get_best_grove: Get grove from a 'datelifeResult' object that can be...

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Get grove from a datelifeResult object that can be converted to phylo from a median summary matrix

Description

Get grove from a datelifeResult object that can be converted to phylo from a median summary matrix

Usage

get_best_grove(datelife_result, criterion = "taxa", n = 2)

Arguments

datelife_result	A datelifeResult object. Only needed for criterion = "taxa".
criterion	Defaults to criterion = "taxa". Used for chronogram summarizing, i.e., obtaining a single summary chronogram from a group of input chronograms. For summarizing approaches that return a single summary tree from a group of phylogenetic trees, it is necessary that the latter form a grove, roughly, a sufficiently overlapping set of taxa between trees, see Ané et al. (2009) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s00026-009-0017-x")}. In rare cases, a group of trees can have multiple groves. This argument indicates whether to get the grove with the most trees (criterion = "trees") or the most taxa (criterion = "taxa").
n	The degree of taxon name overlap among input chronograms. Defaults to n = 2, i.e., at least two overlapping taxon names.

Value

A list of two elements:

best_grove

A datelifeResult object filtered to only include one grove of trees that can be summarized with median or sdm.

overlap

The degree of taxon names overlap among trees in the best grove.

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.