{"id":13724483,"url":"https://github.com/MoBiodiv/mobr","last_synced_at":"2025-05-07T18:32:29.382Z","repository":{"id":33120866,"uuid":"36759899","full_name":"MoBiodiv/mobr","owner":"MoBiodiv","description":"Tools for analyzing changes in diversity across scales","archived":false,"fork":false,"pushed_at":"2024-10-29T02:49:12.000Z","size":6497,"stargazers_count":23,"open_issues_count":13,"forks_count":18,"subscribers_count":13,"default_branch":"master","last_synced_at":"2024-10-29T22:31:45.618Z","etag":null,"topics":["biodiversity","conservation","ecology","rarefaction","species","statistics"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MoBiodiv.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}},"created_at":"2015-06-02T20:28:37.000Z","updated_at":"2024-10-25T17:30:46.000Z","dependencies_parsed_at":"2024-01-12T04:52:19.934Z","dependency_job_id":"454fc498-e381-4393-b025-aaeff0a13614","html_url":"https://github.com/MoBiodiv/mobr","commit_stats":{"total_commits":593,"total_committers":8,"mean_commits":74.125,"dds":"0.45699831365935917","last_synced_commit":"93b8127a4e59a9efb7e16c0b0fc575319959b19a"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MoBiodiv%2Fmobr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MoBiodiv%2Fmobr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MoBiodiv%2Fmobr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MoBiodiv%2Fmobr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MoBiodiv","download_url":"https://codeload.github.com/MoBiodiv/mobr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":222155740,"owners_count":16940399,"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","conservation","ecology","rarefaction","species","statistics"],"created_at":"2024-08-03T01:01:58.025Z","updated_at":"2025-05-07T18:32:29.364Z","avatar_url":"https://github.com/MoBiodiv.png","language":"R","funding_links":[],"categories":["Biosphere"],"sub_categories":["Biodiversity Analysis and Metrics"],"readme":"# mobr\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/mobr)](https://github.com/r-hub/cranlogs.app)\n[![cran version](https://www.r-pkg.org/badges/version/mobr)](https://cran.r-project.org/package=mobr)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4014111.svg)](https://doi.org/10.5281/zenodo.4014111)\n============\n\n# Measurement of Biodiversity in R \n\nThis repository hosts an R package that is actively being developed for \nestimating biodiversity and the components of its change. The key innovations of\nthis R package over other R packages that also carry out rarefaction (e.g.,\n`vegan`, `iNext`) is that `mobr` is focused on 1) making empirical comparisons between \ntreatments or gradients, and 2) our framework emphasizes how changes in \nbiodiversity are linked to changes in community structure: the SAD, total\nabundance, and spatial aggregation. \n\nThe concepts and methods behind this R package are described in three publications.\n\nMcGlinn, D.J., S.A. Blowes, M. Dornelas, T. Engel, I.S. Martins, H. Shimadzu,  N.J. Gotelli,  A. Magurran,  B.J. McGill,  and J.M. Chase. 2025. Disentangling non-random structure from random placement when estimating β-diversity through space or time. Ecosphere. e70061. https://doi.org/10.1002/ecs2.7006114\n\n\nMcGlinn, D.J. X. Xiao, F. May, N.J Gotelli, T. Engel, S.A Blowes, T.M. Knight, O. Purschke, J.M Chase, and B.J. McGill. 2019. MoB (Measurement of Biodiversity): a method to separate the scale-dependent effects of species abundance distribution, density, and aggregation on diversity change. Methods in Ecology and Evolution. 10:258–269. https://doi.org/10.1111/2041-210X.13102\n\nMcGlinn, D.J. T. Engel, S.A. Blowes, N.J. Gotelli, T.M. Knight, B.J. McGill, N. Sanders, and J.M. Chase. 2020. A multiscale framework for disentangling the roles of evenness, density, and aggregation on diversity gradients. Ecology. https://doi.org/10.1002/ecy.3233\n\nChase, J.M., B. McGill, D.J. McGlinn, F. May, S.A. Blowes, X. Xiao, T. Knight. 2018. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Ecology Letters. 21: 1737–1751. https://doi.org/10.1111/ele.13151 \n\nPlease cite `mobr`. Run the following to get the appropriate citation for the version you're using:\n\n```r\ncitation(package = \"mobr\")\n```\n\n## Installation\n\n```r\ninstall.packages('mobr')\n```\n\nOr, install the Github version\n\n```r\ninstall.packages('remotes')\n```\n\nNow that `remotes` is installed you can install `mobr` using the following R code:\n\n```r\nremotes::install_github('MoBiodiv/mobr')\n```\n\n## Examples\n\nThe package [vignette](https://github.com/MoBiodiv/mobr/blob/master/vignettes/mobr_intro.pdf)\nprovides a useful walk-through the package tools, but below is some example code\nthat uses the two key analyses and related graphics. \n\n```r\nlibrary(mobr)\nlibrary(dplyr)\n\ndata(tank_comm)\ndata(tank_plot_attr)\nindices \u003c- c('N', 'S', 'S_n', 'S_C', 'S_PIE')\ntank_div \u003c- tibble(tank_comm) %\u003e% \n  group_by(group = tank_plot_attr$group) %\u003e% \n  group_modify(~ calc_comm_div(.x, index = indices, effort = 5,\n                               extrapolate = TRUE))\nplot(tank_div)\ntank_mob_in \u003c- make_mob_in(tank_comm, tank_plot_attr, coord_names = c('x', 'y'))\ntank_deltaS \u003c- get_delta_stats(tank_mob_in, 'group', ref_level='low',\n                             type='discrete', log_scale=TRUE, n_perm = 5)\nplot(tank_deltaS, 'b1')\n```\n\n## Meta\n\n* Please [report any issues or bugs](https://github.com/mobiodiv/mobr).\n* License: MIT\n* Get citation information for `mobr` in R doing `citation(package = 'mobr')`\n* Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.\n\n## Thanks\n\n* Gregor Seyer for providing a constructive review of our CRAN submission\n* Kurt Hornik for helping us keep up with CRAN changes. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FMoBiodiv%2Fmobr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FMoBiodiv%2Fmobr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FMoBiodiv%2Fmobr/lists"}