pic.ortho: Phylogenetically Independent Orthonormal Contrasts
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

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

`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.

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.

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.

Emmanuel Paradis

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

pic, varCompPhylip

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)