An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235.
nodiv R package
The package implements Borregaard et al. (2014) method for identifying nodes in a phylogeny associated with divergent distributions. The main algorithm goes through each node in the phylogeny and relates node overlap to a null model. The package also provides functions for preparing the data sets, for exploratory plots and further analysis.
The workflow starts by creating
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
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
summary. The package also provides basic functions for plotting and manipulating data sets that combine spatial distributions with phylogenies, e.g.