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mobr

Tools for analyzing changes in diversity across scales

https://github.com/MoBiodiv/mobr

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 11 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.9%) to scientific vocabulary

Keywords

biodiversity conservation ecology rarefaction species statistics

Keywords from Contributors

macroecology point-pattern-analysis species-abundance-distributions
Last synced: 6 months ago · JSON representation

Repository

Tools for analyzing changes in diversity across scales

Basic Info
  • Host: GitHub
  • Owner: MoBiodiv
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 6.54 MB
Statistics
  • Stars: 24
  • Watchers: 12
  • Forks: 19
  • Open Issues: 13
  • Releases: 5
Topics
biodiversity conservation ecology rarefaction species statistics
Created over 10 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License

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:

r citation(package = "mobr")

Installation

r install.packages('mobr')

Or, install the Github version

r install.packages('remotes')

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

r 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.

```r library(mobr) library(dplyr)

data(tankcomm) data(tankplotattr) indices <- c('N', 'S', 'Sn', 'SC', 'SPIE') tankdiv <- tibble(tankcomm) %>% groupby(group = tankplotattr$group) %>% groupmodify(~ calccommdiv(.x, index = indices, effort = 5, extrapolate = TRUE)) plot(tankdiv) tankmobin <- makemobin(tankcomm, tankplotattr, coordnames = c('x', 'y')) tankdeltaS <- getdeltastats(tankmobin, 'group', reflevel='low', type='discrete', logscale=TRUE, nperm = 5) plot(tankdeltaS, '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

  • Name: Measurement of Biodiversity (MoB)
  • Login: MoBiodiv
  • Kind: organization
  • Email: danmcglinn@gmail.com

The repositories related to an iDiv working group examining best practices in the measurement of biodiversity

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Delete event: 1
  • Push event: 17
  • Pull request event: 8
  • Create event: 2
Last Year
  • Release event: 1
  • Watch event: 1
  • Delete event: 1
  • Push event: 17
  • Pull request event: 8
  • Create event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 668
  • Total Committers: 10
  • Avg Commits per committer: 66.8
  • Development Distribution Score (DDS): 0.424
Past Year
  • Commits: 42
  • Committers: 1
  • Avg Commits per committer: 42.0
  • Development Distribution Score (DDS): 0.0
Top Committers
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 (Top 20 + Academic)
idiv.de: 2 fu-berlin.de: 1 carolines-mbp.knology.net: 1 g.cofc.edu: 1 weecology.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 121
  • Total pull requests: 157
  • 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: 1.56
  • Merged pull requests: 145
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 20 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
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)
Pull Request Authors
  • dmcglinn (88)
  • rueuntal (35)
  • FelixMay (25)
  • caroliver (6)
  • T-Engel (4)
  • olivroy (2)
  • AlbanSagouis (1)
  • oliverpurschke (1)
  • jimjunker1 (1)
Top Labels
Issue Labels
enhancement (38) question (33) bug (18) help wanted (9) ToDo (4) wontfix (3) test (1)
Pull Request Labels
enhancement (4) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 362 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: mobr

Measurement of Biodiversity

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 362 Last month
Rankings
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 43.2%
Downloads: 64.4%
Maintainers (1)
danmcglinn@gmail.com
Last synced: 6 months ago

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