congruify_and_check: Congruify and Check.

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

Congruify and Check.

Description

Congruify and Check.

Usage

congruify_and_check(
  reference,
  target,
  taxonomy = NULL,
  tol = 0.01,
  option = 2,
  scale = "pathd8",
  attempt_fix = TRUE
)

Arguments

reference	an ultrametric tree used to time-scale the target
target	a phylogram that is sought to be ultrametricized based on the reference phylogeny
taxonomy	a linkage table between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny
tol	branching time in reference above which secondary constraints will be applied to target
option	an integer (1 or 2; see details).
scale	NA, "PATHd8" or "treePL" (if PATHd8 or "treePL" are available in the R PATH)
attempt_fix	Default to TRUE. If congruification results in NA branch lengths, it will attempt to fix them.

datelife documentation built on July 10, 2023, 2:02 a.m.