The 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 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
.