spacodi.permutplot: EXPERIMENTAL: plotting observed and expected community...
In spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

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

spacodi.permutplot is a function used to plot departures from null expectations of diversity turnover, nodewise for a phylogeny.

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  spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgray"), 
  bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfile = NULL, ...)

`spacodi.permutations`	a list-object generated by `spacodi.by.nodes`
`cex`	a named list of scalings for node symbols (`pch`), permutations (`rand`), `node` labels, and `legend`
`transp`	degree of color transparency: `transp=1` is opaque
`col`	a list of two elements: colors to be used for plotting observed and expected community structure
`bg`	a list of background (fill) colors to be used for plotting observed and expected community structure
`all.points`	Boolean; whether all permutation estimates are to be plotted
`add.id`	Boolean; whether `node.labels` are placed near nodewise estimates of community structure
`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
`envelope`	Boolean; whether a smooth-spline envelope is drawn around permutation estimates of structure
`outfile`	an optional .pdf file to which to write output
`...`	additional plotting parameters to be optionally supplied

This function generates a plot of diversity turnover, evaluated for each subtree of the supplied phylogeny. If all.points=TRUE, empirical estimates of structure as well as those expected from permuted community datasets are plotted together. Several methods are available for data permutation when using spacodi.by.nodes, typically the function used to generate spacodi.permutations.

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

Jonathan Eastman

spacodi.calc for further details on diversity structure; spacodi.by.nodes; smooth.spline

# load a species-by-plots matrix, along with a tree
data(sp.example)
attach(sp.example)
spl
phy

# generate a plot of observed and expected Bst
sp.permut=spacodi.by.nodes(sp.plot=spl, phy=phy, n.rep=10)
spacodi.permutplot(sp.permut,bty="n")