phylANOVA

Simulation based phylogenetic ANOVA following Garland et al. (1993), with post-hoc tests.

Simulation

Statistics

phylogenetics

comparative method

least squares

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, 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 trait data. 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 phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range 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=2.3-0" 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=2.3-0" 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