phangorn-internal: Internal phangorn Functions

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Internal phangorn Functions

Description

Internal phangorn functions.

Usage

threshStateC(x, thresholds)

assert_phylo(x, has_edge_length = FALSE, is_rooted = FALSE,
  is_ultrametric = FALSE)

assert_multiPhylo(x, is_ultrametric = FALSE, is_rooted = FALSE,
  same_labels = FALSE, has_edge_length = FALSE)

assert_phyDat(x, contains_label = !is.null(label), label = NULL)

assert_pml(x)

assert_dist(x, finite = FALSE, missing = FALSE)

assert_treeish(x, null.ok = FALSE)

clean_phylo(x, unroot = FALSE, multi2di = FALSE,
  collapse.singles = FALSE, reorder = FALSE)

clean_multiPhylo(x, unroot = FALSE, multi2di = FALSE,
  collapse.singles = FALSE, reorder = FALSE, compress = FALSE)

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)

KlausVigo/phangorn documentation built on Feb. 14, 2025, 8:24 a.m.