From d3189eafb03e92695ca9c8510b83c04516142475 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Thu, 8 May 2008 05:18:09 +0000
Subject: [PATCH] doc for corBlomberg

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@31 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 man/corBlomberg.Rd | 47 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 man/corBlomberg.Rd

diff --git a/man/corBlomberg.Rd b/man/corBlomberg.Rd
new file mode 100644
index 0000000..ae60db4
--- /dev/null
+++ b/man/corBlomberg.Rd
@@ -0,0 +1,47 @@
+\name{corBlomberg}
+\alias{corBlomberg}
+\alias{coef.corBlomberg}
+\alias{corMatrix.corBlomberg}
+\title{Blomberg et al.'s Correlation Structure}
+\usage{
+corBlomberg(value, phy, form = ~1, fixed = FALSE)
+\method{corMatrix}{corBlomberg}(object, covariate = getCovariate(object),
+                   corr = TRUE, ...)
+\method{coef}{corBlomberg}(object, unconstrained = TRUE, \dots)
+}
+\arguments{
+  \item{value}{the (initial) value of the parameter \eqn{g}{g}.}
+  \item{phy}{an object of class \code{"phylo"}.}
+  \item{form}{(ignored).}
+  \item{fixed}{a logical specifying whether \code{gls} should
+    estimate \eqn{\gamma}{gamma} (the default) or keep it fixed.}
+  \item{object}{an (initialized) object of class \code{"corBlomberg"}.}
+  \item{covariate}{(ignored).}
+  \item{corr}{a logical value specifying whether to return the
+    correlation matrix (the default) or the variance-covariance matrix.}
+  \item{unconstrained}{a logical value. If \code{TRUE} (the default),
+    the coefficients are returned in unconstrained form (the same used
+    in the optimization algorithm). If \code{FALSE} the coefficients are
+    returned in ``natural'', possibly constrained, form.}
+  \item{\dots}{further arguments passed to or from other methods.}
+}
+\description{
+  The ``ACDC'' (accelerated/decelerated) model assumes that continuous
+  traits evolve under a Brownian motion model which rates accelerates
+  (if \eqn{g}{g} < 1) or decelerates (if \eqn{g}{g} > 1) through
+  time. If \eqn{g}{g} = 1, then the model reduces to a Brownian motion
+  model.
+}
+\value{
+  an object of class \code{"corBlomberg"}, the coefficients from an
+  object of this class, or the correlation matrix of an initialized
+  object of this class. In most situations, only \code{corBlomberg} will
+  be called by the user.
+}
+\author{Emmanuel Paradis}
+\references{
+  Blomberg, S. P., Garland, Jr, T., and Ives, A. R. (2003) Testing for
+  phylogenetic signal in comparative data: behavioral traits are more
+  labile. \emph{Evolution}, \bold{57}, 717--745.
+}
+\keyword{models}
-- 
2.39.2