{"id":16704250,"url":"https://github.com/rekyt/biodiversity_facets_tutorial","last_synced_at":"2026-04-28T15:31:47.330Z","repository":{"id":78725444,"uuid":"381663816","full_name":"Rekyt/biodiversity_facets_tutorial","owner":"Rekyt","description":"Repository for practical session on \"Biodiversity facets in macro-space\" https://s.42l.fr/biodiv https://s.42l.fr/nulldata","archived":false,"fork":false,"pushed_at":"2023-04-26T15:18:09.000Z","size":33535,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-21T03:41:23.389Z","etag":null,"topics":["biodiversity","biodiversity-data","ecology","functional-diversity","functional-trait","practical-sessions"],"latest_commit_sha":null,"homepage":"https://rekyt.github.io/biodiversity_facets_tutorial/","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/Rekyt.png","metadata":{"files":{"readme":"README.Rmd","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}},"created_at":"2021-06-30T10:30:05.000Z","updated_at":"2023-04-11T10:55:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"a229b65d-39a6-424e-92e0-be91d01eae9b","html_url":"https://github.com/Rekyt/biodiversity_facets_tutorial","commit_stats":{"total_commits":154,"total_committers":1,"mean_commits":154.0,"dds":0.0,"last_synced_commit":"d24b1c78405931aa6fb9f7426014088b3164cab0"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rekyt%2Fbiodiversity_facets_tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rekyt%2Fbiodiversity_facets_tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rekyt%2Fbiodiversity_facets_tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rekyt%2Fbiodiversity_facets_tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Rekyt","download_url":"https://codeload.github.com/Rekyt/biodiversity_facets_tutorial/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243551326,"owners_count":20309300,"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":["biodiversity","biodiversity-data","ecology","functional-diversity","functional-trait","practical-sessions"],"created_at":"2024-10-12T19:12:01.134Z","updated_at":"2025-12-29T15:45:57.349Z","avatar_url":"https://github.com/Rekyt.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: Biodiversity Facets Practical Session\nauthor: \"Matthias Grenié \u0026 Marten Winter\"\ndate: \"`r format(Sys.time(), '%B %d %Y')`\"\nalways_allow_html: true\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\n```\n\nThis the first practical session in the course \"Macroecology under Global Change\". This it the practical session companion to the lectures on biodiversity facets.\n\n**Year**: 2023\n\n**Instructors**: Matthias Grenié \u0026 Marten Winter\n\nContact us via Slack or email for any further questions.\n\n\n## Goals\n\n* Manipulate research open data;\n* Learn how to compute functional diversity indices with `fundiversity` (load trait data, build a functional space, compute indices);\n* Learn how to compute phylogenetic diversity indices with `ape` and `picante` (load phylogenetic tree, visualize phylogenetic tree, compute indices);\n* Familiarize with null models;\n* Know the difference between facets of functional and phylogenetic diversity indices;\n* Visualize biodiversity facets on the map;\n* Show the effect of logging in a tropical forest context on some biodiversity facets.\n\n## How to use it?\n\n1. **Online** It is accessible online at https://rekyt.github.io/biodiversity_facets_tutorial/ click on `Setup` in the navigation bar to access the tutorial.\n1. **Online** if the website have issue you can access a similar version with the following command: https://htmlpreview.github.io/?https://github.com/Rekyt/biodiversity_facets_tutorial/blob/main/docs/index.html\n1. **Offline** You can download the merged `diversity_facets_tutorial.Rmd` file by clicking the button below.\n1. **Offline** You can also open the `diversity_facets_tutorial.R` file in RStudio to get only the code to execute exactly the codes here.\n\n\n```{r download-single-rmd-file, eval = TRUE, echo = FALSE}\ndownloadthis::download_link(\n  link = \"https://github.com/Rekyt/biodiversity_facets_tutorial/raw/main/diversity_facets_tutorial.Rmd\",\n  button_label = \"Download Single Rmd file\",\n  button_type = \"danger\",\n  has_icon = TRUE,\n  icon = \"fa fa-save\",\n  self_contained = FALSE\n)\n```\n\n```{r download-single-r-file, eval = TRUE, echo = FALSE}\ndownloadthis::download_link(\n  link = \"https://github.com/Rekyt/biodiversity_facets_tutorial/raw/main/diversity_facets_tutorial.R\",\n  button_label = \"Download Single R file\",\n  button_type = \"danger\",\n  has_icon = TRUE,\n  icon = \"fa fa-save\",\n  self_contained = FALSE\n)\n```\n\n## Data provenance\n\nThe data we'll be using throughout the tutorial comes from the following article: \n\n\u003e Döbert, T.F., Webber, B.L., Sugau, J.B., Dickinson, K.J.M. and Didham, R.K. (2017), Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rain forest. J Ecol, 105: 1235-1245. https://doi.org/10.1111/1365-2745.12794\n\nThe data has been deposited on a open data repository called dryad with the following reference:\n\n\u003e Döbert, Timm F. et al. (2018), Data from: Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rainforest, Dryad, Dataset, https://doi.org/10.5061/dryad.f77p7\n\n```{r download-data, echo = FALSE, eval = TRUE}\ndownloadthis::download_link(\n  link = \"https://datadryad.org/stash/downloads/download_resource/5179\",\n  button_label = \"Download Original Data Files\",\n  button_type = \"danger\",\n  has_icon = TRUE,\n  icon = \"fa fa-save\",\n  self_contained = FALSE\n)\n```\n\n## Going Further\n\nOther courses on biodiversity facets and potential interesting papers \u0026 tools:\n\n* The [`FD`](https://cran.r-project.org/package=FD) package is the reference package to compute functional diversity indices.\n* The [Modern concepts and methods in Macroecology and Biogeography](https://github.com/patrickweigelt/MCMMB/) course accessible with this link: http://htmlpreview.github.io/?https://github.com/patrickweigelt/MCMMB/blob/master/index.html.\n* The [Legras et al. 2018 paper](https://doi.org/10.1016/j.actao.2018.02.007) on functional diversity concepts.\n* The [Community Phylogenetics in R Workshop](https://pedrohbraga.github.io/CommunityPhylogenetics-Workshop/CommunityPhylogenetics-Workshop.html) by Pedro Henrique P. Braga and Katherine Hébert.\n\n\n## License\n\n[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) Matthias Grenié\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frekyt%2Fbiodiversity_facets_tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frekyt%2Fbiodiversity_facets_tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frekyt%2Fbiodiversity_facets_tutorial/lists"}