{"id":17844844,"url":"https://github.com/dombennett/project-karenina","last_synced_at":"2025-08-21T12:19:49.843Z","repository":{"id":27718996,"uuid":"31206216","full_name":"DomBennett/Project-karenina","owner":"DomBennett","description":":snowflake::deciduous_tree: Testing the Tolstoyan nature of ED species","archived":false,"fork":false,"pushed_at":"2019-09-20T12:21:25.000Z","size":8830,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-08T06:13:03.811Z","etag":null,"topics":["evolutionary-distinctness","fossil-data","living-fossil","mammals","phylogeny","pipeline","r"],"latest_commit_sha":null,"homepage":"","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/DomBennett.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}},"created_at":"2015-02-23T11:57:05.000Z","updated_at":"2019-09-20T12:21:27.000Z","dependencies_parsed_at":"2022-07-13T21:34:16.356Z","dependency_job_id":null,"html_url":"https://github.com/DomBennett/Project-karenina","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-karenina","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-karenina/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-karenina/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-karenina/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/Project-karenina/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246837685,"owners_count":20841903,"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":["evolutionary-distinctness","fossil-data","living-fossil","mammals","phylogeny","pipeline","r"],"created_at":"2024-10-27T21:33:13.775Z","updated_at":"2025-04-02T15:12:43.243Z","avatar_url":"https://github.com/DomBennett.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# How Do Evolutionary Distinct Species Arise?\n\nAre evolutionarily distinct species distinct for much the same reasons, or\nare each evolutionarily distinct species distinct in their own unique way?\nWe answer this by modelling the evolutioanry distinctness of clades between\ntwo time points.\n\n![](https://upload.wikimedia.org/wikipedia/commons/8/8a/Porc_formiguer.JPG)\n\n\u003e Aardvark (*Orycteropus afer*): An evolutionarily distinct mammal featured\nhere to make the page more visually interesting.\n\n## Details\n\n**Study group**: mammals\n\n**Data**: phylogeny and fossil\n\n**OS**: UNIX\n\n## Reproduce\n\nDownload repository and initial data files (`0_data`). Once directory structure is\nsetup, pipeline can be re-run from terminal:\n\n```{bash}\nRscript run.R \u0026\u003e log \u0026\n```\n\n## Process\n\n* Download fossil records\n* Add fossils stochastically to time-calibrated molecular phylogeny with a taxonomy constraint\n* Calculate evolutionary distinctness at different different epochs for all clades\n* Model change in evolutionary distinctness of clades between epochs\n\n## Stages\n\n* 1_pin: add fossils to molecular phylogeny\n* 2_slice: calculate evolutionary distinctness at different epochs\n* 3_wrngl: wrangle and merge data for modelling\n* 4_model: model results\n\n### Additional analysis\n\n`additional_analysis` contains extra scripts for producing time slices using different simulated\nbirth-death trees.\n\n## Dir Structure\n\n```\n0_data/\n   mammalia.tre\nstages/\n   1_pin.R\n   2_slice.R\n   3_wrngl.R\n   4_model.R\ntools/\n   pin_tools.R\n   slice_tools.R\n   wrngl_tools.R\n```\n\nResults from each stage will be saved in folders named after each stage.\n\n\n## Key Packages\n\n* [treeman](https://github.com/DomBennett/treeman)\n* [paleobioDB](https://github.com/ropensci/paleobioDB)\n\n## Data Sources\n\n* [Bininda-Edmonds et al. (2007)](http://www.nature.com/nature/journal/v446/n7135/abs/nature05634.html)\n* [The Paleobiology Database (2016)](https://paleobiodb.org/#/)\n\n## Reference\n\nBennett DJ, Sutton MD, Turvey ST. 2019 How the past impacts the future: modelling the performance of evolutionarily distinct mammals through time. *Phil. Trans. R. Soc. B* 20190210. [DOI](http://dx.doi.org/10.1098/rstb.2019.0210)\n\n## Author\n\nD.J. Bennett\n\n### Notes\n\nProject name originates from the first line of [Tolstoy's \"Anna Karenina\"](https://en.wikipedia.org/wiki/Anna_Karenina): *Happy families are all alike; every unhappy family is unhappy in its own way.* Are evolutionarily distinct taxa each distinct in their own way?\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-karenina","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fproject-karenina","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-karenina/lists"}