[Caic-commits] r94 - in pkg: . R man

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

Author: davidorme
Date: 2009-05-12 12:28:23 +0200 (Tue, 12 May 2009)
New Revision: 94

Modified:
   pkg/DESCRIPTION
   pkg/R/phylo.d.R
   pkg/man/phylo.d.Rd
Log:
Added method dispatch for phylo.d output, minor changes to man page for phylo.d

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-05-05 16:52:12 UTC (rev 93)
+++ pkg/DESCRIPTION	2009-05-12 10:28:23 UTC (rev 94)
@@ -1,7 +1,7 @@
 Package: CAIC
 Type: Package
 Title: Comparative Analyses using Independent Contrasts
-Version: 1.0.4-93
+Version: 1.0.4-94
 Date: 2008-10-01
 Author: David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz
 Maintainer: David Orme <d.orme at imperial.ac.uk>

Modified: pkg/R/phylo.d.R
===================================================================
--- pkg/R/phylo.d.R	2009-05-05 16:52:12 UTC (rev 93)
+++ pkg/R/phylo.d.R	2009-05-12 10:28:23 UTC (rev 94)
@@ -134,6 +134,8 @@
 	dvals$phyName <- phyName
 	dvals$dsName <- dsName
 	dvals$nPermut <- permut
+	
+	class(dvals) <- 'phylo.d'
 	return(dvals)
 	
 }

Modified: pkg/man/phylo.d.Rd
===================================================================
--- pkg/man/phylo.d.Rd	2009-05-05 16:52:12 UTC (rev 93)
+++ pkg/man/phylo.d.Rd	2009-05-12 10:28:23 UTC (rev 94)
@@ -58,14 +58,14 @@
 # plot the data
 par(mfrow=c(1,2))
 tipOrd <- match(shorebird.data$Species, shorebird.tree$tip.label)
-plot(shorebird.tree, show.tip.label=FALSE) 
+plot(shorebird.tree, show.tip.label=FALSE, main='Random') 
 tiplabels(tip=tipOrd, pch=21, bg=ifelse(shorebird.data$threat==0, 'white','black'))
-plot(shorebird.tree, show.tip.label=FALSE) 
+plot(shorebird.tree, show.tip.label=FALSE, main='Clustered') 
 tiplabels(tip=tipOrd, pch=21, bg=ifelse(shorebird.data$clustered==0, 'white','black'))
 
-# an example where D is not significantly different from a brownian threshold model of evolution (0)
+# an example where D is significantly different from a brownian threshold model of evolution (0)
 ex1 <- phylo.d(shorebird.data, shorebird.tree, threat, Species, permut=100)
-# an example where D is not significantly different from random (1)
+# an example where D is significantly different from random (1)
 ex2 <- phylo.d(shorebird.data, shorebird.tree, clustered, Species, permut=100)
 }