MPSEM-package: Modelling Phylogenetic Signals using Eigenvector Maps

In MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps

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 (InflMat), and simulate trait values (see trait-simulator).

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

From version 0.6-1, no new features will be added to MPSEM. A new package is currently under development to replace MPSEM as a platform for future PEM development. We will continue to maintain MPSEM to provide backward compatibility for old scripts. The release of the new package under development will be announced here along with reference to any relevant research article.

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Author(s)

Guillaume Guénard [aut, cre] (ORCID: <https://orcid.org/0000-0003-0761-3072>), Pierre Legendre [ctb] (ORCID: <https://orcid.org/0000-0002-3838-3305>) Maintainer: Guillaume Guénard <[e-mail]>

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")

MPSEM documentation built on June 8, 2025, 1:56 p.m.