[Mattice-commits] r235 - pkg/man

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

Author: andrew_hipp
Date: 2009-09-14 16:56:42 +0200 (Mon, 14 Sep 2009)
New Revision: 235

Modified:
   pkg/man/carex.Rd
Log:
fixing error in example: used wrong tree for drawing branch colors on simulation in last version

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2009-09-10 05:28:44 UTC (rev 234)
+++ pkg/man/carex.Rd	2009-09-14 14:56:42 UTC (rev 235)
@@ -50,21 +50,22 @@
   data(carex)
   # tree comes in in phylo format, but we need an ouchtree object
   trees <- lapply(carex$ovales.bayesTrees[1:10], ape2ouch) 
+  contree <- ape2ouch(carex$ovales.tree)
   # for expedience, only tests for changes at up to 2 of the first 4 nodes on 10 trees visited in the MCMC phylogenetic analysis
   trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2) 
   summary(trialBayesTrees) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
   # same analysis as above, but on a single tree
-  trialBayesConsensus <- runBatchHansen(ape2ouch(carex$ovales.tree), carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2)
+  trialBayesConsensus <- runBatchHansen(contree, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2)
   # compares five different models of character change at node 2
   multiModel(carex$ovales.tree, carex$ovales.data, carex$ovales.nodes[[2]])
   # simulates the evolution of the chromosome number under the model-averaged values
-  trialSim <- ouSim(trialBayesConsensus, ape2ouch(carex$ovales.tree)) 
+  trialSim <- ouSim(trialBayesConsensus, contree) 
   # plots the character simulation, with all branches black
   plot(trialSim) 
   # plots the character simulation, with branch colors changing at all 8 nodes
-  plot(trialSim, colors = paintBranches(carex$ovales.nodes[1:4], trees[[1]])) 
+  plot(trialSim, colors = paintBranches(carex$ovales.nodes[1:4], contree)) 
   # plots the character simulation, with branch colors changing only at node 2
-  plot(trialSim, colors = paintBranches(list(carex$ovales.nodes[[2]]), trees[[1]])) 
+  plot(trialSim, colors = paintBranches(list(carex$ovales.nodes[[2]]), contree)) 
 }
 \author{Andrew L. Hipp <ahipp at mortonarb.org>}
 \keyword{datasets}                                            
\ No newline at end of file