fix in drop.tip() and new option in pic()

[ape.git] / man / ace.Rd

diff --git a/man/ace.Rd b/man/ace.Rd
index 126a21604047e56ed508433fddae6c55633aa112..15bd38758e42de2c7ede2fb709125350ced28b62 100644 (file)
--- a/man/ace.Rd
+++ b/man/ace.Rd
@@ -6,6 +6,22 @@
 \alias{AIC.ace}
 \alias{anova.ace}
 \title{Ancestral Character Estimation}
+\description{
+  This function estimates ancestral character states, and the associated
+  uncertainty, for continuous and discrete characters.
+
+  \code{logLik}, \code{deviance}, and \code{AIC} are generic functions
+  used to extract the log-likelihood, the deviance, or the Akaike
+  information criterion of a fitted object. If no such values are
+  available, \code{NULL} is returned.
+
+  \code{anova} is another generic function which is used to compare
+  nested models: the significance of the additional parameter(s) is
+  tested with likelihood ratio tests. You must ensure that the models
+  are effectively nested (if they are not, the results will be
+  meaningless). It is better to list the models from the smallest to the
+  largest.
+}
 \usage{
 ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     model = if (type == "continuous") "BM" else "ER",
@@ -23,8 +39,8 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   \item{type}{the variable type; either \code{"continuous"} or
     \code{"discrete"} (or an abbreviation of these).}
   \item{method}{a character specifying the method used for
-    estimation. Three choices are possible: \code{"ML"}, \code{"pic"},
-    or \code{"GLS"}.}
+    estimation. Four choices are possible: \code{"ML"}, \code{"REML"},
+    \code{"pic"}, or \code{"GLS"}.}
   \item{CI}{a logical specifying whether to return the 95\% confidence
     intervals of the ancestral state estimates (for continuous
     characters) or the likelihood of the different states (for discrete
@@ -47,22 +63,6 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     information criterion.}
   \item{\dots}{further arguments passed to or from other methods.}
 }
-\description{
-  This function estimates ancestral character states, and the associated
-  uncertainty, for continuous and discrete characters.
-
-  \code{logLik}, \code{deviance}, and \code{AIC} are generic functions
-  used to extract the log-likelihood, the deviance (-2*logLik), or the
-  Akaike information criterion of a tree. If no such values are
-  available, \code{NULL} is returned.
-
-  \code{anova} is another generic function that is used to compare
-  nested models: the significance of the additional parameter(s) is
-  tested with likelihood ratio tests. You must ensure that the models
-  are effectively nested (if they are not, the results will be
-  meaningless). It is better to list the models from the smallest to the
-  largest.
-}
 \details{
   If \code{type = "continuous"}, the default model is Brownian motion
   where characters evolve randomly following a random walk. This model
@@ -74,14 +74,23 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   given through a correlation structure with the option
   \code{corStruct}.
 
-  In the default setting (i.e., \code{method = "ML"} and \code{model =
-  "BM"}) the maximum likelihood estimation is done simultaneously on
-  the ancestral values and the variance of the Brownian motion process;
+  In the default setting (\code{method = "ML"} and \code{model = "BM"})
+  the maximum likelihood estimation is done simultaneously on the
+  ancestral values and the variance of the Brownian motion process;
   these estimates are then used to compute the confidence intervals in
-  the standard way (see the package \pkg{geiger} for a different
-  implementation). If \code{method = "pic"} or \code{"GLS"}, the
-  confidence intervals are computed using the expected variances under
-  the model, so they depend only on the tree.
+  the standard way. The REML method first estimates the ancestral value
+  at the root (aka, the phylogenetic mean), then the variance of the
+  Brownian motion process is estimated by optimizing the residual
+  log-likelihood. The ancestral values are finally inferred from the
+  likelihood function giving these two parameters. If \code{method =
+  "pic"} or \code{"GLS"}, the confidence intervals are computed using
+  the expected variances under the model, so they depend only on the
+  tree.
+
+  It could be shown that, with a continous character, REML results in
+  unbiased estimates of the variance of the Brownian motion process
+  while ML gives a downward bias. Therefore the former is recommanded,
+  even though it is not the default.
 
   For discrete characters (\code{type = "discrete"}), only maximum
   likelihood estimation is available (Pagel 1994). The model is
@@ -101,7 +110,7 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   is determined from the data.
 }
 \value{
-  a list with the following elements:
+  an object of class \code{"ace"} with the following elements:
 
   \item{ace}{if \code{type = "continuous"}, the estimates of the
     ancestral character values.}
@@ -144,7 +153,7 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   Likelihood of ancestor states in adaptive radiation. \emph{Evolution},
   \bold{51}, 1699--1711.
 }
-\author{Emmanuel Paradis, Ben Bolker \email{bolker@zoo.ufl.edu}}
+\author{Emmanuel Paradis, Ben Bolker}
 \seealso{
   \code{\link{corBrownian}}, \code{\link{corGrafen}},
   \code{\link{corMartins}}, \code{\link{compar.ou}},