phylo: S3 class placeholder definition (list) for phylogenetic...
In phyloseq: Handling and analysis of high-throughput microbiome census data

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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.