{"id":24182977,"url":"https://github.com/ms609/ms609","last_synced_at":"2025-08-03T12:16:14.050Z","repository":{"id":90542400,"uuid":"484474020","full_name":"ms609/ms609","owner":"ms609","description":"Config files for my GitHub profile.","archived":false,"fork":false,"pushed_at":"2025-07-01T08:13:59.000Z","size":8,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-07-01T09:26:07.679Z","etag":null,"topics":["config","github-config"],"latest_commit_sha":null,"homepage":"https://github.com/ms609","language":null,"has_issues":false,"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/ms609.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,"zenodo":null}},"created_at":"2022-04-22T14:59:20.000Z","updated_at":"2025-07-01T08:14:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"f0813f17-fd50-4b4a-9099-169dd8f422b9","html_url":"https://github.com/ms609/ms609","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ms609/ms609","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Fms609","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Fms609/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Fms609/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Fms609/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ms609","download_url":"https://codeload.github.com/ms609/ms609/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Fms609/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268543897,"owners_count":24267154,"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":"2025-08-03T02:00:12.545Z","response_time":2577,"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":["config","github-config"],"created_at":"2025-01-13T08:45:55.253Z","updated_at":"2025-08-03T12:16:14.036Z","avatar_url":"https://github.com/ms609.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Martin R. Smith\n\nI am a Professor in Durham University's Department of Earth Sciences.  I use the fossil record to \nilluminate the origins of life's complexity.  To this end, I have developed and implemented a number of \nmethods to improve the inference of phylogenetic history (\"evolutionary family trees\"), mainly in R/C++.\n\nSee https://smithlabdurham.github.io/ for more about my group's research interests.\n\n# Repo highlights\n\n##  R packages\n\n- [Ternary](https://github.com/ms609/Ternary/): create ternary plots and Holdridge diagrams.\n\n- Packages for calculating and evaluating distances between phylogenetic trees: \n[TreeDist](https://github.com/ms609/TreeDist/),\n[TBRDist](https://github.com/ms609/TBRDist/), [Quartet](https://github.com/ms609/Quartet/).\n\n- [MapTrees](https://ms609.github.io/TreeDist/dev/articles/treespace.html): an interactive user\ninterface for the creation, visualization and evaluation of tree landscapes.\n\n- [TreeTools](https://github.com/ms609/TreeTools/): utilities for the creation, modification and\nanalysis of phylogenetic trees.\n\n- [TreeSearch](https://github.com/ms609/TreeSearch/): phylogenetic tree search in R, with an \nappropriate treatment of ‘inapplicable’ characters.\n\n- [Rogue](https://github.com/ms609/Rogue/): Identify rogue taxa to improve consensus trees.\n\n## Student resources\n\n- [Concentration](https://github.com/ms609/Concentration/): Strategies to improve concentration and maximize productivity.\n\n- [Ancient Life and its Environment](https://smithlabdurham.github.io/GEOL2301): Teaching resources for a \n  palaeontological half-module.\n  \n- [preferences](https://github.com/ms609/preferences): Default configurations for scientific research software.\n\n- [dictionary](https://github.com/smithlabdurham/dictionary): Personal wordlist of scientific terms to supplement spell-checkers.\n\n- [module-map](https://module-map.github.io/): JavaScript interface to navigate Earth Science degree pathways.\n\n## Reproducible research\n\n- [phylo-workflow](https://github.com/smithlabdurham/phylo-workflow): Workflow for semi-automatic phylogenetic analysis of morphological data.\n\n- [hyoliths](https://github.com/ms609/hyoliths): Supplementary dataset for Sun _et al._ (2018): a useful template for\n  morphological phylogenetic analysis.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Fms609","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fms609%2Fms609","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Fms609/lists"}