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

[ape.git] / man / pic.Rd

diff --git a/man/pic.Rd b/man/pic.Rd
index 0c9de0ba5ce040f424a512dc1f1625f664942eb5..80a421ec97da05fa432156e75e1958063076c4ac 100644 (file)
--- a/man/pic.Rd
+++ b/man/pic.Rd
@@ -2,15 +2,19 @@
 \alias{pic}
 \title{Phylogenetically Independent Contrasts}
 \usage{
-pic(x, phy, scaled = TRUE, var.contrasts = FALSE)
+pic(x, phy, scaled = TRUE, var.contrasts = FALSE,
+    rescaled.tree = FALSE)
 }
 \arguments{
   \item{x}{a numeric vector.}
   \item{phy}{an object of class \code{"phylo"}.}
   \item{scaled}{logical, indicates whether the contrasts should be
-    scaled with their expected variance (default to \code{TRUE}).}
+    scaled with their expected variances (default to \code{TRUE}).}
   \item{var.contrasts}{logical, indicates whether the expected
-    variance of the contrasts should be returned (default to \code{FALSE}).}
+    variances of the contrasts should be returned (default to
+    \code{FALSE}).}
+  \item{rescaled.tree}{logical, if \code{TRUE} the rescaled tree is
+    returned together with the main results.}
 }
 \description{
   Compute the phylogenetically independent contrasts using the method
@@ -22,16 +26,21 @@ pic(x, phy, scaled = TRUE, var.contrasts = FALSE)
   than the tip labels of \code{phy}.
 
   The user must be careful here since the function requires that both
-  series of names perfectly match, so this operation may fail if there
-  is a typing or syntax error. If both series of names do not match, the
-  values in the \code{x} are taken to be in the same order than the tip
-  labels of \code{phy}, and a warning message is issued.
+  series of names perfectly match. If both series of names do not match,
+  the values in the \code{x} are taken to be in the same order than the
+  tip labels of \code{phy}, and a warning message is issued.
 }
 \value{
   either a vector of phylogenetically independent contrasts (if
   \code{var.contrasts = FALSE}), or a two-column matrix with the
   phylogenetically independent contrasts in the first column and their
-  expected variance in the second column (if \code{var.contrasts = TRUE}).
+  expected variance in the second column (if \code{var.contrasts =
+  TRUE}). If the tree has node labels, these are used as labels of the
+  returned object.
+
+  If \code{rescaled.tree = TRUE}, a list is returned with two elements
+  named ``contr'' with the above results and ``rescaled.tree'' with the
+  tree and its rescaled branch lengths (see Felsenstein 1985).
 }
 \references{
   Felsenstein, J. (1985) Phylogenies and the comparative method.
@@ -39,7 +48,9 @@ pic(x, phy, scaled = TRUE, var.contrasts = FALSE)
 }
 \author{Emmanuel Paradis}
 \seealso{
-  \code{\link{read.tree}}, \code{\link{compar.gee}}, \code{\link{compar.lynch}}
+  \code{\link{read.tree}}, \code{\link{compar.gee}},
+  \code{\link{compar.lynch}}, \code{\link{pic.ortho}},
+  \code{\link{varCompPhylip}}
 }
 \examples{
 ### The example in Phylip 3.5c (originally from Lynch 1991)