PEM-functions: Phylogenetic Eigenvector Maps

In guenardg/MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps

Phylogenetic Eigenvector Maps

Description

Functions to calculate and manipulate Phylogenetic Eigenvector Maps (PEM), which are sets of eigenfunctions describing the structure of a phylogenetic graph. Each computation function is briefly described in section Functions below.

Usage

PEMweights(d, a = 0, psi = 1)

Arguments

d	A numeric vector of the evolutionary distances (PEMweights) or a character string specifying the row name of the edge table (located in the graph-class object's attribute edge) where the evolutionary distances (edge lengths) can be found.
a	The steepness parameter describing whether changes occur, on average: progressively long edges (a close to 0) or abruptly at vertices (a close to 1; default: 0).
psi	Relative evolution rate along the edges. This parameter only becomes relevant when multiple values are assigned to different portions of the phylogeny (default: 1).

Value

The returned value depends on the function:

PEMweights

A set of numeric value to be used as weights during PEM calculation.

Functions

• PEMweights(): PEM Weighting

  A power function to obtain the edge weights used during PEM calculation.

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 <[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

Makarenkov, V., Legendre, L. & 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

See Also

PEM-class

guenardg/MPSEM documentation built on April 14, 2025, 3:53 p.m.