phyloSignalBS

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.

A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.

Francois Keck

phylosignal

Exploring the Phylogenetic Signal in Continuous Traits

phyloSignalBS function

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

Arguments

Computes phylogenetic signal for bootstrapped replicates of a phylogeny. — phyloSignalBS

<dl>

<dt>p4d</dt>
<dd>a <code>phylo4d</code> object.</dd>


<dt>multiphylo</dt>
<dd>a <code>multiphylo</code> object containing bootstrapped trees of <code>p4d</code>.</dd>


<dt>methods</dt>
<dd>a character vector giving the methods to compute phylogenetic signal (see <code>phyloSignal</code>).</dd>


<dt>reps</dt>
<dd>an integer. The number of repetitions for the estimation of p.values with randomization.</dd>


<dt>W</dt>
<dd>an optional matrix of phylogenetic weights to compute Moran's I. By default the matrix
is computed with the function <code>proxTips</code> with patristic distances.</dd>


<dt>pb</dt>
<dd>a logical. Should a progress bar be printed? (default <code>TRUE</code>).</dd>

</dl>

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

Description

Usage

Value

Arguments

Details