[Vegan-commits] r1451 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-01-10 17:00:38 +0100 (Mon, 10 Jan 2011)
New Revision: 1451

Modified:
   pkg/vegan/R/predict.rda.R
   pkg/vegan/inst/ChangeLog
Log:
predicty type = 'working' for capscale returns now scaled scores like was documented

Modified: pkg/vegan/R/predict.rda.R
===================================================================
--- pkg/vegan/R/predict.rda.R	2011-01-10 15:34:11 UTC (rev 1450)
+++ pkg/vegan/R/predict.rda.R	2011-01-10 16:00:38 UTC (rev 1451)
@@ -31,9 +31,12 @@
         }
         if (inherits(object, "capscale")) {
             if (take > 0) {
-                out <- dist(u %*% slam/sqrt(nr))
-                if (!is.null(object$ac))
-                    out <- out - object$ac
+                out <- u %*% slam/sqrt(nr)
+                if (type == "response") {
+                    out <- dist(out)
+                    if (!is.null(object$ac))
+                        out <- out - object$ac
+                }
             }
         } else {
             if (take > 0) 

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-01-10 15:34:11 UTC (rev 1450)
+++ pkg/vegan/inst/ChangeLog	2011-01-10 16:00:38 UTC (rev 1451)
@@ -10,6 +10,10 @@
 	subtracted from the estimated distances when 'add = TRUE' was used
 	in capscale().
 
+	* predict.rda: type = "working" for capscale returns now scaled
+	scores that produce the dissimilarities as Euclidean distances --
+	like was claimed in the help page.
+
 Version 1.18-20 (closed January 9, 2011)
 
 	* base of vegan release 1.17-6 (released on Jan 10, 2011).