enve.prune.dist | R Documentation |
Automatically prunes a tree, to keep representatives of each clade.
enve.prune.dist( t, dist.quantile = 0.25, min_dist, quiet = FALSE, max_iters = 100, min_nodes_random = 40000, random_nodes_frx = 1 )
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, |
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 |
random_nodes_frx |
Fraction of the nodes to be sampled if more than |
Returns a pruned phylo object.
Luis M. Rodriguez-R [aut, cre]
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