Yesterday & this morning I pushed a couple of new phytools updates to GitHub (1, 2).
Among the two updates, (1) I fixed a bug in fitPagel for cases in
which not all pairwise states of the two binary characters (0|0, 0|1, 1|0, and
1|1) are represented in the dataset. I fixed this bug for
method="fitMk" (the default), but it may persist for the other two
model-fitting methods. I also fixed a bug in dotTree for
data.type="discrete" that was producing a really weird result in
terms of the color scheme and legend.
(2) I made a small update for consensus.edges so that instead of
checking if the tree is rooted for method="least.squares", the
function checks if the trees are all ultrametric. This is done because the
internally used function, nnls.tree(...,rooted=TRUE), will return
ultrametric branches - which does not make sense if the original trees were not
ultrametric!
That's it. These updates can be obtained by installing phytools from GitHub as follows:
library(devtools)
install_github("liamrevell/phytools")
library(phytools)
Amazing timing. This is just what I was hoping for.
ReplyDeleteThank you!