\code{compar.gee} returns an object of class \code{"compar.gee"} with
the following components:
\item{call}{the function call, including the formula.}
- \code{effect.assign}{a vector of integers assigning the coefficients
+ \item{effect.assign}{a vector of integers assigning the coefficients
to the effects (used by \code{drop1}).}
\item{nobs}{the number of observations.}
\item{coefficients}{the estimated coefficients (or regression parameters).}
Classes of phylogenetic correlation structures (\code{"corPhyl"})
available in \pkg{ape}.
- \item{corBrownian}{Brownian motion model (Felsenstein 1985)}
- \item{corMartins}{The covariance matrix defined in Martins and Hansen
- (1997)}
- \item{corGrafen}{The covariance matrix defined in Grafen (1989)}
- \item{corPagel}{The covariance matrix defined in Freckelton et al. (2002)}
- \item{corBlomberg}{The covariance matrix defined in Blomberg et al. (2003)}
+ \itemize{
+ \item{corBrownian}{Brownian motion model (Felsenstein 1985)}
+ \item{corMartins}{The covariance matrix defined in Martins and Hansen
+ (1997)}
+ \item{corGrafen}{The covariance matrix defined in Grafen (1989)}
+ \item{corPagel}{The covariance matrix defined in Freckelton et al. (2002)}
+ \item{corBlomberg}{The covariance matrix defined in Blomberg et al. (2003)}
+ }
See the help page of each class for references and detailed
description.
brief description is given below; more details can be found in the
References.
+\itemize{
\item{``raw'', ``N''}{This is simply the proportion or the number of
sites that differ between each pair of sequences. This may be useful
to draw ``saturation plots''. The options \code{variance} and
\item{``paralin''}{Lake (1994) developed the paralinear distance which
can be viewed as another variant of the Barry--Hartigan distance.}
-}
+}}
\value{
an object of class \link[stats]{dist} (by default), or a numeric
matrix if \code{as.matrix = TRUE}. If \code{model = "BH87"}, a numeric
\code{plot.phylo} returns invisibly a list with the following
components which values are those used for the current plot:
- \item{type}
- \item{use.edge.length}
- \item{node.pos}
- \item{show.tip.label}
- \item{show.node.label}
- \item{font}
- \item{cex}
- \item{adj}
- \item{srt}
- \item{no.margin}
- \item{label.offset}
- \item{x.lim}
- \item{y.lim}
- \item{direction}
- \item{tip.color}
- \item{Ntip}
- \item{Nnode}
+ \item{type}{}
+ \item{use.edge.length}{}
+ \item{node.pos}{}
+ \item{show.tip.label}{}
+ \item{show.node.label}{}
+ \item{font}{}
+ \item{cex}{}
+ \item{adj}{}
+ \item{srt}{}
+ \item{no.margin}{}
+ \item{label.offset}{}
+ \item{x.lim}{}
+ \item{y.lim}{}
+ \item{direction}{}
+ \item{tip.color}{}
+ \item{Ntip}{}
+ \item{Nnode}{}
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
sequential formats, see below). The names of the sequences are read in
the file unless the `seq.names' option is used. Particularities for
each format are detailed below.
-
+
+\itemize{
\item{Interleaved:}{the function starts to read the sequences when it
finds 10 contiguous characters belonging to the ambiguity code of
the IUPAC (namely A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, and
leading spaces before this character). These lines are taken as taxa
names after removing the ``>'' and the possible leading and trailing
spaces. All the data in the file before the first sequence is ignored.}
-}
+}}
\value{
a matrix or a list (if \code{format = "fasta"}) of DNA sequences
stored in binary format, or of mode character (if \code{as.character =
returns invisibly for each subtree a list with the following
components:
- \item{tip.label}
- \item{node.label}
- \item{Ntip}
- \item{Nnode}
+ \item{tip.label}{}
+ \item{node.label}{}
+ \item{Ntip}{}
+ \item{Nnode}{}
}
\examples{
### Random tree with 12 leaves
With the interleaved and sequential formats, the sequences must be all
of the same length. The names of the sequences are not truncated.
- The argument `indent' specifies how the rows of nucleotides are
+ The argument \code{indent} specifies how the rows of nucleotides are
indented. In the interleaved and sequential formats, the rows with
the taxon names are never indented; the subsequent rows are indented
- with 10 spaces by default (i.e. if `indent = NULL)'. In the FASTA
+ with 10 spaces by default (i.e., if \code{indent = NULL}). In the FASTA
format, the rows are not indented by default. This default behaviour
- can be modified by specifying a value to `indent': the rows are then
- indented with `indent' (if it is a character) or `indent' spaces (if
- it is a numeric). For example, specifying `indent = " "' or `indent
- = 3' will have exactly the same effect (use `indent = "\t"' for a
- tabulation).
+ can be modified by specifying a value to \code{indent}: the rows are then
+ indented with ``indent'' (if it is a character) or `indent' spaces (if
+ it is a numeric). For example, specifying \code{indent = " "} or
+ \code{indent = 3} will have the same effect (use \code{indent = "\\t"}
+ for a tabulation).
The different options are intended to give flexibility in formatting
the sequences. For instance, if the sequences are very long it may be
The function needs three things:
+\itemize{
\item a phylogenetic tree which may contain multichotomies;
\item a formula which specifies the predictors of the model described
order than for the labels, then the values for the nodes sequentially
from the root to the most terminal nodes (i.e. in the order given by
\code{phy$edge}).
+}
- The user must obtain the values for the nodes separately.
+The user must obtain the values for the nodes separately.
Note that the method in its present implementation assumes that the
change in a species trait is more or less continuous between two nodes
projects / ape.git / commitdiff