ape: pic.ortho – R documentation

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pic.ortho

Phylogenetically Independent Orthonormal Contrasts

Description

This function computes the orthonormal contrasts using the method described by Felsenstein (2008). Only a single trait can be analyzed; there can be several observations per species.

Usage

pic.ortho(x, phy, var.contrasts = FALSE, intra = FALSE)

Arguments

`x`	a numeric vector or a list of numeric vectors.
`phy`	an object of class `"phylo"`.
`var.contrasts`	logical, indicates whether the expected variances of the contrasts should be returned (default to `FALSE`).
`intra`	logical, whether to return the intraspecific contrasts.

Details

The data x can be in two forms: a vector if there is a single observation for each species, or a list whose elements are vectors containing the individual observations for each species. These vectors may be of different lengths.

If x has names, its values are matched to the tip labels of phy, otherwise its values are taken to be in the same order than the tip labels of phy.

Value

either a vector of contrasts, or a two-column matrix with the contrasts in the first column and their expected variances in the second column (if var.contrasts = TRUE). If the tree has node labels, these are used as labels of the returned object.

If intra = TRUE, the attribute "intra", a list of vectors with the intraspecific contrasts or NULL for the species with a one observation, is attached to the returned object.

Author(s)

Emmanuel Paradis

References

Felsenstein, J. (2008) Comparative methods with sampling error and within-species variation: Contrasts revisited and revised. American Naturalist, 171, 713–725.

Examples

tr <- rcoal(30)
### a single observation per species:
x <- rTraitCont(tr)
pic.ortho(x, tr)
pic.ortho(x, tr, TRUE)
### different number of observations per species:
x <- lapply(sample(1:5, 30, TRUE), rnorm)
pic.ortho(x, tr, intra = TRUE)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24