phyndr_taxonomy: Phyndr taxonomic

Description

Taxonomic method of phyndr that works with generalised sets of taxonomic information. Requires a nested set of taxonomic classes (e.g, genus, family, order, etc) but does not assume that these classes are necessarily monophyletic. phyndr_genus does this for the genus level only but attempts to automatically detect genera from the tree (assuming that tips are all genus/species pairs, with genus and species separated by either an underscore or space).

Usage

phyndr_taxonomy(phy, data_species, taxonomy)
phyndr_genus(phy, data_species)

Arguments

phy

An ape phylogeny

data_species

A vector of species names for which we have trait data. Species names in both the tree and in this vector must be separated with underscores, not with spaces.

taxonomy

A data.frame with taxonomic information. Row names must be present and must list every species in phy and every species in data_species. One or more columns must be present; the first column is the lowest (finest) taxonomic grouping and the last column is the highest (coarsest) taxonomic grouping. The names are arbitrary but will be used in creating mangled names in the resulting phylogeny.

Details

The algorithm (not including recursion and substitute whatever taxonomic level for genus).

1: drop genera if there is a species match for that genus, but don't drop the actual matches.

2: work out which genera can be collapsed to a single tip due to monophyly.

2a. For each genus, determine if they are monophyletic

2b. Then, for genera that are not monophyletic determine which can be made monophyletic by dropping groups that are not represented in the data set.

2c. Collapse each genus down, dropping only genera that are required to achieve monophyly.

3. For each collapsed node we'll mangle the name to "genus::name" and then make a list of suitable species in the tree and data set; for now stored as clades.