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Residual-resampling bootstrap tree(s) from a distance matrix (UPGMA)

Source: R/bootstrapTree.R
residualBootstrapTree.Rd

Build a reference tree from a distance matrix using UPGMA, then perform residual-resampling bootstrap to obtain replicate trees and map clade support onto the reference.

Usage

residualBootstrapTree(D, n_bootstrap = 1000L, clamp_zero = TRUE)

Arguments

D

A square numeric distance matrix with identical row/column names, or a dist object.

n_bootstrap

Integer number of bootstrap replicates (default 1000).

clamp_zero

Logical; clamp negative distances in resampled matrices to 0 (recommended).

Value

A list with:

  • tree: Reference tree (phylo) built from D with UPGMA. Node labels contain bootstrap %.

  • bootstrap_trees: List of replicate trees (phylo).

  • support: Numeric vector of bootstrap percentages per internal node (aligned to tree$node.label).

  • call: Matched call.

Author

Anika Mittal

Examples

out <- residualBootstrapTree(Halo_PercentDiff, n_bootstrap = 200)
plot(out$tree, show.node.label = TRUE)