The R package ebswp was developed for doing stock assessments of eastern Bering Sea walleye pollock for the AFSC. The stock assessment model was coded using the Autodif Model Builder (ADMB) software.

Cloning the repository (optional)

The R package ebswp lives on a private GitHub repository. The repository can be cloned to your computer from the command line or using a user interface. From the command line using Linux the repository can be cloned using:

git clone https://github.com/afsc-assessments/ebs_pollock

Installation

There are several options for installing the ebswp R package.

Option 1

The ebswp package can be installed from within R using:

devtools::install_github(repo = "afsc-assessments/ebs_pollock", dependencies = TRUE, 
                         build_vignettes = TRUE, auth_token = "your_PAT")

Option 2

The GitHub repository can be cloned to your computer and the package installed from the command line. From Linux this would involve:

git clone https://github.com/afsc-assessments/ebs_pollock
R CMD INSTALL ebswp

Option 3

This time from within R using:

devtools::install("ebs_pollock")

Help

Help for all ebswp functions and data sets can be found on the R help pages associated with each function and data set. Help for a specific function can be viewed using ?function_name, for example:

?run_model
?tab_fit
?plot_sel

Alternatively, to see a list of all available functions and data sets use:

help(package = "ebswp")

Examples

The package vignettes are a great place to see what ebswp can do. You can view the package vignettes from within R using:

browseVignettes(package = "ebswp")
vignette(topic = "ebswp", package = "ebswp")

Website

All of the vignettes and the help pages for each function are bundled together and published on the website https://afsc-assessments.github.io/ebs_pollock/.

Developers

Developers will want to do things slightly differently. See the Model development vignette.

Acronymns

NOAA: National Oceanic and Atmospheric Administration
NMFS: National Marine Fisheries Service
AFSC: Alaska Fisheries Science Center
REFM: Resource and Ecology and Fisheries Management

NOAA README

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NOAA License

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

NOAA Fisheries

U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries