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Life and Fishery","monthly_downloads":432,"total_dependent_repos":19,"total_dependent_packages":3,"readme":"# r4ss: R code for Stock Synthesis\n\n[![release date](https://img.shields.io/github/last-commit/r4ss/r4ss)](https://github.com/r4ss/r4ss/commits/main)\n[![call-r-cmd-check](https://github.com/r4ss/r4ss/actions/workflows/call-r-cmd-check.yml/badge.svg)](https://github.com/r4ss/r4ss/actions/workflows/call-r-cmd-check.yml)\n[![codecov](https://codecov.io/gh/r4ss/r4ss/branch/main/graph/badge.svg)](https://app.codecov.io/gh/r4ss/r4ss)\n\u003c!-- # commenting out version badges which were misleading (CRAN not recommended and GitHub number is only most recent release, not the current code) --\u003e\n\u003c!-- [![cran version](http://www.r-pkg.org/badges/version/r4ss)](https://cran.r-project.org/package=r4ss)\n[![github](https://img.shields.io/github/v/release/r4ss/r4ss?color=brightgreen\u0026label=GitHub)](https://github.com/r4ss/r4ss/releases/latest) --\u003e\n\u003c!-- [![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/r4ss?)](https://github.com/metacran/cranlogs.app) --\u003e\n\u003c!-- [![](https://cranlogs.r-pkg.org/badges/r4ss?color=FFD700)](https://www.r-pkg.org/pkg/r4ss) --\u003e\n\nStock Synthesis is a fisheries stock assessment model written in ADMB by\nRick Methot. The Stock Synthesis software and many other associated\nmaterials 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).\nThe r4ss package is a collection of R functions for interacting with\nStock Synthesis. It is based on the original work of Ian Stewart begun\naround 2005 and released as an open source R package in 2009. The\npackage has a long list of authors and has benefited from a large\ncommunity of users making suggestions and reporting issues.\n\n*This code comes with no warranty or guarantee of accuracy. It merely\nrepresents an ongoing attempt to integrate output plotting, statistics\nand diagnostics. It is absolutely necessary that prior to use with a new\napplication, the user checks the output manually to verify that there\nare no plotting or statistical bugs which could incorrectly represent\nthe output files being analyzed.*\n\n## Installation\n\nThere is a CRAN version of r4ss but it is out of date \n(last updated in May 2022). Installing directly from github via either the \n{pak} package or {remotes} will get the most recent main branch which should \nalways work with the latest version of Stock Synthesis (as well as many older \nversions). Sometimes one or the other of these installations doesn't work, in\nthat case find where your R packages are stored using `.libPaths()`, navigate \nthere and manually delete the previously downloaded {r4ss} package. Then, \nrestart R and use the other installation method to download {r4ss}. \nThis manual deletion approach may also for dependent packages if updating them\nis causing errors in the installation of r4ss.\n\n```S\n# option 1: install via {pak}\ninstall.packages(\"pak\")\npak::pkg_install(\"r4ss/r4ss\")\n\n# option 2: install via {remotes}\ninstall.packages(\"remotes\")\nremotes::install_github(\"r4ss/r4ss\")\n```\n\nOnce you have installed the r4ss package, it can be loaded using:\n\n```S\nlibrary(r4ss)\n```\n\nTo get notifications about r4ss, you can watch this GitHub project or\nfollow issues and discussions in the [Stock Synthesis GitHub repository](https://github.com/nmfs-ost/ss3-source-code).\nAdditionally, you can follow messages on the [forums on Stock Synthesis\nVLab](https://vlab.noaa.gov/web/stock-synthesis/public-forums), however, \nmost communications about Stock Synthesis are distributed via GitHub rather than VLab. \nNote that to subscribe to the Stock Synthesis VLab forums, an account is\nrequired, but those without an account may still view and post forum\nmessages.\n\nThe r4ss website \u003chttps://r4ss.github.io/r4ss\u003e includes a vignette explaining \nthe use of common functions and \n[example r4ss plots](https://r4ss.github.io/r4ss/BigSkate) from a 2019 \nBig Skate stock assessment for the U.S. West Coast \n(which used SS version 3.30.13.02 and r4ss version 1.39.0). \n\n## Citing r4ss\n\nPlease cite r4ss as:\n\nIan G. Taylor, Kathryn L. Doering, Kelli F. Johnson, Chantel R. Wetzel,\nIan J. Stewart, 2021. Beyond visualizing catch-at-age models: Lessons\nlearned from the r4ss package about software to support stock\nassessments, Fisheries Research, 239:105924.\n\u003chttps://doi.org/10.1016/j.fishres.2021.105924\u003e.