The `nodiv`

R package

## nodiv -
Node-based analysis of species distributions

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`

.