{"id":45368989,"url":"https://github.com/cjabradshaw/silurodevoniancommunities","last_synced_at":"2026-02-21T15:20:03.540Z","repository":{"id":239121458,"uuid":"798602660","full_name":"cjabradshaw/SiluroDevonianCommunities","owner":"cjabradshaw","description":"Lithofacies and temporal variation predict composition of Siluro-Devonian vertebrate, invertebrate, and plant communities","archived":false,"fork":false,"pushed_at":"2024-06-19T15:18:28.000Z","size":34323,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-10T03:06:30.209Z","etag":null,"topics":["community-ecology","continental-drift","devonian","invertebrates","lithofacies","palaeoecology","palaeoenvironment","palaeontology","plants","sedimentology","silurian","tectonics","vertebrates"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cjabradshaw.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-05-10T05:30:03.000Z","updated_at":"2024-06-19T15:16:48.000Z","dependencies_parsed_at":"2024-06-20T02:09:23.836Z","dependency_job_id":"78b56b99-92fc-4146-8b04-5e2fcd09e2ba","html_url":"https://github.com/cjabradshaw/SiluroDevonianCommunities","commit_stats":null,"previous_names":["cjabradshaw/silurodevoniancommunities"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/cjabradshaw/SiluroDevonianCommunities","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cjabradshaw%2FSiluroDevonianCommunities","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cjabradshaw%2FSiluroDevonianCommunities/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cjabradshaw%2FSiluroDevonianCommunities/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cjabradshaw%2FSiluroDevonianCommunities/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cjabradshaw","download_url":"https://codeload.github.com/cjabradshaw/SiluroDevonianCommunities/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cjabradshaw%2FSiluroDevonianCommunities/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29684392,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T14:31:22.911Z","status":"ssl_error","status_checked_at":"2026-02-21T14:31:22.570Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["community-ecology","continental-drift","devonian","invertebrates","lithofacies","palaeoecology","palaeoenvironment","palaeontology","plants","sedimentology","silurian","tectonics","vertebrates"],"created_at":"2026-02-21T15:20:02.917Z","updated_at":"2026-02-21T15:20:03.516Z","avatar_url":"https://github.com/cjabradshaw.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Siluro-Devonian Communities\n\u003cimg align=\"right\" src=\"www/ageyr perm.jpg\" width=\"400\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e\nLithofacies and temporal variation predict composition of Siluro-Devonian vertebrate, invertebrate, and plant communities. Includes multiple imputation of community data using chained equations.\n\u003cbr\u003e\n\u003cbr\u003e\nlead: \u003ca href=\"https://globalecologyflinders.com/people/#DIRECTOR\"\u003eCorey Bradshaw\u003c/a\u003e\u003cbr\u003e\ncollaborators: \u003ca href=\"https://www.uqar.ca/universite/a-propos-de-l-uqar/departements/departement-de-biologie-chimie-et-geographie/cloutier-richard\"\u003eRichard Cloutier\u003c/a\u003e, \u003ca href=\"https://prc.msu.ac.th/eng/personnel-palaeontological-research-and-education-centre-msu/\"\u003eClive Burrett\u003c/a\u003e, \u003ca href=\"https://prc.msu.ac.th/eng/personnel-palaeontological-research-and-education-centre-msu/\"\u003eMongkol Udchachon\u003c/a\u003e, \u003ca href=\"https://www.uu.se/en/contact-and-organisation/staff?query=N3-984\"\u003ePer Ahlberg\u003c/a\u003e\n\u003cbr\u003e\n## Abstract\nWhile Siluro-Devonian vertebrate communities have been well-described, co-variation in invertebrate and plant communities from the same period has not been adequately assessed. Using methods from community ecology, we tested how the combined vertebrate, invertebrate, and plant communities from 