[Mattice-commits] r191 - pkg/inst/doc

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

Author: andrew_hipp
Date: 2009-05-06 16:21:59 +0200 (Wed, 06 May 2009)
New Revision: 191

Modified:
   pkg/inst/doc/maticce.Rnw
Log:
updating vignette to incorporate Marcial's comments

Modified: pkg/inst/doc/maticce.Rnw
===================================================================
--- pkg/inst/doc/maticce.Rnw	2009-03-03 06:18:35 UTC (rev 190)
+++ pkg/inst/doc/maticce.Rnw	2009-05-06 14:21:59 UTC (rev 191)
@@ -10,7 +10,7 @@
 \newcommand{\code}{\texttt}
 \newcommand{\pkg}{\textsf}
 \title{Utilizing \pkg{maticce} to estimate transitions in continuous character evolution}
-\author{Andrew Hipp}
+\author{Andrew Hipp and Marcial Escudero}
 \date{\today}
 \begin{document}
 \maketitle
@@ -40,14 +40,13 @@
 In case you aren't familiar with \code{R}, the following commands will get you started.
 
 <<startAnalysis, fig=FALSE>>=
-library(maticce)
-library(ape)
-data(carex)
-attach(carex)
+library(maticce) # load maticce and required packages
+data(carex) # load dataset
+attach(carex) # 
 ovales.tree <- ape2ouch(ovales.tree) # make the tree an ouchtree object
 @
 
-Note that although the sample tree provided (\code{carex[['ovales.tree']]}) is ultrametric, this is not strictly required. 
+Note that although the sample tree provided (\code{carex[['ovales.tree']]}) is ultrametric, this is not strictly required. The tree itself is a partial phylogeny of sedges; for information about the tree, you can use \code{help(carex)} or \code{?carex} to call the help file for the dataset, which includes the reference. The data associated with this tree (\code{carex[['ovales.data']]}) are log-transformed mean chromosome data. Because the model underlying \pkg{maticce} is a generalized least squares regression model, standard assumptions about data normality apply and should be considered at the outset of any analysis.
 
 \section{Extracting information from trees}
 
@@ -75,7 +74,7 @@
   >   }
 \end{verbatim}
 
-These functions are all documented under \code{isMonophyletic}.
+These functions are all documented under \code{isMonophyletic}. Note that for many analyses that you might want to perform over a set of trees, you will need to determine for each tree whether each node of interest is present on the tree. There are alternative ways to do this (for example, a relatively new function in \pkg{ape} (\code{makeNodeLabel}) generates node labels by sorting and saving the descendents of each node to a file, then using \code{md5sum} to get a unique node label that uniquely identifies all the nodes in a tree with respect to its descendents. In \pkg{maticce}, node identity is checked automatically during batch analyses (see section \sQuote{Batch analyses} below by defining nodes based on their descendents, then checking for monophyly on each tree. For standard analyses in \pkg{maticce}, you do not have to worry about this yourself, but isn't it nice to think about?
 
 \section{Painting regimes}