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Analysis and Metrics","monthly_downloads":222,"total_dependent_repos":0,"total_dependent_packages":0,"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","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.4014111","https://doi.org/10.1002/ecs2.7006114","https://doi.org/10.1111/2041-210X.13102","https://doi.org/10.1002/ecy.3233","https://doi.org/10.1111/ele.13151"],"works":{"https://doi.org/10.5281/zenodo.4014111":null,"https://doi.org/10.1111/2041-210X.13102":{"id":"https://openalex.org/W2951826941","doi":"https://doi.org/10.1111/2041-210x.13102","title":"Measurement of Biodiversity (MoB): A method to separate the scale‐dependent effects of species abundance distribution, density, and aggregation on diversity change","display_name":"Measurement of Biodiversity (MoB): A method to separate the scale‐dependent effects of species abundance distribution, density, and aggregation on diversity change","publication_year":2018,"publication_date":"2018-11-12","ids":{"openalex":"https://openalex.org/W2951826941","doi":"https://doi.org/10.1111/2041-210x.13102","mag":"2951826941"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1111/2041-210x.13102","pdf_url":null,"source":{"id":"https://openalex.org/S1131227","display_name":"Methods in Ecology and Evolution","issn_l":"2041-210X","issn":["2041-210X"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310320503","host_organization_name":"Wiley-Blackwell","host_organization_lineage":["https://openalex.org/P4310320503","https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley-Blackwell","Wiley"],"type":"journal"},"license":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://scholarworks.uvm.edu/cgi/viewcontent.cgi?article=1069\u0026context=casfac","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048639514","display_name":"Daniel J. 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