[Vegan-commits] r429 - in branches/1.13: . R inst

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

Author: jarioksa
Date: 2008-06-16 11:24:18 +0200 (Mon, 16 Jun 2008)
New Revision: 429

Modified:
   branches/1.13/DESCRIPTION
   branches/1.13/R/print.summary.cca.R
   branches/1.13/R/scores.rda.R
   branches/1.13/inst/ChangeLog
   branches/1.13/inst/NEWS
Log:
merger r425 (rda scores scaling = 0 fix) and r427 (capscale summary fix) to branches/1.13-2

Modified: branches/1.13/DESCRIPTION
===================================================================
--- branches/1.13/DESCRIPTION	2008-06-16 09:16:31 UTC (rev 428)
+++ branches/1.13/DESCRIPTION	2008-06-16 09:24:18 UTC (rev 429)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.13-1
-Date: June 11, 2008
+Version: 1.13-2
+Date: June 16, 2008
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
   M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: branches/1.13/R/print.summary.cca.R
===================================================================
--- branches/1.13/R/print.summary.cca.R	2008-06-16 09:16:31 UTC (rev 428)
+++ branches/1.13/R/print.summary.cca.R	2008-06-16 09:24:18 UTC (rev 429)
@@ -8,9 +8,9 @@
     }
     cat("\nCall:\n")
     cat(deparse(x$call), "\n")
-    statnam <- if (x$method == "rda") 
-        "sums"
-    else "averages"
+    statnam <- if (x$method == "cca") 
+        "averages"
+    else "sums"
     cat("\nPartitioning of ", x$inertia, ":\n", sep = "")
     out <- c(Total = x$tot.chi, Conditioned = x$partial.chi, 
              Constrained = x$constr.chi, Unconstrained = x$unconst.chi)
@@ -52,7 +52,7 @@
     if (x$scaling < 0) {
         if (x$method == "cca") 
             cat("* Hill scaling performed on both scores\n")
-        if (x$method == "rda") 
+        else 
             cat("* Species scores divided by species standard deviations\n")
         cat("  so that they no longer are biplot scores\n")
     }
@@ -79,4 +79,3 @@
     cat("\n")
     invisible(x)
 }
-

Modified: branches/1.13/R/scores.rda.R
===================================================================
--- branches/1.13/R/scores.rda.R	2008-06-16 09:16:31 UTC (rev 428)
+++ branches/1.13/R/scores.rda.R	2008-06-16 09:24:18 UTC (rev 429)
@@ -33,24 +33,27 @@
                 v <- sweep(v, 1, x$colsum, "/")
                 v <- v * sqrt(x$tot.chi / (max(nrow(x$CA$u), nrow(x$CCA$u)) - 1 ))
             }
+            v <- const * v
         }
-        sol$species <- const * v
+        sol$species <- v
     }
     if ("sites" %in% take) {
         wa <- cbind(x$CCA$wa, x$CA$u)[, choices, drop=FALSE]
         if (scaling) {
             scal <- list(slam, 1, sqrt(slam))[[abs(scaling)]]
             wa <- sweep(wa, 2, scal, "*")
+            wa <- const * wa
         }
-        sol$sites <- const * wa
+        sol$sites <- wa
     }
     if ("constraints" %in% take) {
         u <- cbind(x$CCA$u, x$CA$u)[, choices, drop=FALSE]
         if (scaling) {
             scal <- list(slam, 1, sqrt(slam))[[abs(scaling)]]
             u <- sweep(u, 2, scal, "*")
+            u <- const * u
         }
-        sol$constraints <- const * u
+        sol$constraints <- u
     }
     if ("biplot" %in% take && !is.null(x$CCA$biplot)) {
         b <- matrix(0, nrow(x$CCA$biplot), length(choices))
@@ -70,8 +73,9 @@
             if (scaling) {
                 scal <- list(slam, 1, sqrt(slam))[[abs(scaling)]]
                 cn <- sweep(cn, 2, scal, "*")
+                cn <- const * cn
             }
-            sol$centroids <- const * cn
+            sol$centroids <- cn
         }
     }  
     if (length(sol) == 1) 

Modified: branches/1.13/inst/ChangeLog
===================================================================
--- branches/1.13/inst/ChangeLog	2008-06-16 09:16:31 UTC (rev 428)
+++ branches/1.13/inst/ChangeLog	2008-06-16 09:24:18 UTC (rev 429)
@@ -3,6 +3,13 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
+Version 1.13-2 (opened June 16, 2008)
+
+	* merged r425: scores.rda scaling=0 really returns unmodified
+	scores like documented.
+
+	* merged r427: summary for capscale result similar as for rda.
+
 Version 1.13-1 (released June 11, 2008)
 
 	* adonis: speed-up and doc updates.

Modified: branches/1.13/inst/NEWS
===================================================================
--- branches/1.13/inst/NEWS	2008-06-16 09:16:31 UTC (rev 428)
+++ branches/1.13/inst/NEWS	2008-06-16 09:24:18 UTC (rev 429)
@@ -3,6 +3,13 @@
 			VEGAN RELEASE VERSIONS 
 		       	======================
 
+		       CHANGES IN VEGAN 1.13-2
+
+    - summary of capscale identical to the summary of rda.
+
+    - scores of rda and capscale with scaling = 0 really return the
+      unmodified scores.	
+
 		       CHANGES IN VEGAN 1.13-1
 
 GENERAL