spacodi.treeplot: EXPERIMENTAL: plotting diversity turnover on trees
In spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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, ...)

`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

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).

a plot of diversity structure estimates for a phylogeny, with the option to direct output to a .pdf file

Timothy Paine and Jonathan Eastman

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 spacodi.by.nodes for estimating phylogenetic turnover on trees with community-level sampling; spacodi.permutplot; phy.dotplot

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)