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Internal phangorn Functions

Source: R/RcppExports.R, R/candidate_tree.R, R/hash_phylo.R, and 6 more
phangorn-internal.Rd

Internal phangorn functions.

Usage

threshStateC(x, thresholds)

candidate_tree(x, method = c("unrooted", "ultrametric", "tipdated"),
  eps = 1e-08, tip.dates = NULL, ...)

hash(x, ...)

map_duplicates(x, dist = length(x) < 500, ...)

edQt(Q = c(1, 1, 1, 1, 1, 1), bf = c(0.25, 0.25, 0.25, 0.25))

pml.free()

pml.init(data, k = 1L)

coords(obj, dim = "3D")

pmlPen(object, lambda, ...)

relabel(x, ref)