{"id":32403528,"url":"https://github.com/sergeitarasov/morphomodels","last_synced_at":"2026-07-09T04:31:30.906Z","repository":{"id":131279532,"uuid":"361825387","full_name":"sergeitarasov/MorphoModels","owner":"sergeitarasov","description":"Embedded Dependency (ED) models for inapplicable characters","archived":false,"fork":false,"pushed_at":"2024-02-26T07:59:59.000Z","size":14064,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-02-26T09:24:08.759Z","etag":null,"topics":["anatomy","bayesian","ed-models","inapplicable-characters","likelihood","markov","morphology","phylogenetics","revbayes"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sergeitarasov.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}},"created_at":"2021-04-26T16:49:43.000Z","updated_at":"2024-02-26T09:24:12.742Z","dependencies_parsed_at":null,"dependency_job_id":"ded8b90c-b85d-438e-a54e-873f6537fccd","html_url":"https://github.com/sergeitarasov/MorphoModels","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sergeitarasov/MorphoModels","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sergeitarasov%2FMorphoModels","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sergeitarasov%2FMorphoModels/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sergeitarasov%2FMorphoModels/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sergeitarasov%2FMorphoModels/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sergeitarasov","download_url":"https://codeload.github.com/sergeitarasov/MorphoModels/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sergeitarasov%2FMorphoModels/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35287396,"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":"2026-07-09T02:00:07.329Z","response_time":57,"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":["anatomy","bayesian","ed-models","inapplicable-characters","likelihood","markov","morphology","phylogenetics","revbayes"],"created_at":"2025-10-25T10:50:46.081Z","updated_at":"2026-07-09T04:31:30.894Z","avatar_url":"https://github.com/sergeitarasov.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Embedded Dependency (ED) models for inapplicable morphological characters\n\n \u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/sergeitarasov/MorphoModels/blob/main/vignettes/Fig_icon.png\" width=\"700\" title=\"hover text\"\u003e\n\u003c/p\u003e  \n\n# Content\n\nThis repository contains [vignette](https://github.com/sergeitarasov/MorphoModels/wiki/Constructing-rate-matrices-for-ED-models) and **scripts** for setting up and running Embedded Dependency (ED) models for phylogenetic inference with inapplicable morphological data [(Tarasov 2022)](https://www.biorxiv.org/content/10.1101/2021.04.26.441495v3).\n\n* [Here is a vignette](https://github.com/sergeitarasov/MorphoModels/wiki/Constructing-rate-matrices-for-ED-models) for setting up ED models and rate matrices to run in RevaBayes or other R packages.\n* Below are the **scripts** for reproducing analyses from [Tarasov (2022)](https://www.biorxiv.org/content/10.1101/2021.04.26.441495v3).\n \n## The scripts used in [Tarasov (2022)](https://www.biorxiv.org/content/10.1101/2021.04.26.441495v3)\n\nYou can download the entire repository by clicking on the green `Code` button and then selecting `Download ZIP` in the upper right corner. Or by using this command from within terminal:\n\n``` bash\ngit clone https://github.com/sergeitarasov/MorphoModels\n```\n\n- **1_ED_model_performance** The scripts for \"1. ED models and SMMs: fixed data\".\n- - RevBayes scripts for running tree inference with the ED models and calculating marginal likelihood under fixed data.\n\n- **2_EDvsHMM** The scripts for \"1. ED models and SMMs: fixed data\".\n- - RevBayes scripts for tree inference (and marginal likelihood calculation) with expanded ED models and SMM  under fixed data. \n\n- **3_ED_TailColor_problem** The scripts for \"3. ED and Tail Color Problem\".\n- - RevBayes scripts to test the resolution of LTC in the tail color problem under fixed data. \n\n- **4a_EDvsHMM_topology** The scripts for \"2. ED models vs. SMMs: simulated data\".\n- - R scripts (in *RB_run_1/4a_R*) to simulate trees and characters under the ED6 model.\n- - RevBayes scripts to perform tree inferences under the ED6, ED3, and two SMMs.\n- - R scripts (in *RB_run_1/4a_R*) to calculate boostrapped p-values.\n\n\n# References\n\nTarasov, S., 2023. New phylogenetic Markov models for inapplicable morphological characters. *Systematic Biology*, 72(3), pp.681-693.\n\u003chttps://academic.oup.com/sysbio/article/72/3/681/7036827\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsergeitarasov%2Fmorphomodels","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsergeitarasov%2Fmorphomodels","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsergeitarasov%2Fmorphomodels/lists"}