[Mattice-commits] r189 - pkg/inst/doc

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

Author: andrew_hipp
Date: 2009-02-27 21:22:01 +0100 (Fri, 27 Feb 2009)
New Revision: 189

Modified:
   pkg/inst/doc/maticce.Rnw
Log:
minor formatting change

Modified: pkg/inst/doc/maticce.Rnw
===================================================================
--- pkg/inst/doc/maticce.Rnw	2009-02-27 19:02:27 UTC (rev 188)
+++ pkg/inst/doc/maticce.Rnw	2009-02-27 20:22:01 UTC (rev 189)
@@ -40,7 +40,7 @@
 In case you aren't familiar with \code{R}, the following commands will get you started.
 
 <<startAnalysis, fig=FALSE>>=
-library(maticce) # load the maticce package into memory; also loads the required ouch package
+library(maticce)
 library(ape)
 data(carex)
 attach(carex)
@@ -62,8 +62,8 @@
 These functions can be used interactively to identify nodes on the tree for analysis. Because the batch-analysis functions in \pkg{maticce} identify nodes based on taxa (see explanation in the section on 'Performing batch analyses'), nodes are provided as a list of vectors, each vector containing all taxa descendent from the node of interest. You can generate these lists manually by typing lists of names into vectors, or you could use the following if you want to explicitly designate all taxa for each node by selecting from a list:
 
 \begin{verbatim}
-  > nodes <- list(8) # assuming you want 8 nodes}
-  > for(i in 1:length(nodes)) nodes[[i]] <- select.list(otree at nodelabels, multiple = T)}
+  > nodes <- list(8) # assuming you want 8 nodes
+  > for(i in 1:length(nodes)) nodes[[i]] <- select.list(otree at nodelabels, multiple = T)
 \end{verbatim}
 
 Alternatively, if you want to designate the node more quickly by just selecting the most recent common ancestor of a set of taxa: