{"id":17844835,"url":"https://github.com/dombennett/project-edbmm","last_synced_at":"2025-04-02T15:12:39.825Z","repository":{"id":68567010,"uuid":"21008474","full_name":"DomBennett/Project-EDBMM","owner":"DomBennett","description":":evergreen_tree::ghost: Testing the phylogenetic reality of the living fossil with an EDBMM","archived":false,"fork":false,"pushed_at":"2017-01-07T19:41:14.000Z","size":29624,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-08T06:13:03.734Z","etag":null,"topics":["evolutionary-distinctness","living-fossil","markov-model","phylogeny","pipeline","r"],"latest_commit_sha":null,"homepage":"https://www.cambridge.org/core/journals/paleobiology/article/div-classtitleevolutionarily-distinct-living-fossils-require-both-lower-speciation-and-lower-extinction-ratesdiv/895514AC2A88019CB206CC6D83C11943","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2014-06-19T17:01:03.000Z","updated_at":"2017-02-28T14:55:54.000Z","dependencies_parsed_at":null,"dependency_job_id":"f67be825-0d61-4dc2-bfcb-1fa9db442729","html_url":"https://github.com/DomBennett/Project-EDBMM","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-EDBMM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-EDBMM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-EDBMM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-EDBMM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/Project-EDBMM/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","living-fossil","markov-model","phylogeny","pipeline","r"],"created_at":"2024-10-27T21:33:11.402Z","updated_at":"2025-04-02T15:12:39.808Z","avatar_url":"https://github.com/DomBennett.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Evolutionary Distinctness Biased Markov Model (EDBMM)\n\nAn R pipeline for exploring how an evolutionary distinctness bias in a tree-growth Markov model affects tree shape in order to test the reality of the living fossil, see the published article ['Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates'](https://doi.org/10.1017/pab.2016.36).\n\nThe pipeline uses a Markov-Model to grow trees with extinction and speciation rates determined by a tip's evolutionary distinctness.\n\n![EDBMM](https://raw.githubusercontent.com/DomBennett/Project-EDBMM/master/other/EDBMM.png \"Evolutionary Distinctness Biased Markov Model\")\n\nData and results files are not provided in this repository, only the code is.\nAll results and starting datasets can be found in the [Dryad repository](https://datadryad.org/resource/doi:10.5061/dryad.hm55b). The repository\nholds a large (5GB) compressed file in five parts. These parts must all be downloaded,\ncombined and then uncompressed to produce the folders.\n\n```{bash}\n# recombine and uncompress (UNIX)\ncat xaa xab xac xad xae \u003e data_results.tar.gz\ntar zxvf data_results.tar.gz\n```\n\n\n**System requirements**\n\nRun the `install_deps.R` script to install all dependent packages automatically.\n\n* OS\n  + UNIX (but readily modifiable for Windows)\n* R version\n  + 3+\n* R packages (version used)\n  + `plyr` (1.8.1)\n  + `ape` (3.2)\n  + `geiger` (2.0.3)\n  + `apTreeshape` (1.4.5)\n  + `ggplot2` (1.0.0)\n  + `MoreTreeTools` (0.0.1)\n  + `outliers` (0.14)\n  + `doMC` (1.3.3, not for Windows)\n  + `foreach` (1.4.2)\n  + `test_that` (0.9.1, optional)\n* External\n  + [PATHd8](http://www2.math.su.se/PATHd8/)\n  \nPlease note, [MoreTreeTools](https://github.com/DomBennett/MoreTreeTools) is in development and can only be installed via GitHub.\nIt is best to install using the EDBMM branch:\n\n```{R}\nlibrary(devtools)\ninstall_github('DomBennett/MoreTreeTools', ref='edbmm')  # install edbmm branch\n```\n\n**Directory structure**\n\n```\n-- data/\n---- raw_trees/\n------ literature/\n-------- [manually added]\n------ treebase/\n---- parsed_trees/\n---- treestats/\n-- parameters/\n---- [all analysis parameters]\n-- stages/\n---- [all stage .R scripts]\n-- tools/\n---- [all tool .R scripts]\n-- results/\n----- [all folders named by analysis as specified in run.R]\n-- other/\n-- sanity_checks/\n-- PATHd8\n----- [excutable if parsing trees]\n```\n\n**Pipeline**\n\nThe pipeline works by calling the pipeline scripts `setup.R` and `run.R`. These scripts call\nstage scripts which can be found in [`/stages`](https://github.com/DomBennett/Project-EDBMM/tree/master/stages).\nThe stages scripts depend on custom functions found in the [`/tools`](https://github.com/DomBennett/Project-EDBMM/tree/master/tools) folder.\n\n![flow-diagram](https://raw.githubusercontent.com/DomBennett/Project-EDBMM/master/other/flow_diagram.png \"Flow diagram\")\n\n**setup.R**\n\nThis phase of the pipeline sources and calculates statistics from empirical\ntrees:\n\n1. Download trees from TreeBase\n2. Parse trees (make ultramteric using different methods)\n3. Calculate tree shape statistics\n4. Determine the taxonomic identities of downloaded trees\n\n**run.R**\n\nThis phase models trees for determining how model parameters affect tree shape:\n\n1. Read in parameters from [`parameters/`](https://github.com/DomBennett/Project-EDBMM/tree/master/parameters)\n2. Model trees according to parameters in `run.R`\n3. Calculate tree shape statistics\n\n**Analysis**\n\nThe final stage script is user interactive. All plots and analysis presented in the publication\nare generated with this script.\n\n**Clade analysis**\n\nIn addition to setup and run, there are additional clade analysis stages: `clade.R` and `analyse_clades.R`.\n\n**Testing**\n\nRun `test.R` to make sure core functions are working.\n\n**Reference**\n\nBennett, D.J., Sutton, M.D. \u0026 Turvey, S.T., 2016. Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates. Paleobiology, pp.1–15. Available at: http://www.journals.cambridge.org/abstract_S0094837316000361.\n\n**Author**\n\nDom Bennett\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-edbmm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fproject-edbmm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-edbmm/lists"}