enve.prune.dist {enveomics.R}

Enveomics: Prune Dist

Description

Automatically prunes a tree, to keep representatives of each clade.

Usage

enve.prune.dist(
  t,
  dist.quantile = 0.25,
  min_dist,
  quiet = FALSE,
  max_iters = 100,
  min_nodes_random = 40000,
  random_nodes_frx = 1
)

Arguments

t

A phylo object or a path to the Newick file.

dist.quantile

The quantile of edge lengths.

min_dist

The minimum distance to allow between two tips. If not set, dist.quantile is used instead to calculate it.

quiet

Boolean indicating if the function must run without output.

max_iters

Maximum number of iterations.

min_nodes_random

Minimum number of nodes to trigger tip-pairs nodes sampling. This sampling is less reproducible and more computationally expensive, but it's the only solution if the cophenetic matrix exceeds 2^31-1 entries; above that, it cannot be represented in R.

random_nodes_frx

Fraction of the nodes to be sampled if more than min_nodes_random.

Value

Returns a pruned phylo object.

Author(s)

Luis M. Rodriguez-R [aut, cre]