[Vegan-commits] r428 - in pkg: R inst

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

Author: jarioksa
Date: 2008-06-16 11:16:31 +0200 (Mon, 16 Jun 2008)
New Revision: 428

Modified:
   pkg/R/print.summary.cca.R
   pkg/R/scores.rda.R
   pkg/inst/ChangeLog
Log:
scores.rda returns scaling const as an attribute and summary prints it

Modified: pkg/R/print.summary.cca.R
===================================================================
--- pkg/R/print.summary.cca.R	2008-06-16 08:28:47 UTC (rev 427)
+++ pkg/R/print.summary.cca.R	2008-06-16 09:16:31 UTC (rev 428)
@@ -56,6 +56,10 @@
             cat("* Species scores divided by species standard deviations\n")
         cat("  so that they no longer are biplot scores\n")
     }
+    if (x$method != "cca") {
+        cat("* General scaling constant of scores: ",
+            attr(x, "const"), "\n")
+    }
     if (!is.null(x$species)) {
         cat("\n\nSpecies scores\n\n")
         hcat(x$species, head=head, tail=tail, digits = digits, ...)

Modified: pkg/R/scores.rda.R
===================================================================
--- pkg/R/scores.rda.R	2008-06-16 08:28:47 UTC (rev 427)
+++ pkg/R/scores.rda.R	2008-06-16 09:16:31 UTC (rev 428)
@@ -81,5 +81,6 @@
     }  
     if (length(sol) == 1) 
         sol <- sol[[1]]
+    attr(sol, "const") <- const
     return(sol)
 }

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-06-16 08:28:47 UTC (rev 427)
+++ pkg/inst/ChangeLog	2008-06-16 09:16:31 UTC (rev 428)
@@ -9,7 +9,15 @@
 	constant. Gains argument 'const' for user-settable general scaling
 	constant of the scores. The default 'const' is found internally to
 	giv a biplot scaling so that species and site scores together
-	approximate the original data.
+	approximate the original data. The value of 'const' is returned as
+	an attribute of 'scores'.
+
+	* summary.cca: prints the value of general scaling constant used
+	in 'rda' or 'capscale'.
+
+	* summary.cca: prints 'capscale' like 'rda' (used to have some
+	'cca' style output, like calling site scores "weighted averages"
+	instead of "weigthed sums").
 	
 Version 1.14-4 (closed June 12, 2008)