Node_analysis {nodiv}

Calculate GND and SOS scores for a phylogeny and community data set

Description

Goes through each node in the phylogeny, and compares the distribution overlap of sister clades to that expected from a null mode that considers node size, species richness and range size.

Usage

Node_analysis(nodiv_data, repeats = 100, method = c("rdtable", "quasiswap"), 
                cores = 1, log_parallel_progress = FALSE)
## S3 method for class 'nodiv_result'
summary(object, ...)
## S3 method for class 'nodiv_result'
print(x, printlen = 4, ...)
## S3 method for class 'nodiv_result'
plot(x, label = nodenumbers(x), zlim = 0:1, ...)

Arguments

nodiv_data

An object created by the nodiv_data function

repeats

Number of null communities to create at each node

method

The null model algorithm used to simulate random communities

cores

The number of cores to use in the computation. Note that multi-core processing is yet unimplemented.

log_parallel_progress

If this is TRUE, the results from each node will be saved as an '.rda' file in the working directory. Useful for large parallel computations.

object

The nodiv_result object

x

The nodiv_result object

printlen

The number of species to print to screen

label

The text to use for labelling nodes in the plot

zlim

The values of GND to use for the extremes of the color scale on the plot

...

Further arguments to be passed to the function

Details

The "rdtable" algorithm is efficient, but may underestimate the deviation between nodes. It should primarily be used for exploratory data analysis. Note that the more robust "quasiswap" algorithm may take days to run on larger data sets.

The plot function for nodiv_result plots the phylogenetic tree with colored symbols at the nodes. The color and size the nodes are proportional with the GND value of the node.

Value

The result is an object of type nodiv_result, which has the following components:

GND

A numeric vector between 0 and 1 describing the distributional divergence associated with a node

SOS

A numeric matrix given the SOS of values, which expresses the difference between empirical and expected species richness of each clade at each site

It also includes all the elements of the nodiv_data object:

coords

A SpatialPointsDataFrame or SpatialPixelsDataFrame (from sp) with spatial coordinates, and one column named sites containing the site names

comm

The community matrix

type

A character vector describing the type of data

species

A list of species names

shape

An optional slot detailing a shapefile object for plotting the data

phylo

A phylogeny of type phylo from package ape

Author(s)

Michael Krabbe Borregaard

References

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. DOI: 10.1111/2041-210X.12283

See Also

plotSOS

Examples

data(coquettes)
res <- Node_analysis(coquettes, 50, "rdtable")
opar <- par(mfrow = c(1,2))
plot(res)
plotSOS(res, 28, shapefill = terrain.colors(64))
summary(res)
par(opar)