rosenberg: Rosenberg's probability of reciprocal monophyly

In boopsboops/spider: Species Identity and Evolution in R

Rosenberg's probability of reciprocal monophyly

Description

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

Usage

rosenberg(phy)

Arguments

phy	A tree of class ‘phylo’.

Details

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.

Value

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

Author(s)

Samuel Brown <[e-mail]>

References

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

See Also

nodelabels.

Examples

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)

boopsboops/spider documentation built on June 2, 2025, 7:28 a.m.