Congruify and Check.

Usage

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

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.