final corrections for ape 3.0-6

[ape.git] / man / ace.Rd

diff --git a/man/ace.Rd b/man/ace.Rd
index 1fc5d0147f791682af8aca4605888caeee006db0..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}
 \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",
 \usage{
 ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     model = if (type == "continuous") "BM" else "ER",


@@ -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.}
 }
     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
 \details{
   If \code{type = "continuous"}, the default model is Brownian motion
   where characters evolve randomly following a random walk. This model


@@ -74,8 +74,8 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   given through a correlation structure with the option
   \code{corStruct}.
 
   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
+  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. The REML method first estimates the ancestral value
   ancestral values and the variance of the Brownian motion process;
   these estimates are then used to compute the confidence intervals in
   the standard way. The REML method first estimates the ancestral value


@@ -89,8 +89,8 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
 
   It could be shown that, with a continous character, REML results in
   unbiased estimates of the variance of the Brownian motion process
 
   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
-  over the latter, even though it is not the default.
+  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
 
   For discrete characters (\code{type = "discrete"}), only maximum
   likelihood estimation is available (Pagel 1994). The model is


@@ -110,7 +110,7 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   is determined from the data.
 }
 \value{
   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.}
 
   \item{ace}{if \code{type = "continuous"}, the estimates of the
     ancestral character values.}


@@ -153,7 +153,7 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   Likelihood of ancestor states in adaptive radiation. \emph{Evolution},
   \bold{51}, 1699--1711.
 }
   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}},
 \seealso{
   \code{\link{corBrownian}}, \code{\link{corGrafen}},
   \code{\link{corMartins}}, \code{\link{compar.ou}},