Computes phylogenetic signal with different methods

Description

This function computes phylogenetic signal statistics (Blomberg's K and K*, Abouheif's Cmean, Moran's I, and Pagel's Lambda) for traits in phylo4d objects.

Usage

1
2
phyloSignal(p4d, methods = c("all", "I", "Cmean", "Lambda", "K", "K.star"),
  reps = 999, W = NULL)

Arguments

p4d

a phylo4d object.

methods

a character vector giving the methods to compute phylogenetic signal (see Details).

reps

an integer. The number of repetitions for the estimation of p.values with randomization.

W

an optional matrix of phylogenetic weights to compute Moran's I. By default the matrix is computed with the function proxTips with patristic distances.

Details

p4d must be a phylo4d object as defined in phylobase package. By default, the methods argument is set to "all" and all the available methods are used. The user can specify which method(s) to use. Possible methods are "I" (Gittleman & Kot 1990), "Cmean" (Abouheif 1999)", "Lambda" (Pagel 1999), "K" and "K.star" (Blomberg et al. 2003).

Value

A list of two dataframes with the values of statistics and associated p.values for each tested trait and method.

Author(s)

This function is a general wrapper for C++ subroutines. C++ code is adapted from R functions in Pavoine and Ricotta (2013) and Revell (2012).

References

Abouheif E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1, 895-909. Blomberg S.P., Garland Jr T. & Ives A.R. (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57, 717-745. Gittleman J.L. & Kot M. (1990) Adaptation: Statistics and a null model for estimating phylogenetic effects. Systematic Biology 39, 227-241. Pagel M. (1999) Inferring the historical patterns of biological evolution. Nature 401, 877-884. Revell L.J. (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3, 217-223. Pavoine S. & Ricotta C. (2013) Testing for Phylogenetic Signal in Biological Traits: The Ubiquity of Cross-Product Statistics. Evolution 67, 828-840.

See Also

phyloSimSignal .

Examples

1
2
3
4
5
6
require(ape)
require(phylobase)
data(navic)
tipData(navic)$rand <- rnorm(17)
tipData(navic)$BM <- rTraitCont(as(navic, "phylo"))
phyloSignal(navic)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.