[Mattice-commits] r121 - pkg/inst/doc

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

Author: andrew_hipp
Date: 2008-12-30 08:09:19 +0100 (Tue, 30 Dec 2008)
New Revision: 121

Modified:
   pkg/inst/doc/maticce.Rnw
Log:
adding analysis details to vignette

Modified: pkg/inst/doc/maticce.Rnw
===================================================================
--- pkg/inst/doc/maticce.Rnw	2008-12-30 06:45:38 UTC (rev 120)
+++ pkg/inst/doc/maticce.Rnw	2008-12-30 07:09:19 UTC (rev 121)
@@ -118,5 +118,23 @@
 \caption{Simulated character on \code{ovales.tree} at model-averaged theta values, with coloring according to \code{ou2}}
 \end{figure}
 
+What is the relative support for the brownian motion vs. OU-2 model? We find which model has a change only at node 2 by inspecting the regime matrix
 
+<<ha, fig = FALSE, echo = TRUE>>=
+ha.4.2[['regMatrix']][['overall']]
+@
+
+Then we can find the likelihood of these models on a given tree:
+
+<<haLnl, fig = FALSE, echo = TRUE>>=
+ha.4.2[['hansens']][[1]] 
+@
+
+or the information criterion weights:
+
+<<haWeights, fig=FALSE, echo=TRUE>>=
+summary(ha.4.2)[['modelsMatrix']][[1]]
+@
+
+
 \end{document}