spacodiR (version 0.13.0115)

spacodi.treeplot: EXPERIMENTAL: plotting diversity turnover on trees

Description

spacodi.treeplot is used to plot departures from expectations for diversity turnover on a phylogeny

Usage

spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, cols = list("white", "gray", "black"), main = TRUE, outfile = NULL, add.id = FALSE, ...)

Arguments

spacodi.permutations

a list-object generated by spacodi.by.nodes

phy

a phylogenetic tree of class phylo; see read.tree

cex

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

Value

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).

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

Examples

data(sp.example)
attach(sp.example)

# plot PIst 
PI=spacodi.by.nodes(sp.plot=spl, sp.parm="PIst", phy=phy, return.all=TRUE, method="1s")
spacodi.treeplot(PI, phy, sig.plot=TRUE, add.id=FALSE)
spacodi.treeplot(PI, phy, sig.plot=FALSE, add.id=FALSE)