The workflow starts by creating a nodiv_data data object, which makes sure that the phylogeny, the species distributions and the spatial coordinates of sites are matched correctly. The function takes a number of data types. There are several functions for exploratory data analysis, including plot, summary, richness, Node_occupancy, Node_size etc. The core of the package are the functions Nodesig, which compares the distributions of the two clades descending from a node, and Node_analysis, which applies this function to all nodes in the phylogeny and summarizes the results as a nodiv_result object. There is a set of functions for interpretation of the results, including plot, plotSOS, and summary. The package also provides basic functions for plotting and manipulating data sets that combine spatial distributions with phylogenies, e.g. subsample, plot_grid and plot_points.
Note that the package may still be unstable - if you experience problems, try cloning the github repository instead: library(devtools); install_github("mkborregaard/nodiv"), or feel free to contact the maintainer.