Run the GMYC Species Delimitation Analysis

Usage

gmyc(tree, method = "single", interval = c(0, 5), quiet = TRUE, tol = 1e-06)

Arguments

tree: A "phylo" object (ape).
method: Analysis method: only "single" is implemented.
interval: Optimisation interval for the null model scaling exponent (used only for the pure-R fallback; C engine always searches [0, 5]).
quiet: Suppress per-threshold progress output (default TRUE).
tol: Ultrametricity tolerance (default 1e-6).

Value

A named list of class "gmyc", with the same structure as splits::gmyc(): method, likelihood (per-threshold vector), parameters, entity, cluster, MRCA, threshold.time, and tree.

References

Fujisawa & Barraclough (2013). Syst. Biol. 62(5), 707–724.