MPSEM-package: Modelling Phylogenetic Signals using Eigenvector Maps
| MPSEM-package | 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.
The package provides low-level utility functions for performing operations on
graphs (see graph-functions), calculate influence matrix
(InflMat), and so on.
A phylogenetic modelling tutorial using MPSEM is available as a
package vignette. See example below.
The DESCRIPTION file:
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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")
