a named list of character scalings for node-associated symbols (pch), tip labels (tip), and the legend (legend)
transp
degree of color transparency: transp=1 is opaque
sig.plot
Boolean; whether nodes are colored by significance of observed and expected estimates of structure
cut.off
a value, if sig.plot=TRUE, distinguishing observed from expected estimates of structure
cols
a list of three elements if using sig.plot: the first color is for values not different than expected; the second and third for values greater and less than expected
main
Boolean; whether a title is plotted
outfile
an optional .pdf file to which to write output
add.id
Boolean; whether node.labels are placed near nodes; see nodelabels
...
additional plotting parameters to be optionally supplied
Details
This function will compute and plot estimates of diversity structure on the tree, with color-coded values.
Note: this function requires a spacodi.permutations with data for all nodes. If using, for instance, spacodi.by.nodes to
generate these data, the option obs.only=TRUE will ensure that data are returned for all nodes (see Examples below).
Value
a plot of diversity structure estimates for a phylogeny, with the option to direct output to a .pdf file
Author(s)
Timothy Paine and Jonathan Eastman
References
HARDY OJ and B SENTERRE. 2007. Characterizing the
phylogenetic structure of communities by an additive partitioning of
phylogenetic diversity. Journal of Ecology 95:493-506.
HARDY OJ. 2008. Testing the spatial phylogenetic
structure of local communities: statistical performances of
different null models and test statistics on a locally neutral
community. Journal of Ecology 96:914-926.
See Also
see spacodi.by.nodes for estimating phylogenetic turnover on trees with community-level sampling;
spacodi.permutplot; phy.dotplot