105 fossiliferous sites around the world varied relative to lithofacies and time. We built logistic linear models to examine variation in the three main communities (vertebrates, invertebrates, plants). We found that the type of lithofacies (6 categories) explained the most variation (% deviance explained [%DE] = 6.4), followed by geological period (4 categories); however, community type had little explanatory power (%DE = 0.05). Variation among most lithofacies expalined variation in presence probability. There was little support for a period×lithofacies interaction. Lithofacies explained most variation among communities when divided  by major palaeo-environmental category (marine, alluvial/deltaic, freshwater/estuarine). We then applied a stochastic variant of a permutation analysis of variance to the entire community (10 vertebrate, 20 invertebrate, 7 plant taxa) to examine the relative explanatory power of lithofacies and temporal variation on composition. There was an effect of the lithofacies (R\u003csup\u003e2\u003c/sup\u003e\u003csub\u003eperm\u003c/sub\u003e = 14.0%; \u003cem\u003ep\u003c/em\u003e\u003csub\u003eperm\u003c/sub\u003e = 0.0002; driven mainly by limestone) and categorical period (R\u003csup\u003e2\u003c/sup\u003e\u003csub\u003eperm\u003c/sub\u003e = 10.3%; \u003cem\u003ep\u003c/em\u003e\u003csub\u003eperm\u003c/sub\u003e = 0.0001; driven mainly by the Silurian, Middle Devonian, and Late Devonian) (but not their interaction: \u003cem\u003ep\u003c/em\u003e\u003csub\u003eperm\u003c/sub\u003e = 0.1652) on community composition. Treating time as a continuous variable (age) also demonstrated an effect on community composition (R\u003csup\u003e2\u003c/sup\u003e\u003csub\u003eperm\u003c/sub\u003e = 14.7%; \u003cem\u003ep\u003c/em\u003e\u003csub\u003eperm\u003c/sub\u003e = 0.0004), with incidence tending to rise in most taxa from 435 to 360 million years ago. Model predictions can now be used to show spatial variation in the relative presence probability for any of the taxa we modelled provided detailed distribution maps of lithofacies are available.\n\n## \u003ca href=\"https://github.com/cjabradshaw/SiluroDevonianCommunities/tree/main/scripts\"\u003eScripts\u003c/a\u003e\n- \u003ccode\u003esilurodev.R\u003c/code\u003e: main code to generate results\n- \u003ccode\u003er.squared.R\u003c/code\u003e: functions to estimate goodness of fit for linear models\n- \u003ccode\u003enew_lmer_AIC_tables3.r\u003c/code\u003e: functions to compare linear models\n- \u003ccode\u003epalaeocoords.ipynb\u003c/code\u003e: Jupyter Notebook with Python code to project current-era lat/lon coordinates to palaeo-coordinates, with corresponding plate tectonics, for anytime in the last 1 billion years (modified code supplied by @\u003ca href=\"https://github.com/amer7632\"\u003eamer7632\u003c/a\u003e; detailed instructions \u003ca href=\"https://github.com/GPlates/gplately/blob/master/Notebooks/03-WorkingWithPoints.ipynb\"\u003ehere\u003c/a\u003e)\n\n## \u003ca href=\"https://github.com/cjabradshaw/SiluroDevonianCommunities/tree/main/data\"\u003eData\u003c/a\u003e\n- \u003cem\u003esildevcomp4.txt\u003c/em\u003e: fossiliferous site database\n- \u003ca href=\"https://github.com/cjabradshaw/SiluroDevonianCommunities/tree/main/data/plate-model-repo/\"\u003eplate-model-repo\u003c/a\u003e: data for hindcasted tectonic reconstruction and generation of palaeo coordinates (maintain sub-folder hierarchy \u0026 unzip files in 'Topologies' sub-folder)\n- \u003ca href=\"https://github.com/cjabradshaw/SiluroDevonianCommunities/tree/main/data/sitecoords/\"\u003esitecoords\u003c/a\u003e: .csv files with site coordinates — all: \u003cem\u003esitelocs.csv\u003c/em\u003e; and divided by major period: Silurian (SIL), Lochkovian (LOCH), Emsian (EMS), Eifelian (EIF), Givetian (GIV), Frasnian (FRAS), Famennian (FAM)\n\u003cimg align=\"right\" src=\"www/FAMsites.png\" width=\"400\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e\n\n## R