4 \alias{corMatrix.corPagel}
5 \title{Pagel's ``lambda'' Correlation Structure}
7 corPagel(value, phy, form = ~1, fixed = FALSE)
8 \method{corMatrix}{corPagel}(object, covariate = getCovariate(object),
10 \method{coef}{corPagel}(object, unconstrained = TRUE, \dots)
13 \item{value}{the (initial) value of the parameter
14 \eqn{\lambda}{lambda}.}
15 \item{phy}{an object of class \code{"phylo"}.}
16 \item{form}{(ignored).}
17 \item{fixed}{a logical specifying whether \code{gls} should
18 estimate \eqn{\lambda}{lambda} (the default) or keep it fixed.}
19 \item{object}{an (initialized) object of class \code{"corPagel"}.}
20 \item{covariate}{(ignored).}
21 \item{corr}{a logical value specifying whether to return the
22 correlation matrix (the default) or the variance-covariance matrix.}
23 \item{unconstrained}{a logical value. If \code{TRUE} (the default),
24 the coefficients are returned in unconstrained form (the same used
25 in the optimization algorithm). If \code{FALSE} the coefficients are
26 returned in ``natural'', possibly constrained, form.}
27 \item{\dots}{further arguments passed to or from other methods.}
30 The correlation structure from the present model is derived from the
31 Brownian motion model by multiplying the off-diagonal elements (i.e.,
32 the covariances) by \eqn{\lambda}{lambda}. The variances are thus the
33 same than for a Brownian motion model.
36 an object of class \code{"corPagel"}, the coefficients from an object
37 of this class, or the correlation matrix of an initialized object of
38 this class. In most situations, only \code{corPagel} will be called
41 \author{Emmanuel Paradis}
43 Freckleton, R. P., Harvey, P. H. and M. Pagel, M. (2002) Phylogenetic
44 analysis and comparative data: a test and review of evidence.
45 \emph{American Naturalist}, \bold{160}, 712--726.
47 Pagel, M. (1999) Inferring the historical patterns of biological
48 evolution. \emph{Nature}, \bold{401},877--884.