Compares the Distribution of Sister Clades Through a Phylogeny

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. . Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.


The nodiv R package

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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.

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Reference manual

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install.packages("nodiv")

1.3.0 by Michael Krabbe Borregaard, 8 months ago


https://github.com/mkborregaard/nodiv


Browse source code at https://github.com/cran/nodiv


Authors: Michael Krabbe Borregaard


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


MIT + file LICENSE license


Imports picante, raster, ape, sp, vegan, utils

Suggests RColorBrewer, parallel, testthat, colorspace


See at CRAN