[Adephylo-commits] r183 - in pkg: . R inst man

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

Author: jombart
Date: 2012-10-31 12:25:07 +0100 (Wed, 31 Oct 2012)
New Revision: 183

Removed:
   pkg/inst/doc/
Modified:
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/R/zzz.R
   pkg/man/adephylo.package.Rd
   pkg/man/dibas.Rd
Log:
removing vignette from inst

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-09-26 20:49:55 UTC (rev 182)
+++ pkg/DESCRIPTION	2012-10-31 11:25:07 UTC (rev 183)
@@ -1,6 +1,6 @@
 Package: adephylo
 Version: 1.1-3
-Date: 2012/01/20
+Date: 2012/10/30
 Title: adephylo: exploratory analyses for the phylogenetic comparative method.
 Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, Stephane Dray <stephane.dray at univ-lyon1.fr>
 Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2012-09-26 20:49:55 UTC (rev 182)
+++ pkg/NAMESPACE	2012-10-31 11:25:07 UTC (rev 183)
@@ -11,3 +11,7 @@
   ape,
   ade4
 )
+
+
+# Load DLL
+useDynLib(adephylo)

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2012-09-26 20:49:55 UTC (rev 182)
+++ pkg/R/zzz.R	2012-10-31 11:25:07 UTC (rev 183)
@@ -1,3 +1,3 @@
-.First.lib <- function (lib, pkg){
-  library.dynam("adephylo", pkg, lib)
-}
+## .First.lib <- function (lib, pkg){
+##   library.dynam("adephylo", pkg, lib)
+## }

Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd	2012-09-26 20:49:55 UTC (rev 182)
+++ pkg/man/adephylo.package.Rd	2012-10-31 11:25:07 UTC (rev 183)
@@ -130,8 +130,8 @@
   \tabular{ll}{
     Package: \tab adephylo\cr
     Type: \tab Package\cr
-    Version: \tab 1.1-1\cr
-    Date: \tab 2011-01-17 \cr
+    Version: \tab 1.1-3\cr
+    Date: \tab 2012-10-30 \cr
     License: \tab GPL (>=2)
   }  
 }

Modified: pkg/man/dibas.Rd
===================================================================
--- pkg/man/dibas.Rd	2012-09-26 20:49:55 UTC (rev 182)
+++ pkg/man/dibas.Rd	2012-10-31 11:25:07 UTC (rev 183)
@@ -14,7 +14,7 @@
 \method{dibas}{phylo}(x, grp, method = c("default", "leaveOneOut"),
       metric = c("nNodes", "patristic", "Abouheif", "sumDD"), \ldots)
 
-\method{dibas}{matrix}(x, grp, method = c("default", "leaveOneOut"), ldots)
+\method{dibas}{matrix}(x, grp, method = c("default", "leaveOneOut"), \ldots)
 
 \method{dibas}{dist}(x, grp, method = c("default", "leaveOneOut"), \ldots)
 
@@ -76,14 +76,16 @@
 ## make a tree
 tre <- nj(dist(dat$dat))
 plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],main="simulated data - tree")
+mtext(side=3, text="hand-fan syndrome")
 
 ## use dibas method
-res <- dibas(tre, dat$grp, metric="nNodes")
-res$grp.tab # results OK
-
 res.patri <- dibas(tre, dat$grp, metric="patristic")
 res.patri$grp.tab # poor results
+plot(table(res.patri$groups), main="Group assignment - dibas patristic")
 
+res <- dibas(tre, dat$grp, metric="nNodes")
+res$grp.tab # results OK
+plot(table(res$groups), main="Group assignment - dibas nNodes")
 
 
 
@@ -91,7 +93,7 @@
 #### MORE COMPLEX DATASET ####
 if(require(adegenet)){
 
-dat <- simDatGroups(k=5, p=50, n=c(5,10,10,30,60), mu=1:5, sigma=sample(1:5)/2)
+dat <- simDatGroups(k=5, p=50, n=c(5,10,10,30,60), mu=sample(1:5, 5, replace=TRUE), sigma=sample(1:5)/2)
 names(dat)
 
 ## make a tree
@@ -102,6 +104,9 @@
 res <- dibas(tre, dat$grp, metric="Abouheif")
 res
 
+plot(table(res$groups), main="Group assignment - dibas Abouheif")
+
+
 }
 
 }