MPSEM-package {MPSEM}R Documentation

Modelling Phylogenetic Signals using Eigenvector Maps

Description

Computational tools to represent phylogenetic signals using adapted eigenvector maps.

Details

Phylogenetic eignevector maps (PEM) is a method for using phylogeny to model features of organism, most notably quantitative traits. It consists in calculating sets of explanatory variables (eigenvectors) that are meant to represent different patterns in trait values that are likely to have been inducted by evolution. These patterns are used to model the data, using a linear model for instance.

If one in interested in a ‘target’ species (i.e. a species for which the trait value is unknown), and provided that we know the phylogenetic relationships between that species and those of the model, the method allows us to obtain the scores of that new species on the phylogenetic eigenfunctions underlying a PEM. These scores are used to make empirical predictions of trait values for the target species on the basis of those observed for the species used in the model.

Functions PEM.build, PEM.updater, PEM.fitSimple, and PEM.forcedSimple allow one to build, update (i.e. recalculate with alternative weighting parameters) as well as to estimate or force arbitrary values for the weighting function parameters.

Functions getGraphLocations and Locations2PEMscores allow one to make predictions using method predict.PEM and a linear model. To obtain this linear model, one can use either function lm or auxiliary functions lmforwardsequentialsidak or lmforwardsequentialAICc, which perform forward-stepwise variable addition on the basis of either familiwise type I error rate or the Akaike Information Criterion (AIC), respectively.

The package provides low-level utility functions for performing operations on graphs (see graph-functions), calculate influence matrix (PEMInfluence), and simulate trait values (see trait-simulator).

A phylogenetic modelling tutorial using MPSEM is available as a package vignette. See example below.

The DESCRIPTION file:

Package: MPSEM
Type: Package
Encoding: UTF-8
Title: Modelling Phylogenetic Signals using Eigenvector Maps
Version: 0.4-4
Date: 2024-09-04
Authors@R: c( person( given = "Guillaume", family = "Guénard", role = c("aut","cre"), email = "guillaume.guenard@umontreal.ca", comment = c(ORCID = "0000-0003-0761-3072")), person( given = "Pierre", family = "Legendre", role = "ctb", email = "pierre.legendre@umontreal.ca", comment = c(ORCID = "0000-0002-3838-3305") ) )
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Depends: R (>= 3.0.0), ape
Suggests: knitr, caper, xfun
Imports: MASS
License: GPL-3
LazyLoad: yes
NeedsCompilation: yes
VignetteBuilder: knitr
Repository: CRAN
RoxygenNote: 7.3.1
Author: Guillaume Guénard [aut, cre] (<https://orcid.org/0000-0003-0761-3072>), Pierre Legendre [ctb] (<https://orcid.org/0000-0002-3838-3305>)
Maintainer: Guillaume Guénard <guillaume.guenard@umontreal.ca>

Index of help topics:

MPSEM-package           Modelling Phylogenetic Signals using
                        Eigenvector Maps
PEM-class               Class and Methods for Phylogenetic Eigenvector
                        Maps (PEM)
PEM-functions           Phylogenetic Eigenvector Maps
graph-class             Class and Method for Directed Graphs
graph-functions         MPSEM graph Manipulation Functions
lm-utils                Linear Modelling Utility Functions
trait-simulator         Simulate the Evolution of a Quantitative Trait

Author(s)

Guillaume Guénard [aut, cre] (<https://orcid.org/0000-0003-0761-3072>), Pierre Legendre [ctb] (<https://orcid.org/0000-0002-3838-3305>) Maintainer: Guillaume Guénard <guillaume.guenard@umontreal.ca>

References

Guénard, G., Legendre, P., and Peres-Neto, P. 2013. Phylogenetic eigenvector maps: a framework to model and predict species traits. Methods in Ecology and Evolution 4: 1120-1131

See Also

Makarenkov, V., Legendre, P. & Desdevise, Y. 2004. Modelling phylogenetic relationships using reticulated networks. Zoologica Scripta 33: 89-96

Blanchet, F. G., Legendre, P. & Borcard, D. 2008. Modelling directional spatial processes in ecological data. Ecological Modelling 215: 325-336

Examples

## To view MPSEM tutorial
vignette("MPSEM", package="MPSEM")


[Package MPSEM version 0.4-4 Index]