{"id":15555163,"url":"https://github.com/psolymos/opticut","last_synced_at":"2025-04-23T20:31:32.617Z","repository":{"id":33791384,"uuid":"37479673","full_name":"psolymos/opticut","owner":"psolymos","description":"Likelihood Based Optimal Partitioning","archived":false,"fork":false,"pushed_at":"2024-05-21T16:50:24.000Z","size":9292,"stargazers_count":2,"open_issues_count":4,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-17T05:54:44.211Z","etag":null,"topics":["cran","ecology","indicator-species-analysis","likelihood","optimal-partitioning","r","species"],"latest_commit_sha":null,"homepage":"https://github.com/psolymos/opticut","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/psolymos.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-06-15T17:20:36.000Z","updated_at":"2024-05-21T16:46:39.000Z","dependencies_parsed_at":"2024-05-21T17:08:10.869Z","dependency_job_id":null,"html_url":"https://github.com/psolymos/opticut","commit_stats":{"total_commits":833,"total_committers":1,"mean_commits":833.0,"dds":0.0,"last_synced_commit":"b98a0653e892e5f48a141be6711e2e4977eeb7ed"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psolymos%2Fopticut","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psolymos%2Fopticut/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psolymos%2Fopticut/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psolymos%2Fopticut/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/psolymos","download_url":"https://codeload.github.com/psolymos/opticut/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250509549,"owners_count":21442448,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cran","ecology","indicator-species-analysis","likelihood","optimal-partitioning","r","species"],"created_at":"2024-10-02T15:07:04.534Z","updated_at":"2025-04-23T20:31:32.595Z","avatar_url":"https://github.com/psolymos.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# opticut: Likelihood Based Optimal Partitioning and Indicator Species Analysis\n\n[![CRAN version](https://www.r-pkg.org/badges/version/opticut)](https://CRAN.R-project.org/package=opticut)\n[![CRAN mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/opticut)](https://CRAN.R-project.org/package=opticut)\n[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)\n\nLikelihood based optimal partitioning for indicator species analysis and more.\nFinding the best binary partition for each species based on\nmodel selection, possibly controlling for modifying/confounding\nvariables as described in Kemencei et al. (2014).\n\n![](https://github.com/psolymos/opticut/raw/master/extras/oc-logo.gif)\n\n## Versions\n\nInstall stable version from CRAN:\n\n```R\ninstall.packages(\"opticut\")\n```\n\nInstall development version from GitHub:\n\n```R\ndevtools::install_github(\"psolymos/opticut\")\n```\n\nUser visible changes in the package are listed in the [NEWS](https://github.com/psolymos/opticut/blob/master/NEWS.md) file.\n\n## Report a problem\n\nUse the [issue tracker](https://github.com/psolymos/opticut/issues)\nto report a problem.\n\n## Typical workflow\n\n```R\nlibrary(opticut)\n\n## --- community data ---\ny \u003c- cbind(\n    Sp1 = c(4,6,3,5, 5,6,3,4, 4,1,3,2),\n    Sp2 = c(0,0,0,0, 1,0,0,1, 4,2,3,4),\n    Sp3 = c(0,0,3,0, 2,3,0,5, 5,6,3,4))\n\n## --- stratification ---\ng \u003c-      c(1,1,1,1, 2,2,2,2, 3,3,3,3)\n\n## --- find optimal partitions for each species ---\noc \u003c- opticut(y, strata = g, dist = \"poisson\")\nsummary(oc)\n#  Multivariate opticut results, comb = rank, dist = poisson\n#\n#  Call:\n#  opticut.default(Y = y, strata = g, dist = \"poisson\")\n#\n#  Best supported models with logLR \u003e= 2:\n#      split assoc      I  mu0  mu1 logLR      w\n#  Sp3   2 3    ++ 0.6471 0.75 3.50 4.793 0.6962\n#  Sp2     3   +++ 0.8571 0.25 3.25 9.203 0.9577\n#  2 binary splits\n#  1 species not shown\n\n## --- visualize the results ---\nplot(oc, cut = -Inf)\n\n## --- quantify uncertainty ---\nuc \u003c- uncertainty(oc, type = \"asymp\", B = 999)\nsummary(uc)\n#  Multivariate opticut uncertainty results\n#  type = asymp, B = 999, level = 0.95\n#\n#      split R      I   Lower  Upper\n#  Sp1   1 2 1 0.2860 0.02341 0.5668\n#  Sp3   2 3 1 0.6218 0.21456 0.8813\n#  Sp2     3 1 0.8274 0.51229 0.9680\n```\n\n## Dynamic documents with opticut\n\nHere is a minimal [Rmarkdown](https://rmarkdown.rstudio.com/) example: [Rmd](https://raw.githubusercontent.com/psolymos/opticut/master/extras/opticut-knitr-example.Rmd) source, knitted [PDF](https://github.com/psolymos/opticut/raw/master/extras/opticut-knitr-example.pdf).\n\n## References\n\nKemencei, Z., Farkas, R., Pall-Gergely, B., Vilisics, F., Nagy, A., Hornung,\nE. \u0026 Solymos, P. (2014): Microhabitat associations of land snails in\nforested dolinas: implications for coarse filter conservation.\n_Community Ecology_ **15**:180--186.\n[[link](https://dx.doi.org/10.1556/ComEc.15.2014.2.6), [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPWnBjLUxvcXJVUXc/view?usp=sharing)]\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpsolymos%2Fopticut","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpsolymos%2Fopticut","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpsolymos%2Fopticut/lists"}