[Mattice-commits] r108 - pkg/misc

[noreply at r-forge.r-project.org]

Author: andrew_hipp
Date: 2008-12-23 22:56:29 +0100 (Tue, 23 Dec 2008)
New Revision: 108

Modified:
   pkg/misc/maticce.Rnw
Log:
more on maticce vignette

Modified: pkg/misc/maticce.Rnw
===================================================================
--- pkg/misc/maticce.Rnw	2008-12-22 23:00:16 UTC (rev 107)
+++ pkg/misc/maticce.Rnw	2008-12-23 21:56:29 UTC (rev 108)
@@ -21,22 +21,19 @@
 
 This document also provides a worked example of analyzing a continuous character dataset that illustrates most of the \pkg{maticce} features. Working through this example will I expect address most questions that should come up during a typical analysis.
 
-XXXXXXXXXXXXXXXXXXX
-
 \section{Package Overview}
 
-The phylobase package currently implements the following functions and data structures:
+The \pkg{maticce} package currently implements functions in the following categories:
 
 \begin{itemize}
-  \item Data structures for storing a single tree and multiple trees: \code{phylo4} and \code{multiPhylo4}?
-  \item A data structure for storing a tree with associated tip and node data: \code{phylo4d}
-  \item A data structure for storing multiple trees with one set of tip data: \code{multiPhylo4d}
-  \item Functions for reading nexus files into the above data structures
-  \item Functions for converting between the above data structures and \code{ape phylo} objects as well as \code{ade4 phylog} objects
-  \item Functions for editing trees and data (i.e., subsetting and replacing)
-  \item Functions for plotting trees and trees with data
+  \item Traversing and manipulating \pkg{ouch}-style (S4 class \code{ouchtree}) trees
+  \item Painting regimes on a batch of \pkg{ouch}-style trees
+  \item Performing batch analyses in \pkg{ouch} over trees and over regimes
+  \item Summarizing analyses 
 \end{itemize}
 
+XXXXXXXXXXXXXXXXXXX
+
 \section{Using the S4 help system}
 
 The \code{S4} help system works similarly to the \code{S3} help system with some small differences relating to how \code{S4} methods are written.  The \code{plot()} function is a good example.  When we type \code{?plot} we are provided the help for the default plotting function which expects \code{x} and \code{y}.  \code{R} also provides a way to smartly dispatch the right type of plotting function.  In the case of an \code{ape phylo} object (a \code{S3} class object) \code{R} evaluates the class of the object and finds the correct functions, so the following works correctly.