plotSOS: Gives the SOS values for a given node.

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

Gives the SOS values for a given node.

Description

SOS gives the SOS value for the node, used in the interpretation of node-based analysis of species distributions after running Node_analysis. plotSOS plots the values on a map. GND gives the GND values.

Usage

SOS(nodiv_result, node)
plotSOS(nodiv_result, node, zlim, ...)
GND(nodiv_result, node = NULL)

Arguments

nodiv_result	The result of running Node_analysis
node	The node label or node number specifying the node to plot. Optional for GND
zlim	The values to use for the extremes of the color palette
...	Further arguments to pass to the plotting function

Details

The first descendant clade (i.e. the first returned by a call to Descendants) is associated with positive SOS values, the second descendant clade is associated with negative values. The plot will be done as a spatial grid or as colored points, depending on the type of the nodiv_result object. If the nodiv_result object has a shape object of type raster, this will be plotted normally in the background - but resizing the window will cause the plots/pixels and the underlying raster object to lose alignment, due to a bug in the raster package.

Value

SOS returns a numerical vector with the SOS values. If nodiv_result has type raster, a raster object of the SOS values is returned by plotSOS.

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

Node_analysis

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