sppEdge: Returns

In spiderDev: Species Identity and Evolution in R--development

Description

This function calculates AIC values, weights and model-weighted average number of entities inferred using GMYC.

Usage

sppEdge(phy, sppVector, cols = NULL)

Arguments

phy	An object of class ‘phylo’.
sppVector	The species vector (see sppVector).
cols	Vector to represent the colours for each species. Recycled if necessary.

Details

This function implements equations 3 to 6 in Powell (2011).

Value

A numeric vector giving the descendant tip numbers and (if tips.only = FALSE) node numbers

Author(s)

Samuel Brown <[e-mail]>

See Also

clustGMYC

Examples

data(dolomedes)
doloTr <- nj(dist.dna(dolomedes))
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

edgeCol <- sppEdge(doloTr, doloSpp)
plot(doloTr, edge.color = edgeCol)

data(anoteropsis)
anoTr <- nj(dist.dna(anoteropsis))
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"),  function(x) paste(x[1], x[2], sep="_"))

edgeCol <- sppEdge(anoTr, anoSpp)
plot(anoTr, edge.color = edgeCol)

spiderDev documentation built on May 2, 2019, 5:23 p.m.