department of Commerce (DOC). All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the DOC or DOC bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation, or favoring by the DOC. The DOC seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by the DOC or the United States Government.