phylo: S3 class placeholder definition (list) for phylogenetic trees.
Description
The ape package does not export a version of its
phylo-class, partly because it is not
really defined formally anywhere. Instead, it is an S3
class extended from the base class, list --
this is a very common and easy approach -- and proper
behavior of any method taking an instance of this class
requires exact naming conventions for element names of
the components. The phyloseq package does not provide any
validity checks that a given phylo instance is valid
(conforms to the conventions in the ape package). Yet. If
problems arise, this might be considered, and they could
be defined judiciously and within phyloseq. Similarly, if
a formal definition for the the phylo-class is ever
exported by ape, the current philosophy of phyloseq would
be to remove this internal definition and import the
former. Note that there is still some work going on for
the phylobase package, which is addressing these same
exact issues for S4 phylogenetic tree interaction. A very
large number of packages (around 60 at my last count),
depend on ape, making it easily the de facto standard for
representing phylogenetic trees in R; and the phyloseq
team would prefer to use any exported definitions from
the ape package if possible and available.