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

Description Usage Arguments Details Value

View source: R/phyloSignalExtra.R

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

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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.


phylosignal documentation built on May 30, 2017, 12:50 a.m.

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