Node_analysis: Calculate GND and SOS scores for a phylogeny and community...

In nodiv: Compares the Distribution of Sister Clades Through a Phylogeny

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)

nodiv documentation built on Aug. 21, 2023, 9:10 a.m.