{"id":17844823,"url":"https://github.com/dombennett/predicts-pd","last_synced_at":"2025-10-08T17:10:23.024Z","repository":{"id":23765284,"uuid":"27139971","full_name":"DomBennett/PREDICTS-PD","owner":"DomBennett","description":":evergreen_tree::house: Response of phylogenetic diversity to human impacts in terrestrial ecosystems","archived":false,"fork":false,"pushed_at":"2015-09-28T14:29:40.000Z","size":796,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-17T03:42:52.577Z","etag":null,"topics":[],"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":"2014-11-25T18:31:14.000Z","updated_at":"2018-08-13T11:36:36.000Z","dependencies_parsed_at":"2022-08-22T05:30:21.783Z","dependency_job_id":null,"html_url":"https://github.com/DomBennett/PREDICTS-PD","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/DomBennett/PREDICTS-PD","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FPREDICTS-PD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FPREDICTS-PD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FPREDICTS-PD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FPREDICTS-PD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/PREDICTS-PD/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FPREDICTS-PD/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278981518,"owners_count":26079640,"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","status":"online","status_checked_at":"2025-10-08T02:00:06.501Z","response_time":56,"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":"2024-10-27T21:33:09.454Z","updated_at":"2025-10-08T17:10:23.007Z","avatar_url":"https://github.com/DomBennett.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Response of phylogenetic diversity to human impacts in terrestrial ecosystems\n\nAll code is made available for reproducing the analyses as described in\n[insert paper URL here]. This is code only, for full completed dataset click\nhere (not yet available).\n\n## Pipeline\n\nThe analysis comes in four stages:\n\n![r_pipeline](https://raw.githubusercontent.com/DomBennett/PREDICTS-PD/master/other/r_pipeline.jpg?token=AC0Jh05l2WChD8gM7MaQJYfT5OkuzoZlks5WCRrIwA%3D%3D \"R analysis pipeline\")\n\nEach stage is run once with the exception of `B1_parse.R`, `B2_compare.R` and `B3_metrics.R`\nwhich are each run twice for comparing the results from unconstrained and constrained\npG-lt trees and testing whether there is a difference between total and age\nbranch length normalisation.\n\n## Running\n\nMake sure all relevant packages are installed:\n\n```{bash}\nRscript x_install_deps.R\n```\n\nAdditionally, you will need a compiled version of [pathD8](http://www2.math.su.se/PATHd8/)\nin your working directory.\n\nTo run entire automated pipeline (UNIX OS):\n\n```{bash}\nsh x_run.sh\n```\n\npG-lt step can only be run separately. It was originally run on Imperial's HPC.\nMake sure you have `0_pglt/` before running the calculate step.\n`C1_analysis.R` is an interactive script and it not part of the pipeline.\nNote, setup will take a long time to run as they interact\nwith the [GNR](http://resolver.globalnames.biodinfo.org/).\n\n## Stage details\n\n### Setup\n\nThis is run with the `x_setup.sh` script. You can run pG-lt after it is run.\n\n* `A1_presolve.R`: read in published trees and PREDICTS data, search names\nagainst [GNR](http://resolver.globalnames.biodinfo.org/).\n* `A2_parse.R`: read in published trees and rate-smooth\n* `A3_pgltsetup.R`: identify suitable PREDICTS studies, output into pG-lt friendly\nformat. You can run pG-lt with the resulting folder.\n* `A4_map.R`: use published phylogenies in `0_data` to generate study-level\nphylogenies\n\n### Calculate\n\nThis is run with the `x_calculate.R` script.\n\n* `B1_parse.R`: read in pG-lt and mapped phylogenies, check and rate-smooth\n* `B2_compare.R`: compare mapped and pG-lt phylogenies\n* `B3_metrics.R`: generate PD, PSV and PSE values per site using both pG-lt and\nmapped trees.\n* `B4_plots.R`: community plot PREDICTS data onto pG-lt consensus phylogenies\n\n## Directory (after complete run)\n\n```\n-- 0_data/\n    -- PREDICTS-DATA/\n        -- [site-level PREDICTS data]\n    -- raw_trees/\n        -- [downloaded published trees]\n-- 0_pglt/\n-- A1_preresolve/\n-- A2_parse/\n-- A3_pgltsetup/\n-- A4_map/\n-- B1_parse/\n-- B2_compare/\n-- B3_metrics/\n-- B4_plots/\n-- C1_analysis/\n-- stages/\n    -- [all R stages files]\n-- tools/\n    -- [all custom R functions]\n-- sanity_checks/\n    -- [demonstrations of code accuracy]\n-- other/\n    -- [misc non-essential items]\n```\n\n## Data\n\nAfter cloning this repo to your machine, you can download all missing data files\nwith this link (not yet available).\n\nUncompress files:\n\n```{bash}\nsh x_uncompress.sh\n```\n\nAnd compress again:\n\n```{bash}\nsh x_compress.sh\n```\n\n## Authors\n[Bennett D.J.](https://github.com/DomBennett),\n[De Palma A.](https://github.com/adrianadepalma),\n[Pearse W.D.](https://github.com/willpearse)\nand [Purvis A](https://github.com/AndyPurvis).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fpredicts-pd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fpredicts-pd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fpredicts-pd/lists"}