\n\n## Changes\n\nSee [NEWS.md](https://github.com/r4ss/r4ss/blob/main/NEWS.md) for a (not\nvery complete) log of changes to r4ss, starting with r4ss v1.24.0 from\n2014. The list of commits at \u003chttps://github.com/r4ss/r4ss/commits/main\u003e\nprovides a much more detailed list.\n\n## Contributing to r4ss\n\nInterested in contributing to r4ss? We recognize contributions come in\nmany forms, including but not limited to code, reporting issues,\ncreating examples and/or documentation.\n\nWe strive to follow the [NMFS Fisheries Toolbox Contribution\nGuide](https://github.com/nmfs-fish-tools/Resources/blob/master/CONTRIBUTING.md).\nWe also have included r4ss-specific code contribution information in the\n[Git workflow page of the r4ss\nwiki](https://github.com/r4ss/r4ss/wiki/Git-Workflow). Note that these\nare guidelines, not rules, and we are open to collaborations in other\nways that may work better for you. Please feel free to reach out to us\nby opening an issue in this repository or by emailing the maintainer\n(call `maintainer(\"r4ss\")` in R to view the current maintainer's name\nand email address).\n\nNote that by contributing, you are expect to uphold the [code of\nconduct](#code-of-conduct).\n\n## Reporting problems\n\nPlease report any issues with this package by posting a new github issue\nat \u003chttps://github.com/r4ss/r4ss/issues\u003e. You can also write to\nIan.Taylor@noaa.gov.\n\n## Code of conduct\n\nThis project and everyone participating in it is governed by the [NMFS\nFisheries Toolbox Code of\nConduct](https://github.com/nmfs-fish-tools/Resources/blob/master/CODE_OF_CONDUCT.md).\nBy participating, you are expected to uphold this code. Please report\nunacceptable behavior to\n[fisheries.toolbox@noaa.gov](mailto:fisheries.toolbox@noaa.gov). Note\nthat the maintainers of r4ss do not have access to this email account,\nso unacceptable behavior of maintainers can also be reported here.\n\nThe NMFS Fisheries Toolbox Code of Conduct is adapted from the\n[Contributor Covenant][homepage], version 1.4, available at\n\u003chttps://www.contributor-covenant.org/version/1/4/code-of-conduct.html\u003e\n\n[homepage]: \u003chttps://www.contributor-covenant.org\u003e\n\nFor answers to common questions about this code of conduct, see\n\u003chttps://www.contributor-covenant.org/faq\u003e\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1016/j.fishres.2021.105924"],"works":{"https://doi.org/10.1016/j.fishres.2021.105924":{"id":"https://openalex.org/W3136120226","doi":"https://doi.org/10.1016/j.fishres.2021.105924","title":"Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments","display_name":"Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments","publication_year":2021,"publication_date":"2021-07-01","ids":{"openalex":"https://openalex.org/W3136120226","doi":"https://doi.org/10.1016/j.fishres.2021.105924","mag":"3136120226"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.fishres.2021.105924","pdf_url":"http://manuscript.elsevier.com/S0165783621000527/pdf/S0165783621000527.pdf","source":{"id":"https://openalex.org/S20111203","display_name":"Fisheries Research","issn_l":"0165-7836","issn":["0165-7836","1872-6763"],"is_oa":false,"is_in_doaj":false,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"publisher-specific-oa","version":"acceptedVersion","is_accepted":true,"is_published":false},"type":"article","type_crossref":"journal-article","open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"http://manuscript.elsevier.com/S0165783621000527/pdf/S0165783621000527.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016271275","display_name":"Ian Taylor","orcid":"https://orcid.org/0000-0002-4232-5669"},"institutions":[{"id":"https://openalex.org/I4210166920","display_name":"NOAA National Marine Fisheries Service Northwest Fisheries Science Center","ror":"https://ror.org/05r7z1k40","country_code":"US","type":"government","lineage":["https://openalex.org/I106745318","https://openalex.org/I4210166920"]},{"id":"https://openalex.org/I1308126019","display_name":"National Oceanic and Atmospheric Administration","ror":"https://ror.org/02z5nhe81","country_code":"US","type":"government","lineage":["https://openalex.org/I1308126019","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I106745318","display_name":"NOAA National Marine Fisheries Service","ror":"https://ror.org/033mqx355","country_code":"US","type":"government","lineage":["https://openalex.org/I106745318","https://openalex.org/I1308126019"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ian G. 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