some big fixes for ape 2.7-1

[ape.git] / man / ace.Rd

diff --git a/man/ace.Rd b/man/ace.Rd
index edcab533e32c4a87d6fde5f498318a666cf74787..f440027d34297bcf7857f78ab7b879883a06bf23 100644 (file)
--- a/man/ace.Rd
+++ b/man/ace.Rd
@@ -1,5 +1,6 @@
 \name{ace}
 \alias{ace}
+\alias{print.ace}
 \alias{logLik.ace}
 \alias{deviance.ace}
 \alias{AIC.ace}
@@ -9,13 +10,15 @@
 ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     model = if (type == "continuous") "BM" else "ER",
     scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1)
+\method{print}{ace}(x, digits = 4, ...)
 \method{logLik}{ace}(object, ...)
 \method{deviance}{ace}(object, ...)
 \method{AIC}{ace}(object, ..., k = 2)
 \method{anova}{ace}(object, ...)
 }
 \arguments{
-  \item{x}{a vector or a factor.}
+  \item{x}{a vector or a factor; an object of class \code{"ace"} in the
+    case of \code{print}.}
   \item{phy}{an object of class \code{"phylo"}.}
   \item{type}{the variable type; either \code{"continuous"} or
     \code{"discrete"} (or an abbreviation of these).}
@@ -37,11 +40,12 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     structure to be used (this also gives the assumed model).}
   \item{ip}{the initial value(s) used for the ML estimation procedure
     when \code{type == "discrete"} (possibly recycled).}
+  \item{digits}{the number of digits to be printed.}
   \item{object}{an object of class \code{"ace"}.}
   \item{k}{a numeric value giving the penalty per estimated parameter;
     the default is \code{k = 2} which is the classical Akaike
     information criterion.}
-  \item{...}{further arguments passed to or from other methods.}
+  \item{\dots}{further arguments passed to or from other methods.}
 }
 \description{
   This function estimates ancestral character states, and the associated
@@ -65,9 +69,9 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   can be fitted by maximum likelihood (the default, Schluter et
   al. 1997), least squares (\code{method = "pic"}, Felsenstein 1985), or
   generalized least squares (\code{method = "GLS"}, Martins and Hansen
-  1997). In the latter case, the specification of \code{phy} and
-  \code{model} are actually ignored: it is instead given through a
-  correlation structure with the option \code{corStruct}.
+  1997, Cunningham et al. 1998). In the latter case, the specification
+  of \code{phy} and \code{model} are actually ignored: it is instead
+  given through a correlation structure with the option \code{corStruct}.
 
   For discrete characters (\code{type = "discrete"}), only maximum
   likelihood estimation is available (Pagel 1994). The model is
@@ -108,6 +112,11 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   \item{call}{the function call.}
 }
 \references{
+  Cunningham, C. W., Omland, K. E. and Oakley, T. H. (1998)
+  Reconstructing ancestral character states: a critical
+  reappraisal. \emph{Trends in Ecology & Evolution}, \bold{13},
+  361--366.
+
   Felsenstein, J. (1985) Phylogenies and the comparative
   method. \emph{American Naturalist}, \bold{125}, 1--15.
 
@@ -125,8 +134,7 @@ 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 \email{Emmanuel.Paradis@mpl.ird.fr}, Ben Bolker
-\email{bolker@zoo.ufl.edu}}
+\author{Emmanuel Paradis, Ben Bolker \email{bolker@zoo.ufl.edu}}
 \seealso{
   \code{\link{corBrownian}}, \code{\link{corGrafen}},
   \code{\link{corMartins}}, \code{\link{compar.ou}},