[Mattice-commits] r150 - in pkg: . man misc

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

Author: andrew_hipp
Date: 2009-01-14 04:36:27 +0100 (Wed, 14 Jan 2009)
New Revision: 150

Added:
   pkg/misc/NAMESPACE
Removed:
   pkg/NAMESPACE
Modified:
   pkg/man/carex.Rd
Log:
moved namespace to misc... any change it's causing the problem? shortened carex example

Deleted: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2009-01-13 22:12:18 UTC (rev 149)
+++ pkg/NAMESPACE	2009-01-14 03:36:27 UTC (rev 150)
@@ -1,6 +0,0 @@
-export(informationCriterion, informationCriterion.hansenBatch)
-export(ouSim, ouSim.hansenBatch, ouSim.hansenSummary, ouSim.browntree, ouSim.hansentree, ouSim.ouchtree, ouSim.phylo, plot.ouSim)
-export(regimeVectors, paintBranches)
-export(summary.hansenBatch, print.hansenSummary)
-export(isMonophyletic, nodeDescendents, mrcaOUCH)
-export(runBatchHansen)
\ No newline at end of file

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2009-01-13 22:12:18 UTC (rev 149)
+++ pkg/man/carex.Rd	2009-01-14 03:36:27 UTC (rev 150)
@@ -46,11 +46,11 @@
   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, maxNodes = 3) # for expedience, only allows regime changes at up to 3 nodes
+  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, ovales.tree)) # plots the character simulation, with branch colors changing at all 8 nodes
+  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>}

Added: pkg/misc/NAMESPACE
===================================================================
--- pkg/misc/NAMESPACE	                        (rev 0)
+++ pkg/misc/NAMESPACE	2009-01-14 03:36:27 UTC (rev 150)
@@ -0,0 +1,6 @@
+export(informationCriterion, informationCriterion.hansenBatch)
+export(ouSim, ouSim.hansenBatch, ouSim.hansenSummary, ouSim.browntree, ouSim.hansentree, ouSim.ouchtree, ouSim.phylo, plot.ouSim)
+export(regimeVectors, paintBranches)
+export(summary.hansenBatch, print.hansenSummary)
+export(isMonophyletic, nodeDescendents, mrcaOUCH)
+export(runBatchHansen)
\ No newline at end of file