I made a few minor updates to phytools in the past couple of days.
First, I fixed a bug in plotSimmap
(and, consequently, in
any function that uses plotSimmap
internally, such as
plotTree
). The bug seems to result when the edges of the tree
are neither in "cladewise"
nor in "pruningwise"
order, and I have fixed it by substituting the more standard
"postorder"
edge order (for post-order tree traversal) for
ape's related "pruningwise"
order. The fix can be seen
here.
Second, I updated the phytools function collapse.to.star
which
collapses a user-specified subtree to a star (unsurprisingly) so that it
now accepts trees without edge lengths. Details of this update can be seen
here.
Finally, third, and perhaps most amusingly, I corrected the spelling of
"neighber"
to "neighbor"
in a message printed
to report the number of nearest-neighbor-interchanges required to find the
best tree in the phytools function for unweighted least-squares phylogeny
inference from a distance matrix, optim.phylo.ls
.
That's it.
¿Es necesario reinstalar de nuevo phytools? Lo descargue en septiembre en el workshop que impartiste en México. Saludos
ReplyDeleteSe va a depender en cual tipo de análisis que estás haciendo, pero si todo esta trabajando corectamente, probablemente puedes esperar por la siguiente versión de CRAN. ¡Gracias!
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