phyloregion
Biogeographic regionalization and spatial conservation
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 10 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 17 committers (17.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.0%) to scientific vocabulary
Repository
Biogeographic regionalization and spatial conservation
Basic Info
- Host: GitHub
- Owner: darunabas
- Language: R
- Default Branch: master
- Homepage: http://phyloregion.com/
- Size: 29.2 MB
Statistics
- Stars: 17
- Watchers: 5
- Forks: 12
- Open Issues: 7
- Releases: 0
Metadata Files
README.md
phyloregion 
An R package for biogeographic regionalization (the classification of geographical areas in terms of their biotas) and macroecology. With macroecological datasets of ever increasing size and complexity, phyloregion offers the possibility of handling and executing very large scale analysis of biogeographic regionalization. It also allows fast and memory efficient analysis of standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment. phyloregion can run on any operating system (Mac, Linux, Windows or even high performance computing cluster) with R 3.6.0 (or higher) installed.
How to cite
The original implementation of phyloregion is described in:
Daru, B.H., Karunarathne, P. & Schliep, K. (2020) phyloregion: R package for biogeographic regionalization and macroecology. Methods in Ecology and Evolution 11: 1483-1491. doi: 10.1111/2041-210X.13478.
It is based on the method described in:
Daru, B.H., Farooq, H., Antonelli, A. & Faurby, S. (2020) Endemism patterns are scale dependent. Nature Communications 11: 2115 doi: 10.1038/s41467-020-15921-6.
The original conceptual is described in:
Daru, B.H., Elliott, T.L., Park, D.S. & Davies, T.J. (2017) Understanding the processes underpinning patterns of phylogenetic regionalization. Trends in Ecology & Evolution 32: 845-860. doi: 10.1016/j.tree.2017.08.013
Installation
phyloregion is available from the Comprehensive R Archive Network, so you can use the following line of code to install and run it:
install.packages("phyloregion")
Alternatively, you can install the development version of phyloregion hosted on GitHub. To do this, you will need to install the devtools package. In R, type:
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("darunabas/phyloregion")
Feedback
If you have any questions, suggestions or issues regarding the package, please add them to GitHub issues
License
The license for phyloregion is similar to that of the package on CRAN:
License: AGPL-3
The AGPL-3 license can be found at: https://cran.r-project.org/web/licenses/AGPL-3
Owner
- Login: darunabas
- Kind: user
- Company: Texas A&M University-Corpus Christi
- Website: https://barnabasdaru.com/
- Twitter: Barnabas_Daru
- Repositories: 6
- Profile: https://github.com/darunabas
GitHub Events
Total
- Issues event: 4
- Watch event: 2
- Issue comment event: 4
- Pull request review event: 1
- Pull request event: 1
- Fork event: 1
Last Year
- Issues event: 4
- Watch event: 2
- Issue comment event: 4
- Pull request review event: 1
- Pull request event: 1
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Klaus Schliep | k****p@g****m | 198 |
| Barnabas Daru | b****u@B****l | 102 |
| Barnabas Daru | b****u@B****t | 101 |
| darunabas | d****s | 28 |
| Barnabas Daru | b****u@t****u | 16 |
| piyalkarum | p****l@y****m | 8 |
| Barnabas Daru | d****s@g****m | 8 |
| patarol | l****o@g****m | 4 |
| Barnabas Daru | b****u@b****u | 3 |
| Barnabas Daru | b****u@v****u | 2 |
| Barnabas Daru | b****u@B****n | 2 |
| Barnabas Daru | b****u@c****t | 1 |
| Barnabas Daru | b****u@M****t | 1 |
| Barnabas Daru | b****u@B****l | 1 |
| Barnabas Daru | b****u@D****t | 1 |
| Barnabas Daru | b****u@D****t | 1 |
| GabrielNakamura | g****a@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 12
- Total pull requests: 6
- Average time to close issues: 12 months
- Average time to close pull requests: 12 days
- Total issue authors: 11
- Total pull request authors: 3
- Average comments per issue: 1.75
- Average comments per pull request: 0.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: 4 months
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- joelnitta (2)
- duyuanbao (1)
- rgb459 (1)
- guoguo7896 (1)
- MUBGVic (1)
- Otoliths (1)
- patarol (1)
- shawnlaffan (1)
- rsbivand (1)
- natirubirb (1)
- gfschnei (1)
- Lisark45 (1)
Pull Request Authors
- patarol (4)
- leorjorge (1)
- GabrielNakamura (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 491 last-month
- Total docker downloads: 21,613
- Total dependent packages: 2
- Total dependent repositories: 3
- Total versions: 5
- Total maintainers: 1
cran.r-project.org: phyloregion
Biogeographic Regionalization and Macroecology
- Homepage: https://github.com/darunabas/phyloregion
- Documentation: http://cran.r-project.org/web/packages/phyloregion/phyloregion.pdf
- License: AGPL-3
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Latest release: 1.0.9
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
- Matrix * imports
- ape * imports
- betapart * imports
- clustMixType * imports
- colorspace * imports
- dismo * imports
- gbm * imports
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- parallel * imports
- phangorn * imports
- predicts * imports
- randomForest * imports
- raster * imports
- rgeos * imports
- rpart * imports
- sp * imports
- terra * imports
- vegan * imports
- knitr * suggests
- mapproj * suggests
- phyloseq * suggests
- rJava * suggests
- rmarkdown * suggests
- survival * suggests
- tinytest * suggests