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fisheries fisheries-stock-assessment r rstats stock-synthesis

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README 

        
# r4ss: R code for Stock Synthesis



[![release date](https://img.shields.io/github/last-commit/r4ss/r4ss)](https://github.com/r4ss/r4ss/commits/main)

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[![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/r4ss?)](https://github.com/metacran/cranlogs.app)

[![](https://cranlogs.r-pkg.org/badges/r4ss?color=FFD700)](https://www.r-pkg.org/pkg/r4ss)



Stock Synthesis is a fisheries stock assessment model written in ADMB by

Rick Methot. The Stock Synthesis software and many other associated

materials are available in the [Stock Synthesis GitHub repository](https://github.com/nmfs-ost/ss3-source-code) and other repositories under the [nmfs-ost organization](https://github.com/nmfs-ost).

The r4ss package is a collection of R functions for interacting with

Stock Synthesis. It is based on the original work of Ian Stewart begun

around 2005 and released as an open source R package in 2009. The

package has a long list of authors and has benefited from a large

community of users making suggestions and reporting issues.



*This code comes with no warranty or guarantee of accuracy. It merely

represents an ongoing attempt to integrate output plotting, statistics

and diagnostics. It is absolutely necessary that prior to use with a new

application, the user checks the output manually to verify that there

are no plotting or statistical bugs which could incorrectly represent

the output files being analyzed.*



## Installation



There is a CRAN version of r4ss but it is out of date 

(last updated in May 2022). Installing directly from github via either the 

{pak} package or {remotes} will get the most recent main branch which should 

always work with the latest version of Stock Synthesis (as well as many older 

versions). Sometimes one or the other of these installations doesn't work, in

that case find where your R packages are stored using `.libPaths()`, navigate 

there and manually delete the previously downloaded {r4ss} package. Then, 

restart R and use the other installation method to download {r4ss}. 

This manual deletion approach may also for dependent packages if updating them

is causing errors in the installation of r4ss.



```S

# option 1: install via {pak}

install.packages("pak")

pak::pkg_install("r4ss/r4ss")



# option 2: install via {remotes}

install.packages("remotes")

remotes::install_github("r4ss/r4ss")

```



Once you have installed the r4ss package, it can be loaded using:



```S

library(r4ss)

```



To get notifications about r4ss, you can watch this GitHub project or

follow issues and discussions in the [Stock Synthesis GitHub repository](https://github.com/nmfs-ost/ss3-source-code).

Additionally, you can follow messages on the [forums on Stock Synthesis

VLab](https://vlab.noaa.gov/web/stock-synthesis/public-forums), however, 

most communications about Stock Synthesis are distributed via GitHub rather than VLab. 

Note that to subscribe to the Stock Synthesis VLab forums, an account is

required, but those without an account may still view and post forum

messages.



The r4ss website  includes a vignette explaining 

the use of common functions and 

[example r4ss plots](https://r4ss.github.io/r4ss/BigSkate) from a 2019 

Big Skate stock assessment for the U.S. West Coast 

(which used SS version 3.30.13.02 and r4ss version 1.39.0). 



## Citing r4ss



Please cite r4ss as:



Ian G. Taylor, Kathryn L. Doering, Kelli F. Johnson, Chantel R. Wetzel,

Ian J. Stewart, 2021. Beyond visualizing catch-at-age models: Lessons

learned from the r4ss package about software to support stock

assessments, Fisheries Research, 239:105924.

.



## Changes



See [NEWS.md](https://github.com/r4ss/r4ss/blob/main/NEWS.md) for a (not

very complete) log of changes to r4ss, starting with r4ss v1.24.0 from

2014. The list of commits at 

provides a much more detailed list.



## Contributing to r4ss



Interested in contributing to r4ss? We recognize contributions come in

many forms, including but not limited to code, reporting issues,

creating examples and/or documentation.



We strive to follow the [NMFS Fisheries Toolbox Contribution

Guide](https://github.com/nmfs-fish-tools/Resources/blob/master/CONTRIBUTING.md).

We also have included r4ss-specific code contribution information in the

[Git workflow page of the r4ss

wiki](https://github.com/r4ss/r4ss/wiki/Git-Workflow). Note that these

are guidelines, not rules, and we are open to collaborations in other

ways that may work better for you. Please feel free to reach out to us

by opening an issue in this repository or by emailing the maintainer

(call `maintainer("r4ss")` in R to view the current maintainer's name

and email address).



Note that by contributing, you are expect to uphold the [code of

conduct](#code-of-conduct).



## Reporting problems



Please report any issues with this package by posting a new github issue

at . You can also write to

[email protected].



## Code of conduct



This project and everyone participating in it is governed by the [NMFS

Fisheries Toolbox Code of

Conduct](https://github.com/nmfs-fish-tools/Resources/blob/master/CODE_OF_CONDUCT.md).

By participating, you are expected to uphold this code. Please report

unacceptable behavior to

[[email protected]](mailto:[email protected]). Note

that the maintainers of r4ss do not have access to this email account,

so unacceptable behavior of maintainers can also be reported here.



The NMFS Fisheries Toolbox Code of Conduct is adapted from the

[Contributor Covenant][homepage], version 1.4, available at



[homepage]: 



For answers to common questions about this code of conduct, see