little changes in phangorn

[KlausVigo]

Hi @MichelleKendall and @thibautjombart,
congrats that the paper is finally out (sorry I am late a few weeks). Just wanted you guys let know that I made some small changes to all the RF.dist(), wRF.dist() and KF.dist() which all handle rooted=TRUE, so they use clades instead of bipartitions. The behaviour for the rooted case is in many cases a bit weird. Also densiTree() got a lot of new arguments similar as in plot.phylo(), if you call the arguments it should behave the same, but it may have some interesting new features. All on github now.
Cheers,
Klaus

[thibautjombart]

Hi Klaus,
thanks for the heads up. Just to clarify: is it all backward compatible, or is there anything we should change?

[KlausVigo]

It should be all backward compatible, as long as you use argument names. The argument rooted = FALSE in RF.dist() etc was mostly ignored, at least for the vectorized functions. I thought you may be you guys are interested in comparing clades.
densiTree got additional arguments. Only the use of col changed, if col was a vector it would use different colors for edges, now for trees. I doubt that it was used that way.