[Mattice-commits] r152 - pkg/man

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

Author: andrew_hipp
Date: 2009-01-14 05:46:34 +0100 (Wed, 14 Jan 2009)
New Revision: 152

Modified:
   pkg/man/carex.Rd
Log:
example back in carex.Rd; namespace moved to misc

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2009-01-14 04:10:22 UTC (rev 151)
+++ pkg/man/carex.Rd	2009-01-14 04:46:34 UTC (rev 152)
@@ -42,16 +42,16 @@
 }
 
 \examples{
-  #library(maticce)
-  #data(carex)
-  #attach(carex)
-  #ovales.tree <- ape2ouch(ovales.tree) # tree comes in in phylo format, but we need an ouchtree object
-  #trial <- runBatchHansen(ovales.tree, ovales.data, ovales.nodes[1:3], maxNodes = 2) # for expedience, only tests for changes at up to 2 of the first 4 nodes
-  #summary(trial) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
-  #trialSim <- ouSim(trial, ovales.tree) # simulates the evolution of the chromosome number under the model-averaged values
-  #plot(trialSim) # plots the character simulation, with all branches black
-  #plot(trialSim, colors = paintBranches(ovales.nodes[1:4], ovales.tree)) # plots the character simulation, with branch colors changing at all 8 nodes
-  #plot(trialSim, colors = paintBranches(list(ovales.nodes[[2]]), ovales.tree)) # plots the character simulation, with branch colors changing only at node 2
+  library(maticce)
+  data(carex)
+  attach(carex)
+  ovales.tree <- ape2ouch(ovales.tree) # tree comes in in phylo format, but we need an ouchtree object
+  trial <- runBatchHansen(ovales.tree, ovales.data, ovales.nodes[1:3], maxNodes = 2) # for expedience, only tests for changes at up to 2 of the first 4 nodes
+  summary(trial) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
+  trialSim <- ouSim(trial, ovales.tree) # simulates the evolution of the chromosome number under the model-averaged values
+  plot(trialSim) # plots the character simulation, with all branches black
+  plot(trialSim, colors = paintBranches(ovales.nodes[1:4], ovales.tree)) # plots the character simulation, with branch colors changing at all 8 nodes
+  plot(trialSim, colors = paintBranches(list(ovales.nodes[[2]]), ovales.tree)) # plots the character simulation, with branch colors changing only at node 2
 }
 \author{Andrew L. Hipp <ahipp at mortonarb.org>}
 \keyword{datasets}                                            
\ No newline at end of file