libraries\n\u003ccode\u003eperformance\u003c/code\u003e, \u003ccode\u003esjPlot\u003c/code\u003e, \u003ccode\u003elme4\u003c/code\u003e, \u003ccode\u003eggplot2\u003c/code\u003e, \u003ccode\u003estringr\u003c/code\u003e, \u003ccode\u003evegan\u003c/code\u003e, \u003ccode\u003eparallel\u003c/code\u003e, \u003ccode\u003evcdExtra\u003c/code\u003e, \u003ccode\u003eplyr\u003c/code\u003e, \u003ccode\u003edplyr\u003c/code\u003e, \u003ccode\u003emice\u003c/code\u003e, \u003ccode\u003eVIM\u003c/code\u003e\n\n## GPlately\nInstall \u003ccode\u003e\u003ca href=\"https://github.com/GPlates/gplately?tab=readme-ov-file\"\u003eGPlately\u003c/a\u003e\u003c/code\u003e, a Python interface to accelerate spatio-temporal data analysis leveraging \u003ccode\u003e\u003ca href=\"https://www.gplates.org/docs/pygplates/index.html\"\u003epyGPlates\u003c/a\u003e\u003c/code\u003e and \u003ccode\u003e\u003ca href=\"https://github.com/EarthByte/PlateTectonicTools\"\u003ePlateTectonicTools\u003c/a\u003e\u003c/code\u003e\n(references: \u003ca href=\"https://doi.org/10.1016/j.earscirev.2020.103477\"\u003eMerdith et al.\u003c/a\u003e 2021 \u003cem\u003eEarth-Science Reviews\u003c/em\u003e 214:103477; \u003ca href=\"https://doi.org/10.1002/gdj3.185\"\u003eMather et al.\u003c/a\u003e 2024 \u003cem\u003eGeosciences Data Journal\u003c/em\u003e 11:3-10)\n\n## Python dependencies\n\u003ccode\u003e\u003ca href=\"https://www.gplates.org/docs/pygplates/pygplates_getting_started.html#installation\"\u003epyGPlates\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://pypi.org/project/plate-model-manager/\"\u003eplate-model-manager\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://shapely.readthedocs.io/en/stable/project.html#installing-shapely\"\u003eShapely\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://numpy.org/install/\"\u003eNumPy\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://scipy.org/install/\"\u003eSciPy\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://matplotlib.org/stable/users/installing/index.html\"\u003eMatplotlib\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://scitools.org.uk/cartopy/docs/latest/index.html#getting-started\"\u003eCartopy\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://github.com/fatiando/pooch\"\u003ePooch\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://geopandas.org/en/stable/getting_started.html\"\u003eGeoPandas\u003c/a\u003e\u003c/code\u003e, \u003ccode\u003e\u003ca href=\"https://unidata.github.io/netcdf4-python/#quick-install\"\u003enetCDF4\u003c/a\u003e\u003c/code\u003e\n\n\u003cbr\u003e\n\u003ca href=\"https://www.flinders.edu.au\"\u003e\u003cimg align=\"bottom-left\" src=\"www/Flinders_University_Logo_Horizontal_RGB_Master.png\" alt=\"Flinders University logo\" height=\"40\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u003ca href=\"https://globalecologyflinders.com\"\u003e\u003cimg align=\"bottom-left\" src=\"www/GEL Logo Kaurna New Transp-2.png\" alt=\"GEL logo\" height=\"85\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u003ca href=\"https://www.uqar.ca\"\u003e\u003cimg align=\"bottom-left\" src=\"www/UQARlogo.png\" alt=\"UQAR logo\" height=\"70\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e\u003ca href=\"https://www.msu.ac.th/eng/\"\u003e\u003cimg align=\"bottom-left\" src=\"www/MahasarakhamUlogo.png\" alt=\"MU logo\" height=\"95\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u0026nbsp; \u003ca href=\"https://www.uu.se\"\u003e\u003cimg align=\"bottom-left\" src=\"www/UUlogo.png\" alt=\"Uppsala logo\" height=\"90\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e\u003c/p\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcjabradshaw%2Fsilurodevoniancommunities","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcjabradshaw%2Fsilurodevoniancommunities","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcjabradshaw%2Fsilurodevoniancommunities/lists"}