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Open Sustainable Technology

A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources.

mobr

Tools for analyzing changes in biodiversity across scales.
https://github.com/MoBiodiv/mobr

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

Keywords

biodiversity conservation ecology rarefaction species statistics

Keywords from Contributors

macroecology point-pattern-analysis species-abundance-distributions

Last synced: about 17 hours ago
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Repository metadata

Tools for analyzing changes in diversity across scales

README.md

mobr

Project Status: Active – The project has reached a stable, usable state and is being actively developed.
rstudio mirror downloads
cran version
DOI

Measurement of Biodiversity in R

This repository hosts an R package that is actively being developed for
estimating biodiversity and the components of its change. The key innovations of
this R package over other R packages that also carry out rarefaction (e.g.,
vegan, iNext) is that mobr is focused on 1) making empirical comparisons between
treatments or gradients, and 2) our framework emphasizes how changes in
biodiversity are linked to changes in community structure: the SAD, total
abundance, and spatial aggregation.

The concepts and methods behind this R package are described in three publications.

McGlinn, 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

McGlinn, 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

McGlinn, 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

Chase, 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

Please cite mobr. Run the following to get the appropriate citation for the version you're using:

citation(package = "mobr")

Installation

install.packages('mobr')

Or, install the Github version

install.packages('remotes')

Now that remotes is installed you can install mobr using the following R code:

remotes::install_github('MoBiodiv/mobr')

Examples

The package vignette
provides a useful walk-through the package tools, but below is some example code
that uses the two key analyses and related graphics.

library(mobr)
library(dplyr)

data(tank_comm)
data(tank_plot_attr)
indices <- c('N', 'S', 'S_n', 'S_C', 'S_PIE')
tank_div <- tibble(tank_comm) %>% 
  group_by(group = tank_plot_attr$group) %>% 
  group_modify(~ calc_comm_div(.x, index = indices, effort = 5,
                               extrapolate = TRUE))
plot(tank_div)
tank_mob_in <- make_mob_in(tank_comm, tank_plot_attr, coord_names = c('x', 'y'))
tank_deltaS <- get_delta_stats(tank_mob_in, 'group', ref_level='low',
                             type='discrete', log_scale=TRUE, n_perm = 5)
plot(tank_deltaS, 'b1')

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for mobr in R doing citation(package = 'mobr')
  • 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.

Thanks

  • Gregor Seyer for providing a constructive review of our CRAN submission
  • Kurt Hornik for helping us keep up with CRAN changes.

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 6 days ago

Total Commits: 668
Total Committers: 10
Avg Commits per committer: 66.8
Development Distribution Score (DDS): 0.424

Commits in past year: 42
Committers in past year: 1
Avg Commits per committer in past year: 42.0
Development Distribution Score (DDS) in past year: 0.0

Name Email Commits
Dan McGlinn d****n@g****m 385
Xiao Xiao x****o@w****g 158
FelixMay f****y@i****e 63
Thore Engel t****l@i****e 38
Caroline Oliver o****s@g****u 8
Caroline Oliver c****r@C****t 8
FelixMay f****y@f****e 4
Caroline Oliver c****r@C****l 2
olivroy 5****y 1
AlbanSagouis 2****s 1

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 121
Total pull requests: 158
Average time to close issues: 7 months
Average time to close pull requests: 15 days
Total issue authors: 14
Total pull request authors: 9
Average comments per issue: 4.63
Average comments per pull request: 1.55
Merged pull request: 146
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 7
Past year average time to close issues: N/A
Past year average time to close pull requests: 17 minutes
Past year issue authors: 0
Past year pull request authors: 1
Past year average comments per issue: 0
Past year average comments per pull request: 0.0
Past year merged pull request: 7
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/MoBiodiv/mobr

Top Issue Authors

  • dmcglinn (68)
  • rueuntal (19)
  • valentinitnelav (5)
  • dylancraven (5)
  • T-Engel (5)
  • elslabbert (4)
  • AlbanSagouis (4)
  • FelixMay (4)
  • nathanbaker04 (2)
  • caroliver (1)
  • aornugent (1)
  • jimjunker1 (1)
  • jmchase (1)
  • Kaoping (1)

Top Pull Request Authors

  • dmcglinn (84)
  • rueuntal (35)
  • FelixMay (25)
  • caroliver (6)
  • T-Engel (4)
  • AlbanSagouis (1)
  • jimjunker1 (1)
  • oliverpurschke (1)
  • olivroy (1)

Top Issue Labels

  • enhancement (38)
  • question (33)
  • bug (18)
  • help wanted (9)
  • ToDo (4)
  • wontfix (3)
  • test (1)

Top Pull Request Labels

  • enhancement (4)
  • bug (1)

Package metadata

cran.r-project.org: mobr

Measurement of Biodiversity

  • Homepage: https://github.com/MoBiodiv/mobr
  • Documentation: http://cran.r-project.org/web/packages/mobr/mobr.pdf
  • Licenses: MIT + file LICENSE
  • Latest release: 3.0.0 (published 8 months ago)
  • Last Synced: 2025-04-25T13:32:47.481Z (1 day ago)
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 215 Last month
  • Rankings:
    • Dependent packages count: 29.797%
    • Dependent repos count: 35.455%
    • Average: 43.228%
    • Downloads: 64.432%
  • Maintainers (1)

Dependencies

DESCRIPTION cran
  • R >= 3.0.2 depends
  • dplyr * imports
  • egg * imports
  • geosphere * imports
  • ggplot2 * imports
  • pbapply * imports
  • plotrix * imports
  • purrr * imports
  • rlang * imports
  • scales * imports
  • tibble * imports
  • tidyr * imports
  • vctrs * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests

Score: 11.261382439134321