phylANOVA

This function performs the simulation-based phylogenetic ANOVA of Garland et al. (1993) and (optionally) conducts all posthoc comparisons of means among groups (also obtaining the P-values by phylogenetic simulation).

Simulation

Statistics

phylogenetics

comparative method

least squares

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

phylANOVA function

<dl>	<dt>tree</dt>
<dd>a phylogenetic tree in <code>"phylo"</code> format.</dd>	<dt>x</dt>
<dd>a vector containing the groups.</dd>	<dt>y</dt>
<dd>a vector containing the response variable (continuously valued).</dd>	<dt>nsim</dt>
<dd>an integer specifying the number of simulations (including the observed data).</dd>	<dt>posthoc</dt>
<dd>a logical value indicating whether or not to conduct posthoc tests to compare the mean among groups.</dd>	<dt>p.adj</dt>
<dd>method to adjust P-values for the posthoc tests to account for multiple testing. Options same as <code><a href="/link/p.adjust?package=phytools&version=1.2-0" data-mini-rdoc="phytools::p.adjust">p.adjust</a></code>.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.2-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Phylogenetic ANOVA and post-hoc tests — phylANOVA

<dl>

	<dt>tree</dt>
<dd>a phylogenetic tree in <code>"phylo"</code> format.</dd>

	<dt>x</dt>
<dd>a vector containing the groups.</dd>

	<dt>y</dt>
<dd>a vector containing the response variable (continuously valued).</dd>

	<dt>nsim</dt>
<dd>an integer specifying the number of simulations (including the observed data).</dd>

	<dt>posthoc</dt>
<dd>a logical value indicating whether or not to conduct posthoc tests to compare the mean among groups.</dd>

	<dt>p.adj</dt>
<dd>method to adjust P-values for the posthoc tests to account for multiple testing. Options same as <code><a href='https://rdrr.io/r/stats/p.adjust.html'>p.adjust</a></code>.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

phylANOVA: Phylogenetic ANOVA and post-hoc tests

Description

Usage

Value

Arguments

Author

Details

References

See Also