change dpcoa distance

Change dpcoa distance to square root of patristic distance, which should always be Euclidean. This means we will have to perform the Euclidean correction less often (only if there are numerical problems).

R/ordination-methods.R

@@ -247,12 +247,13 @@ ordinate = function(physeq, method="DCA", distance="bray", formula=NULL, ...){
 #' to perform a
 #' Double Principle Coordinate Analysis (DPCoA), relying heavily on 
 #' the underlying (and more general) function, \code{\link[ade4]{dpcoa}}.
-#' The distance object ultimately provided as the cophenetic/patristic
-#' (\code{\link[ape]{cophenetic.phylo}}) distance between the species. 
-#' 
-#' In most real-life, real-data applications, the phylogenetic tree 
-#' will not provide a Euclidean distance matrix, and so a correction
-#' will be performed, if needed. See \code{correction} argument. 
+#' The distance object ultimately provided is the square root of the 
+#' cophenetic/patristic (\code{\link[ape]{cophenetic.phylo}}) distance 
+#' between the species, which is always Euclidean. 
+#'  
+#' Although this distance is Euclidean, for numerical reasons it 
+#' will sometimes look non-Euclidean, and a correction will be performed. 
+#' See \code{correction} argument. 
 #'
 #' @param physeq (Required). A \code{\link{phyloseq-class}} object
 #'  containing, at a minimum, abundance (\code{\link{otu_table-class}}) and 
@@ -265,14 +266,14 @@ ordinate = function(physeq, method="DCA", distance="bray", formula=NULL, ...){
 #'  and return a new \code{dist}ance object that is Euclidean.
 #'  If testing a distance object, try \code{\link[ade4]{is.euclid}}.
 #' 
-#'  In most real-life, real-data applications, the phylogenetic tree 
-#'  will not provide a Euclidean distance matrix, and so a correction
-#'  will be needed. 
-#'  Two recommended correction methods are
+#'  
+#'  Although the distance matrix should always be Euclidean, for numerical 
+#' reasons it will sometimes appear non-Euclidean and a correction method must 
+#' be applied. Two recommended correction methods are
 #'  \code{\link[ade4]{cailliez}} and \code{\link[ade4]{lingoes}}.
 #'  The default is \code{cailliez},
-#'  but not for any particularly special reason. If the patristic 
-#'  distance matrix turns out to be Euclidian, no correction will be 
+#'  but not for any particularly special reason. If the
+#'  distance matrix is Euclidian, no correction will be 
 #'  performed, regardless of the value of the \code{correction} argument.
 #'
 #' @param scannf (Optional). Logical. Default is \code{FALSE}. This
@@ -335,7 +336,7 @@ DPCoA <- function(physeq, correction=cailliez, scannf=FALSE, ...){
 	if(taxa_are_rows(OTU) ){ OTU <- t(OTU) }
 
 	# get the patristic distances between the species from the tree 
-	patristicDist <- as.dist(cophenetic.phylo(tree))
+	patristicDist <- sqrt(as.dist(cophenetic.phylo(tree)))
 
 	# if the patristic distances are not Euclidean, 
 	# then correct them or throw meaningful error.
@@ -638,4 +639,4 @@ function(physeq, formula, distance, ...){
     return(capscale.phyloseq(physeq, formula, distance, ...))
   }
 })
-################################################################################
+################################################################################