Bootstrap support for a tree — bootstrap

Resamples the markers, traits or alignment sites with replacement, recomputes the distance matrix and the tree for each replicate, and reports how often each group in the original tree is found again (Felsenstein 1985). For rooted trees the groups are clades; for unrooted NJ and BIONJ trees they are bipartitions.

Usage

bootstrap_tree(
  d,
  tree,
  distance = NULL,
  B = 100,
  seed = 1,
  sqrt_binary = FALSE,
  scale = TRUE,
  progress = NULL
)

Arguments

d: The cl_data the tree was built from.
tree: A cl_tree from build_tree().
distance: Distance method used for the tree.
B: Number of bootstrap replicates.
seed: Random seed, so the run can be repeated exactly.
sqrt_binary, scale: Passed to compute_distance().
progress: Optional function called with the share done (0 to 1).

Value

A list with support (percent, one value per internal node of tree$phylo), trees (the replicate trees), B, failed and seed.