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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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