{"id":22188445,"url":"https://github.com/vmikk/selfing-rate","last_synced_at":"2026-06-29T15:31:34.562Z","repository":{"id":81321568,"uuid":"38739309","full_name":"vmikk/Selfing-rate","owner":"vmikk","description":"R functions used to perform the analysis of COLONY and RMES output, and COLONY simulation.","archived":false,"fork":false,"pushed_at":"2016-09-15T07:55:52.000Z","size":32,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-24T20:14:41.909Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vmikk.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2015-07-08T07:38:12.000Z","updated_at":"2021-06-17T08:28:17.000Z","dependencies_parsed_at":null,"dependency_job_id":"5cb2b16b-7144-4475-b6fb-980fe6b96290","html_url":"https://github.com/vmikk/Selfing-rate","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/vmikk/Selfing-rate","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FSelfing-rate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FSelfing-rate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FSelfing-rate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FSelfing-rate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vmikk","download_url":"https://codeload.github.com/vmikk/Selfing-rate/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2FSelfing-rate/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34933498,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-29T02:00:05.398Z","response_time":58,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-12-02T11:10:36.934Z","updated_at":"2026-06-29T15:31:34.534Z","avatar_url":"https://github.com/vmikk.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Selfing-rate\nR functions used to perform the analysis of MLTR, COLONY and RMES output, and COLONY simulation.\n\nLinks to software:  \n- *MLTR*: http://genetics.forestry.ubc.ca/ritland/programs.html  \n- *COLONY2*: https://www.zsl.org/science/software/colony  \n- *RMES*: http://www.cefe.cnrs.fr/index.php/fr/recherche/accueil-dpt-ecologie-evolutive/genetique-et-ecologie-evolutive/800-gge/gge-chercheurs/196-patrice-david  \n\n# Examples:\n## Parsing results produced with MLTR v.3.4\nSingle population - run `MLTR_extract_single-pop.R`\nExample files: MLTR_sample1a.out, MLTR_sample1b.out, MLTR_sample1c.out)\n\nMultiple populations (MLTR grouping was enabled) - run `MLTR_extract_mult-pop.R`\nExample file: MLTR_sample2.out\n\n## Parsing results produced with RMES\nCopy results from the RMES output window and save them to file, run `RMES_extract.R`\nExample file: RMES_default_output.txt\n\n## Extraction of selfers from the COLONY simulation\nTo determine which individuals are the results of selfing in the COLONY simulation - run `Colony_Selfer.R`\nExample file: COLONY_simulation_Selfer.Selfer\n\n## Preparation of selfing matrix for COLONY simulation\n`Colony_PrepareRandomMatingMatrix.R` - these are internal functions which are used in `COLONY_PrepareInputFiles.R`\nInput parameters for the mating.matrix function:\n - n = dimensions of mating matrix (for monoecious plants number of males = number of females)\n - s = desired selfing rate (diagonal elements)\n - cs = vector of known offspring numbers from female (sum of columns)\n\n## Batch preparation of input files for COLONY simulation\nDirectory with input data should contain:\n - Design matrix (\"COLONY_simulation_Descr.txt\")\n - Genetic markers information for each population (\"Markers_\u003cPopulationName\u003e.txt\")\n - Allele frequency data for each population (\"\u003cPopulationName\u003e_AlleleFreq.txt\")\n\n*NB:* Population names should be the same as in design matrix ('Meadow' column)\n\nRun `COLONY_PrepareInputFiles.R`\n\nSeveral folders (5 replicates by default) will be created for each population.\n\nCopy COLONY files (impi.dll, libguide40.dll, libiomp5md.dll, colony2s.exe, simu2.exe) to each folder with input data, run simu2.exe (from batch file).\n\n**NB.** Some of the parameters (path to the COLONY folder, etc.) are hard-coded in `COLONY_PrepareInputFiles.R` and should be tuned for your current project.\n\n## Accuracy estimation of COLONY simulation\nRun `Colony_AccuracyEstimation.R`\nExample file: COLONY_simulation_Accuracy.Accuracy\n\n\n\n# Prerequisites:\nPackages [plyr](https://cran.r-project.org/web/packages/plyr/index.html) and [xlsx](https://cran.r-project.org/web/packages/xlsx/index.html)\n\n `install.packages(c(\"plyr\", \"xlsx\"))`\n\n# Citation:\nDulya O.V., Mikryukov V.S. Genetic variation and selfing rate in *Lychnis flos-cuculi* along an industrial pollution gradient // New Phytologist. 2016. V. 209. № 3. P. 1083-1095. DOI: 10.1111/nph.13636\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvmikk%2Fselfing-rate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvmikk%2Fselfing-rate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvmikk%2Fselfing-rate/lists"}