ape: compar.cheverud – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

compar.cheverud

Cheverud's Comparative Method

Description

This function computes the phylogenetic variance component and the residual deviation for continous characters, taking into account the phylogenetic relationships among species, following the comparative method described in Cheverud et al. (1985). The correction proposed by Rholf (2001) is used.

Usage

compar.cheverud(y, W, tolerance = 1e-06, gold.tol = 1e-04)

Arguments

`y`	A vector containing the data to analyse.
`W`	The phylogenetic connectivity matrix. All diagonal elements will be ignored.
`tolerance`	Minimum difference allowed to consider eigenvalues as distinct.
`gold.tol`	Precision to use in golden section search alogrithm.

Details

Model:

y = rho.W.y + e

where e is the error term, assumed to be normally distributed. rho is estimated by the maximum likelihood procedure given in Rohlf (2001), using a golden section search algorithm. The code of this function is indeed adapted from a MatLab code given in appendix in Rohlf's article, to correct a mistake in Cheverud's original paper.

Value

A list with the following components:

`rhohat`	The maximum likelihood estimate of rho
`Wnorm`	The normalized version of `W`
`residuals`	Error terms (e)

Author(s)

Julien Dutheil dutheil@evolbio.mpg.de

References

Cheverud, J. M., Dow, M. M. and Leutenegger, W. (1985) The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates. Evolution, 39, 1335–1351.

Rohlf, F. J. (2001) Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution, 55, 2143–2160.

Harvey, P. H. and Pagel, M. D. (1991) The Comparative Method in Evolutionary Biology. Oxford University Press.

Examples

### Example from Harvey and Pagel's book:
y<-c(10,8,3,4)
W <- matrix(c(1,1/6,1/6,1/6,1/6,1,1/2,1/2,1/6,1/2,1,1,1/6,1/2,1,1), 4)
compar.cheverud(y,W)
### Example from Rohlf's 2001 article:
W<- matrix(c(
  0,1,1,2,0,0,0,0,
  1,0,1,2,0,0,0,0,
  1,1,0,2,0,0,0,0,
  2,2,2,0,0,0,0,0,
  0,0,0,0,0,1,1,2,
  0,0,0,0,1,0,1,2,
  0,0,0,0,1,1,0,2,
  0,0,0,0,2,2,2,0
),8)
W <- 1/W
W[W == Inf] <- 0
y<-c(-0.12,0.36,-0.1,0.04,-0.15,0.29,-0.11,-0.06)
compar.cheverud(y,W)

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