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entropart

An R package that provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
https://github.com/EricMarcon/entropart

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

Keywords

biodiversity diversity entropy-partitioning estimator measure species

Keywords from Contributors

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Last synced: about 19 hours ago
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Repository metadata

Entropy Partitioning to Measure Diversity

README.md

Entropy Partitioning to Measure Diversity

CRAN version


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entropart is an R package that provides functions to calculate alpha, beta and gamma diversity of communities,
including phylogenetic and functional diversity.

Estimation-bias corrections are available.

Details

In the entropart package, individuals of different species are counted in several communities which may (or not)
be agregated to define a metacommunity.
In the metacommunity, the probability to find a species in the weighted average of probabilities in communities.
This is a naming convention, which may correspond to plots in a forest inventory or any data organized the same way.

Basic functions allow computing diversity of a community.
Data is simply a vector of probabilities (summing up to 1) or of abundances (integer values that are numbers of individuals).
Calculate entropy with functions such as Tsallis, Shannon, Simpson, Hurlbert or GenSimpson
and explicit diversity (i.e. effective number of species) with Diversity and others.
By default, the best available estimator of diversity will be used, according to the data.

Communities can be simulated by rCommunity, explicitely declared as a species distribution (as.AbdVector or as.ProbaVector),
and plotted.

Phylogenetic entropy and diversity can be calculated if a phylogenetic (or functional), ultrametric tree is provided.
See PhyloEntropy, Rao for examples of entropy and PhyloDiversity to calculate phylodiversity,
with the state-of-the-art estimation-bias correction.
Similarity-based diversity is calculated with Dqz, based on a similarity matrix.

Vignettes

A quick introduction is in vignette("entropart").

A full documentation is available online, in the "Articles" section of the web site of the vignette.
It is a continuous update of the paper published in the Journal of Statistical Software (Marcon & Hérault, 2015).

The development version documentation is also available.

Reference

Marcon, E. and Herault, B. (2015). entropart: An R Package to Measure and Partition Diversity.
Journal of Statistical Software. 67(8): 1-26.

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Last synced: 5 days ago

Total Commits: 416
Total Committers: 3
Avg Commits per committer: 138.667
Development Distribution Score (DDS): 0.007

Commits in past year: 13
Committers in past year: 2
Avg Commits per committer in past year: 6.5
Development Distribution Score (DDS) in past year: 0.154

Name Email Commits
Eric Marcon e****n@e****f 413
Teun van den Brand t****d@g****m 2
Matthias Grenié m****e@e****r 1

Committer domains:

Issue and Pull Request metadata

Last synced: 2 days ago

Total issues: 1
Total pull requests: 2
Average time to close issues: 11 days
Average time to close pull requests: about 5 hours
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 1.0
Average comments per pull request: 1.0
Merged pull request: 2
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 1
Past year average time to close issues: N/A
Past year average time to close pull requests: about 3 hours
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: 1.0
Past year merged pull request: 1
Past year bot issues: 0
Past year bot pull requests: 0

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

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  • tothzoltan81 (1)

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  • teunbrand (1)
  • Rekyt (1)

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Package metadata

cran.r-project.org: entropart

Entropy Partitioning to Measure Diversity

  • Homepage: https://ericmarcon.github.io/entropart/
  • Documentation: http://cran.r-project.org/web/packages/entropart/entropart.pdf
  • Licenses: GPL-2 | GPL-3 [expanded from: GNU General Public License]
  • Latest release: 1.4.1 (published over 9 years ago)
  • Last Synced: 2025-04-25T12:07:34.773Z (2 days ago)
  • Versions: 28
  • Dependent Packages: 4
  • Dependent Repositories: 11
  • Downloads: 748 Last month
  • Docker Downloads: 42,767
  • Rankings:
    • Dependent repos count: 8.819%
    • Dependent packages count: 9.104%
    • Forks count: 12.335%
    • Average: 13.929%
    • Downloads: 18.664%
    • Stargazers count: 20.725%
  • Maintainers (1)

Dependencies

DESCRIPTION cran
  • EntropyEstimation * imports
  • ape * imports
  • ggplot2 * imports
  • ggpubr * imports
  • grDevices * imports
  • graphics * imports
  • parallel * imports
  • reshape2 * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • utils * imports
  • vegan * imports
  • ade4 * suggests
  • knitr * suggests
  • pkgdown * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/check.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/rhub.yaml actions
  • r-hub/actions/checkout v1 composite
  • r-hub/actions/platform-info v1 composite
  • r-hub/actions/run-check v1 composite
  • r-hub/actions/setup v1 composite
  • r-hub/actions/setup-deps v1 composite
  • r-hub/actions/setup-r v1 composite

Score: 13.977180327027357