several fixes

[ape.git] / R / vcv.phylo.R

diff --git a/R/vcv.phylo.R b/R/vcv.phylo.R
index 09e4dc3248bb4b356cce6b585ac1c160e976c93e..2473280424f7545ba9ae08e8be20bf422c538958 100644 (file)
--- a/R/vcv.phylo.R
+++ b/R/vcv.phylo.R
@@ -1,16 +1,16 @@
-## vcv.phylo.R (2006-10-04)
+## vcv.phylo.R (2009-11-19)
 
 ##   Phylogenetic Variance-Covariance or Correlation Matrix
 
-## Copyright 2002-2006 Emmanuel Paradis
+## Copyright 2002-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-vcv.phylo <- function(phy, model = "Brownian", cor = FALSE)
+vcv <- function(phy, ...) UseMethod("vcv")
+
+vcv.phylo <- function(phy, model = "Brownian", corr = FALSE, ...)
 {
-    if (class(phy) != "phylo")
-      stop('object "phy" is not of class "phylo"')
     if (is.null(phy$edge.length))
       stop("the tree has no branch lengths")
 
@@ -37,6 +37,7 @@ vcv.phylo <- function(phy, model = "Brownian", cor = FALSE)
         }
     }
 
+    phy <- reorder(phy)
     n <- length(phy$tip.label)
     n.node <- phy$Nnode
     N <- n.node + n
@@ -44,7 +45,7 @@ vcv.phylo <- function(phy, model = "Brownian", cor = FALSE)
     foo(n + 1, 0, dim(phy$edge)[1])
 
     vcv <- vcv[1:n, 1:n]
-    if (cor) {
+    if (corr) {
         ## This is inspired from the code of `cov2cor' (2005-09-08):
         M <- vcv
         Is <- sqrt(1/M[1 + 0:(n - 1)*(n + 1)])
@@ -54,3 +55,12 @@ vcv.phylo <- function(phy, model = "Brownian", cor = FALSE)
     rownames(vcv) <- colnames(vcv) <- phy$tip.label
     vcv
 }
+
+vcv.corPhyl <- function(phy, corr = FALSE, ...)
+{
+    labels <- attr(phy, "tree")$tip.label
+    dummy.df <- data.frame(1:length(labels), row.names = labels)
+    res <- nlme::corMatrix(Initialize.corPhyl(phy, dummy.df), corr = corr)
+    dimnames(res) <- list(labels, labels)
+    res
+}