{"id":17844856,"url":"https://github.com/dombennett/masters-project-pipeline","last_synced_at":"2025-04-02T15:12:39.861Z","repository":{"id":68566916,"uuid":"21288781","full_name":"DomBennett/Masters-project-pipeline","owner":"DomBennett","description":"BIG MRes (2012-13, Silwood park) project code pipeline","archived":false,"fork":false,"pushed_at":"2014-06-27T20:47:24.000Z","size":128,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-08T06:13:04.956Z","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","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":"2014-06-27T20:47:20.000Z","updated_at":"2015-02-23T10:59:52.000Z","dependencies_parsed_at":"2023-02-21T07:46:10.442Z","dependency_job_id":null,"html_url":"https://github.com/DomBennett/Masters-project-pipeline","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%2FMasters-project-pipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FMasters-project-pipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FMasters-project-pipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FMasters-project-pipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/Masters-project-pipeline/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":[],"created_at":"2024-10-27T21:33:15.759Z","updated_at":"2025-04-02T15:12:39.838Z","avatar_url":"https://github.com/DomBennett.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"################################################################################\n################################################################################\nBIG MRes 2013 Project Code and Results\nD.J. Bennett\n05/09/2013\nTesting for non-random phylogenetic responses to urbanisation using mass\n phylogeny estimation (MPE)\n################################################################################\n################################################################################\n\n## Title\nAnalysis\n\n## Required programs\nR (v3+)\n\n## Program packages\nR: ape, reshape, picante, caper, lme4, stringr, RCurl, apTreeshape, phangorn,\n stringdist, ggplot2, maps, mapdata, vioplot\n\n## OS and system\nOriginally coded and run on:\n Ubuntu 13.04 (Intel® Core™ i5-2540M CPU @ 2.60GHz × 4, 7.8 GiB)\n\n## Folders\n0_data --\n\tfiles:\n\t\turban_data.csv (PREDICTS data) and name_modifiers.RData\n\t\tpublished phylogenies and mass produced\n\tfolders:\n\t \tpub_phylos (containing published phylogenies in Newick format \n\t \tand a treecomp.csv specifying the comparisons to be performed),\n\t \tmass_phylos (containing the distribution of trees for each study\n\t \tin Newick format.)\n1_results -- .csv and .RData files of the results\n2_figures -- produced figures for thesis\nfunctions -- EcoDataTools.R (functions for running ecological analysis) +\n\tAP's plot fixed effects function.\n\n## Description\nThese scripts are not for running automatively. Run 0_names.R first to generate\nnames for the taxa present across studies. Move these resultant files to the\n0_names folder in the MPE pipeline. 0_names also produces a prem_taxadata.csv.\nThis contains information for each study to help speed up generation of a \ntaxadata.csv.\nOnce the MPE pipeline has run, move the name_modifiers.RData to the 0_data\nfolder here. And move all resultant trees (from 5_screen in MPE pipeline) to the\nmass_phylos folder in 0_data.\nTo regenerate the results I produced for my thesis, re-run each script in the\norder in which tehy are numbered.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fmasters-project-pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fmasters-project-pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fmasters-project-pipeline/lists"}