README.Rmd

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output: github_document
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<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```


# East Bering Sea pollock <img src="man/figures/logo.png" align="right" height="140/"/>

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:

``` r
git clone https://github.com/afsc-assessments/ebswp
```

## Installation

There are several options for installing the `ebswp` R package.

### Option 1

The `ebswp` package can be installed from within R using:

``` r
devtools::install_github(repo = "afsc-assessments/ebswp", 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:

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

### Option 3

This time from within R using:

``` r
devtools::install("ebswp")
```

## 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:

``` r
?run_model
?tab_fit
?plot_sel
```

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

``` r
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:

``` r
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/ebswp/>.

## 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

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. 
All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. 
Any claims against the Department of Commerce or Department of Commerce 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 Department of Commerce.
The Department of Commerce 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 DOC or the United States Government.

### 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.

<img src="https://raw.githubusercontent.com/nmfs-general-modeling-tools/nmfspalette/main/man/figures/noaa-fisheries-rgb-2line-horizontal-small.png" height="75" alt="NOAA Fisheries">

[U.S. Department of Commerce](https://www.commerce.gov/) | [National
Oceanographic and Atmospheric Administration](https://www.noaa.gov) |
[NOAA Fisheries](https://www.fisheries.noaa.gov/)