Project Status: Active – The project has reached a stable, usable state and is being actively developed. lifecycle

This is a computational infrastructure for biogeographic regionalization (the classification of geographical areas in terms of their biotas) and spatial conservation in the R scientific computing environment. Previously it was only possible to perform analysis of biogeographic regionalization on small datasets, often using tools that are difficult to replicate. With macroecological datasets of ever increasing size and complexity, phyloregion offers the possibility of handling and executing large scale biogeographic regionalization efficiently and with extreme speed. It also allows fast and efficient analysis of more 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 spatial conservation. bioRxiv 2020.02.12.945691 doi: 10.1101/2020.02.12.945691

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

Feedback

If you have any questions, suggestions or issues regarding the package, please add them to GitHub issues

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") 

Then:

devtools::install_github("darunabas/phyloregion")

Load the phyloregion package and you are good to go:

library(phyloregion)

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