Welcome to our page for Machuruku, our R package for phylogenetic niche modeling. Machuruku uses a modified Bioclim niche-modeling method and ancestral character estimation to reconstruct ancestral niches. Input data consists of present-day climate rasters, a time-calibrated phylogeny, and taxon occurrence data for all tips. Ancestral niche models can be projected into additionally provided paleoclimate data to visualize the geographic origins of a lineage. To install Machuruku, simply run the following in R:
install.packages("devtools")
devtools::install_github("wxguillo/machuruku")
If your install fails because of ggtree, install it separately with the following, then reattempt the above:
install.packages("BiocManager")
BiocManager::install("ggtree")
For both quick and detailed tutorials on how to use Machuruku, please visit the tutorial page in this repository.
Software citation and associated manuscript: Guillory WG, Brown JL. 2021. A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions. Systematic Biology, syab016. Link. (Email me at [email protected] for PDF)
