phyloSignalBS: Computes phylogenetic signal for bootstrapped replicates of a...

In fkeck/phylosignal: Exploring the Phylogenetic Signal in Continuous Traits

Computes phylogenetic signal for bootstrapped replicates of a phylogeny.

Description

This function computes phylogenetic signal statistics and p-values for bootsrapped replicates a phylogenetic tree and produce boxplots to represent the results. This can be useful to check the impact of phylogenetic reconstruction uncertainty on phylogenetic signal.

Usage

phyloSignalBS(
  p4d,
  multiphylo,
  methods = c("all", "I", "Cmean", "Lambda", "K", "K.star"),
  reps = 999,
  W = NULL,
  pb = TRUE
)

Arguments

p4d	a phylo4d object.
multiphylo	a multiphylo object containing bootstrapped trees of p4d.
methods	a character vector giving the methods to compute phylogenetic signal (see phyloSignal).
reps	an integer. The number of repetitions for the estimation of p.values with randomization.
W	an optional matrix of phylogenetic weights to compute Moran's I. By default the matrix is computed with the function proxTips with patristic distances.
pb	a logical. Should a progress bar be printed? (default TRUE).

Details

Time consumption can be important if there are many bootraped trees and tested traits.

Value

The data generated are returned invisibly as a list.

fkeck/phylosignal documentation built on June 12, 2025, 3:13 p.m.