joey711/phyloseq — pull request #258 by joey711 (2013-11-05 01:43:17+00:00)
Title: 1.7.7 Tree fixes. Precise ape-import dependency, rather than full

CHANGES IN VERSION 1.7.7
-------------------------

USER-VISIBLE CHANGES

- Tree fixes:
https://github.com/joey711/phyloseq/issues/235
https://github.com/joey711/phyloseq/issues/255

- If a tree has NA branch-length values, they are automatically set to 0.
This occurs within both phyloseq(), and read_tree().

- UniFrac calculations require a rooted tree. While a rooted tree is
not required to be part of a phyloseq object, it is a helpful
default behavior to select a random root when UniFrac is called
and the tree is unrooted, flashing a notice to the user.

- Precise import from ape-package, rather than full-import.
Smaller chance for collisions.
Precisely-defined dependencies listed in NAMESPACE

- As a result of the previous, phyloseq defines a placeholder "phylo" class,
extended from "list". This seems to match the class
from a full import of ape, and is necessary since ape does not
export the "phylo" class.