Science Score: 39.0%
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○CITATION.cff file
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✓.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Keywords
Repository
Entropy Partitioning to Measure Diversity
Basic Info
- Host: GitHub
- Owner: EricMarcon
- Language: R
- Default Branch: master
- Homepage: https://ericmarcon.github.io/entropart/
- Size: 41.7 MB
Statistics
- Stars: 9
- Watchers: 1
- Forks: 5
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Entropy Partitioning to Measure Diversity 
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.
Owner
- Name: Eric Marcon
- Login: EricMarcon
- Kind: user
- Location: Montpellier, France
- Company: AgroParisTech
- Website: https://ericmarcon.github.io/
- Repositories: 11
- Profile: https://github.com/EricMarcon
GitHub Events
Total
- Watch event: 2
- Issue comment event: 1
- Push event: 4
- Pull request event: 2
- Fork event: 1
Last Year
- Watch event: 2
- Issue comment event: 1
- Push event: 4
- Pull request event: 2
- Fork event: 1
Committers
Last synced: 10 months ago
Top Committers
| Name | 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 (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 1
- Total pull requests: 3
- 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: 0.67
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: about 3 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tothzoltan81 (1)
Pull Request Authors
- teunbrand (2)
- Rekyt (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 951 last-month
- Total docker downloads: 42,767
- Total dependent packages: 4
- Total dependent repositories: 11
- Total versions: 28
- Total maintainers: 1
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
- License: GPL-2 | GPL-3 [expanded from: GNU General Public License]
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Latest release: 1.4.1
published over 10 years ago
Rankings
Maintainers (1)
Dependencies
- 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
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- 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