[Adephylo-commits] r72 - in pkg: R man

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

Author: jombart
Date: 2008-12-02 17:41:04 +0100 (Tue, 02 Dec 2008)
New Revision: 72

Modified:
   pkg/R/orthogram.R
   pkg/man/orthogram.Rd
Log:
Orthogram fix


Modified: pkg/R/orthogram.R
===================================================================
--- pkg/R/orthogram.R	2008-12-02 16:36:09 UTC (rev 71)
+++ pkg/R/orthogram.R	2008-12-02 16:41:04 UTC (rev 72)
@@ -3,7 +3,10 @@
                         cfont.main = 1.5, lwd = 2, nclass,
                         high.scores = 0,alter=c("greater", "less", "two-sided")){
 
+    ## some checks and preliminary assignements
     if(!require(ade4)) stop("The ade4 package is not installed.")
+
+    nbos <- length(x)
     if(is.numeric(x)&is.vector(x)){
         type <- "numeric"
         ##  } else if(is.factor(x)){

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2008-12-02 16:36:09 UTC (rev 71)
+++ pkg/man/orthogram.Rd	2008-12-02 16:41:04 UTC (rev 72)
@@ -73,7 +73,7 @@
 x <- phylo4d(tre, cbind.data.frame(afbw, neonatw)) # traits on the phylogeny
 
 ## orthogram for trait afbw
-prox <- proxTips(tre, method="Abouheif") # compute Abouheif's proximities
-orthogram(afbw, )
+myOrthoBasis <- orthobasis.phylo(tre, method="oriAbouheif") # compute Abouheif's proximities
+orthogram(afbw, myOrthoBasis)
 
 }