Biodiverse
A tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matrix-based relationships, as well as related environmental and temporal variations.
https://github.com/shawnlaffan/biodiverse
Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics
Keywords
beta-diversity biodiverse endemism hacktoberfest phylodiversity phylogenetic-diversity phylogenetic-trees phylogeography randomisations spatial-analysis species-turnover
Last synced: about 14 hours ago
JSON representation
Repository metadata
A tool for the spatial analysis of diversity
- Host: GitHub
- URL: https://github.com/shawnlaffan/biodiverse
- Owner: shawnlaffan
- License: gpl-3.0
- Created: 2015-03-27T22:49:20.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2025-03-05T05:07:43.000Z (2 months ago)
- Last Synced: 2025-05-09T02:54:11.010Z (9 days ago)
- Topics: beta-diversity, biodiverse, endemism, hacktoberfest, phylodiversity, phylogenetic-diversity, phylogenetic-trees, phylogeography, randomisations, spatial-analysis, species-turnover
- Language: Perl
- Homepage: http://shawnlaffan.github.io/biodiverse/
- Size: 452 MB
- Stars: 78
- Watchers: 8
- Forks: 19
- Open Issues: 83
- Releases: 18
-
Metadata Files:
- Readme: README.md
- License: LICENSE
README.md
Biodiverse
Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matrix-based (e.g. genetic distance) relationships, as well as related environmental and temporal variations.
DOWNLOAD: Biodiverse can be downloaded from https://github.com/shawnlaffan/biodiverse/wiki/Downloads
Biodiverse supports the following processes:
- Linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces;
- Spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity;
- Spatially constrained agglomerative cluster analyses;
- Spatially constrained region grower analyses;
- Interactive visualisation of turnover patterns (for example beta-diversity); and
- Randomisations for hypothesis testing.
Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface (GUI) and through user written scripts.
More than 300 indices are supported. See the Indices page.
Screen shots can be found on the ScreenShots page.
Example applications can be seen at the publications page.
Help can be located via the help pages (these are also accessible via the wiki link on the right of this page).
A discussion group is at http://groups.google.com.au/group/biodiverse-users and a blog at http://biodiverse-analysis-software.blogspot.com.au/
To cite Biodiverse or acknowledge its use, use the following details, substituting the version of the application that you used for "Version 1.0".
- Laffan, S.W., Lubarsky, E. & Rosauer, D.F. (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography. Vol 33, 643-647 (Version 1.0).
An overview of the system is also provided in Dan Rosauer's talk at TDWG2008:
- Rosauer, D.F. & Laffan, S.W. (2008) Linking phylogenetic trees, taxonomy & geography to map phylogeography using Biodiverse. Taxonomic Data Working Group 2008, Perth, Australia. PPT SWF with audio.
For a list of publications using Biodiverse, see the PublicationsList page.
Installation
Installation instructions can be accessed through the Installation page.
News
See http://shawnlaffan.github.io/biodiverse/#news
Acknowledgements
This research has been supported by Australian Research Council Linkage Grant LP0562070 (Laffan and West) and UNSW FRGP funding to Laffan.
Much of the original GUI coding was by Eugene Lubarsky. Substantial contributions to the project have also been made by Michael Zhou and Anthony Knittel. Unfortunately the code history does not show their contributions as authorship details were lost as we transitioned from Google Code to GitHub.
Persistent URL
http://www.purl.org/biodiverse
Keywords
Biodiversity analysis tool, spatial analysis, phylogeography, spatial analysis, endemism, phylogenetic diversity, beta diversity, species turnover
Owner metadata
- Name:
- Login: shawnlaffan
- Email:
- Kind: user
- Description:
- Website: http://shawnlaffan.github.io/biodiverse/
- Location: Australia
- Twitter:
- Company: @unsw-edu-au
- Icon url: https://avatars.githubusercontent.com/u/1332405?v=4
- Repositories: 61
- Last ynced at: 2023-08-13T06:41:08.322Z
- Profile URL: https://github.com/shawnlaffan
GitHub Events
Total
- Issues event: 12
- Watch event: 3
- Delete event: 6
- Issue comment event: 5
- Push event: 26
- Pull request event: 13
- Gollum event: 23
- Create event: 7
Last Year
- Issues event: 12
- Watch event: 3
- Delete event: 6
- Issue comment event: 5
- Push event: 26
- Pull request event: 13
- Gollum event: 23
- Create event: 7
Committers metadata
Last synced: 8 days ago
Total Commits: 4,505
Total Committers: 14
Avg Commits per committer: 321.786
Development Distribution Score (DDS): 0.091
Commits in past year: 331
Committers in past year: 1
Avg Commits per committer in past year: 331.0
Development Distribution Score (DDS) in past year: 0.0
| Name | Commits | |
|---|---|---|
| Shawn Laffan | s****n@g****m | 4093 |
| Luke Fitzpatrick | l****k@g****m | 202 |
| [email protected] | z****y@g****m@0****0 | 81 |
| Dan Rosauer | D****r | 41 |
| Anderson Ku | a****u@g****m | 40 |
| Jason Mumbulla | j****a@g****m | 37 |
| [email protected] | a****l@g****m@0****0 | 3 |
| Katherine Spice | k****e@c****k | 2 |
| Liuyong Ding | 3****s | 1 |
| Katrin Leinweber | 9****r | 1 |
| Alex Kapranoff | a****x@k****u | 1 |
| Patrice Clement | m****p@g****g | 1 |
| [email protected] | s****0@g****m@0****0 | 1 |
| Anderson Ku | a****u@a****m | 1 |
Committer domains:
- amadeus.com: 1
- gentoo.org: 1
- kapranoff.ru: 1
- coruscant.org.uk: 1
Issue and Pull Request metadata
Last synced: 1 day ago
Total issues: 45
Total pull requests: 53
Average time to close issues: 11 months
Average time to close pull requests: 1 day
Total issue authors: 6
Total pull request authors: 2
Average comments per issue: 1.13
Average comments per pull request: 0.17
Merged pull request: 52
Bot issues: 0
Bot pull requests: 0
Past year issues: 8
Past year pull requests: 15
Past year average time to close issues: 2 days
Past year average time to close pull requests: about 5 hours
Past year issue authors: 1
Past year pull request authors: 1
Past year average comments per issue: 0.13
Past year average comments per pull request: 0.0
Past year merged pull request: 15
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- shawnlaffan (37)
- GoogleCodeExporter (4)
- eortizb (1)
- vmikk (1)
- luishdez35 (1)
- FranckLejzerowicz (1)
Top Pull Request Authors
- shawnlaffan (52)
- vmikk (1)
Top Issue Labels
- GUI (20)
- enhancement (16)
- randomisations (5)
- trees (5)
- auto-migrated (4)
- bug (4)
- data import (3)
- indices (2)
- needs blog post (2)
- Refactor (1)
- spatial conditions (1)
- Priority-Medium (1)
- Type-Enhancement (1)
- OpSys-OSX (1)
- executable (1)
- Gtk3 (1)
Top Pull Request Labels
- metadata (1)
Dependencies
- actions/cache v3 composite
- actions/checkout v3 composite
- shogo82148/actions-setup-perl v1 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/cache v3 composite
- actions/checkout v3 composite
Score: 7.720461694599722