This document describes the phyloregion package for the R software.
phyloregion 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. Previous
analyses of biogeographical regionalization were either focused on smaller
datasets or slower particularly when the number of species or geographic scale
is very large. 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 for 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.
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. Coming soon.
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 and Evolution 32: 845-860.
If you have any questions, suggestions or issues regarding the package, please add them to GitHub issues
phyloregion is an open-source and free package hosted on
GitHub.
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:
library(phyloregion)
Barnabas Daru thanks Texas A&M University-Corpus Christi for financial and logistic support.