Hi!
I used phytools to perform a stochastic character mapping on a list of
phylogenetic trees (make.simmap function). Does phytools include a function
somehow analogous to the densiTree function of the R package phangorn that
allows superimposing in a single plot the graphical outputs of the
Josef - this is awesome. I tried it out. Very cool. I don't know if my
brain is able to parse the mixtures of colors along edges into
probabilities of being in each state, but nonetheless - super cool.
Marina - there is also a function in phytools that does this for a two
state character.
Marina,
I actually wrote a function to do this the other day. Hope it's helpful:
densiMap - function(simmap.trees, pal=rainbow, alpha=10, ...){
# Palette is the color palette to draw from, alpha is the
transparency of each plot. ... passed to plotSimmap.
states -
