[Vegan-commits] r2501 - in pkg/vegan: R inst man src

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

Author: jarioksa
Date: 2013-05-05 19:36:48 +0200 (Sun, 05 May 2013)
New Revision: 2501

Modified:
   pkg/vegan/R/vegdist.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/vegdist.Rd
   pkg/vegan/src/vegdist.c
Log:
add Mahalanobis to vegdist

Modified: pkg/vegan/R/vegdist.R
===================================================================
--- pkg/vegan/R/vegdist.R	2013-05-05 17:07:39 UTC (rev 2500)
+++ pkg/vegan/R/vegdist.R	2013-05-05 17:36:48 UTC (rev 2501)
@@ -7,7 +7,8 @@
         method <- "euclidean"
     METHODS <- c("manhattan", "euclidean", "canberra", "bray", 
                  "kulczynski", "gower", "morisita", "horn", "mountford", 
-                 "jaccard", "raup", "binomial", "chao", "altGower", "cao")
+                 "jaccard", "raup", "binomial", "chao", "altGower", "cao",
+                 "mahalanobis")
     method <- pmatch(method, METHODS)
     inm <- METHODS[method]
     if (is.na(method)) 
@@ -25,6 +26,8 @@
                 dQuote(inm))
     if (method == 6) # gower, but no altGower
         x <- decostand(x, "range", 2, na.rm = TRUE, ...)
+    if (method == 16) # mahalanobis
+        x <- veganMahatrans(scale(x, scale = FALSE))
     if (binary) 
         x <- decostand(x, "pa")
     N <- nrow(x <- as.matrix(x))

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-05-05 17:07:39 UTC (rev 2500)
+++ pkg/vegan/inst/ChangeLog	2013-05-05 17:36:48 UTC (rev 2501)
@@ -22,6 +22,8 @@
 	variance (Euclidean) or range (Manhattan), and the scaling is
 	already inbuilt in Mahalanobis and Gower.
 
+	* vegdist: added Mahalanobis distance.
+
 Version 2.1-29 (closed April 19, 2013)
 
 	* ordisurf: significant changes were made to this function:

Modified: pkg/vegan/man/vegdist.Rd
===================================================================
--- pkg/vegan/man/vegdist.Rd	2013-05-05 17:07:39 UTC (rev 2500)
+++ pkg/vegan/man/vegdist.Rd	2013-05-05 17:36:48 UTC (rev 2501)
@@ -28,7 +28,7 @@
     \code{"euclidean"}, \code{"canberra"}, \code{"bray"}, \code{"kulczynski"},
      \code{"jaccard"}, \code{"gower"}, \code{"altGower"}, \code{"morisita"}, 
      \code{"horn"}, \code{"mountford"}, \code{"raup"} , \code{"binomial"}, 
-     \code{"chao"} or \code{"cao"}.}
+     \code{"chao"}, \code{"cao"} or \code{"mahalanobis"}.}
   \item{binary}{Perform presence/absence standardization before analysis
     using \code{\link{decostand}}.}
   \item{diag}{Compute diagonals. }
@@ -209,6 +209,13 @@
   Morisita index can be used with genuine count data (integers) only. Its
   Horn--Morisita variant is able to handle any abundance data.
 
+  Mahalanobis distances are Euclidean distances of a matrix where
+  columns are centred, have unit variance, and are uncorrelated.  The
+  index is not commonly used for community data, but it is sometimes
+  used for environmental variables. The calculation is based on
+  transforming data matrix and then using Euclidean distances
+  following Mardia et al. (1979).
+
   Euclidean and Manhattan dissimilarities are not good in gradient
   separation without proper standardization but are still included for
   comparison and special needs.
@@ -272,6 +279,9 @@
 
   Krebs, C. J. (1999). \emph{Ecological Methodology.} Addison Wesley Longman.
 
+  Mardia, K.V., Kent, J.T. and Bibby, J.M. (1979). \emph{Multivariate analysis}.
+  Academic Press.
+
   Mountford, M. D. (1962). An index of similarity and its application to
   classification problems. In: P.W.Murphy (ed.),
   \emph{Progress in Soil Zoology}, 43--50. Butterworths.

Modified: pkg/vegan/src/vegdist.c
===================================================================
--- pkg/vegan/src/vegdist.c	2013-05-05 17:07:39 UTC (rev 2500)
+++ pkg/vegan/src/vegdist.c	2013-05-05 17:36:48 UTC (rev 2501)
@@ -44,6 +44,7 @@
 #define CHAO 13
 #define GOWERDZ 14
 #define CAO 15
+#define MAHALANOBIS 16
 #define MATCHING 50
 #define NOSHARED 99
 
@@ -125,7 +126,9 @@
      return dist;
 }
 
-/* Euclidean distance: duplicates base R */
+/* Euclidean distance: duplicates base R. If Mahalanobis
+ * transformation was performred in the calling routine, this will
+ * give Mahalanobis distances. */
 
 double veg_euclidean(double *x, int nr, int nc, int i1, int i2)
 {
@@ -631,6 +634,7 @@
 	distfun = veg_manhattan;
 	break;
     case EUCLIDEAN:
+    case MAHALANOBIS:
 	distfun = veg_euclidean;
 	break;
     case CANBERRA: