This document describes the
phyloregion package for the R software.
phyloregion is a computational infrastructure for biogeographic
(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
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 macroecology. Methods in Ecology and Evolution 11, 1483-1491.
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.
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
You will need to install the
devtools package. In
if (!requireNamespace("devtools", quietly = TRUE))
Load the phyloregion package:
Barnabas Daru thanks Texas A&M University-Corpus Christi for financial and logistic support.