rosenberg: Rosenberg's probability of reciprocal monophyly
In spider: Species Identity and Evolution in R

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

This function computes Rosenberg's probability of reciprocal monophyly for each dichotomous node of a phylogenetic tree.

1	rosenberg(phy)

phy

A tree of class ‘phylo’.

Because ape plots node labels in a different manner to the method in which they are stored, when plotting the node labels made by rosenberg, make sure the node argument is given as shown in the examples below.

A numeric vector with names giving the node numbers of phy.

Samuel Brown <s_d_j_brown@hotmail.com>

Rosenberg, N. A. (2007). Statistical tests for taxonomic distinctiveness from observations of monophyly. _Evolution_ *61* (2), 317-323.

nodelabels.

data(anoteropsis)
anoTr <- ape::nj(ape::dist.dna(anoteropsis))
anoLab <- rosenberg(anoTr)
ape::plot.phylo(anoTr)
ape::nodelabels(round(anoLab,3), node=as.numeric(names(anoLab)))

data(dolomedes)
doloTr <- ape::nj(ape::dist.dna(dolomedes))
doloRose <- rosenberg(doloTr)
ape::plot.phylo(doloTr)
ape::nodelabels(round(doloRose, 3))

#Colour circles for nodes with a probability < 0.005
doloNodes <- doloRose < 0.005
doloLabs <- doloRose
doloLabs[doloNodes] <- "blue"
doloLabs[!doloNodes] <- "red"
ape::plot.phylo(doloTr, cex=0.7)
ape::nodelabels(pch=21, bg=doloLabs, node=as.numeric(names(doloLabs)), cex=2)
graphics::legend(x=0.015, y=16.13, legend=c("significant", "not significant"), pch=21, 
    pt.bg=c("blue", "red"), bty="n", pt.cex=2)