[Vegan-commits] r658 - in branches/1.15: . R inst

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

Author: jarioksa
Date: 2009-01-14 15:08:14 +0100 (Wed, 14 Jan 2009)
New Revision: 658

Modified:
   branches/1.15/DESCRIPTION
   branches/1.15/R/print.summary.cca.R
   branches/1.15/R/summary.cca.R
   branches/1.15/inst/ChangeLog
Log:
merged r652, r657 to branches/1.15-2 (fix ouput of summary.cca for unconstrained models)

Modified: branches/1.15/DESCRIPTION
===================================================================
--- branches/1.15/DESCRIPTION	2009-01-14 13:58:49 UTC (rev 657)
+++ branches/1.15/DESCRIPTION	2009-01-14 14:08:14 UTC (rev 658)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.15-1
-Date: December 19, 2008
+Version: 1.15-2
+Date: January 14, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: branches/1.15/R/print.summary.cca.R
===================================================================
--- branches/1.15/R/print.summary.cca.R	2009-01-14 13:58:49 UTC (rev 657)
+++ branches/1.15/R/print.summary.cca.R	2009-01-14 14:08:14 UTC (rev 658)
@@ -25,8 +25,10 @@
     out <- rbind("Eig.value" = c(x$ev.con, x$ev.uncon),
                  "Accounted" = c(x$ev.con.account, x$ev.uncon.account))
     print(out, digits = digits, ...)
-    cat("\nAccumulated constrained eigenvalues\n")
-    print(x$cca.acc, digits = digits, ...)
+    if (!is.null(x$cca.acc)) {
+        cat("\nAccumulated constrained eigenvalues\n")
+        print(x$cca.acc, digits = digits, ...)
+    }
     cat("\nScaling", x$scaling, "for species and site scores\n")
     if (abs(x$scaling) == 2) {
         ev.ent <- "Species"

Modified: branches/1.15/R/summary.cca.R
===================================================================
--- branches/1.15/R/summary.cca.R	2009-01-14 13:58:49 UTC (rev 657)
+++ branches/1.15/R/summary.cca.R	2009-01-14 14:08:14 UTC (rev 658)
@@ -28,10 +28,12 @@
     ev.account <- summ$tot.chi
     if (!is.null(object$pCCA)) 
         ev.account <- ev.account - summ$partial.chi
-    summ$ev.con.account <- cumsum(summ$ev.con)/ev.account
+    if (!is.null(object$CCA))
+        summ$ev.con.account <- cumsum(summ$ev.con)/ev.account
     summ$ev.uncon.account <-
-        (summ$constr.chi + cumsum(summ$ev.uncon))/ev.account
-    summ$cca.acc <- cumsum(summ$ev.con)/summ$constr.chi
+        (max(summ$constr.chi, 0) + cumsum(summ$ev.uncon))/ev.account
+    if (!is.null(object$CCA))
+        summ$cca.acc <- cumsum(summ$ev.con)/summ$constr.chi
     summ$ev.head <- c(summ$ev.con, summ$ev.uncon)[1:axes]
     summ$scaling <- scaling
     summ$digits <- digits

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-01-14 13:58:49 UTC (rev 657)
+++ branches/1.15/inst/ChangeLog	2009-01-14 14:08:14 UTC (rev 658)
@@ -3,8 +3,13 @@
 
 VEGAN STABLE VERSIONS
 
-Version 1.15-1 (opened October 10, 2008)
+Version 1.15-2 (opened January 14, 2009)
 
+	* merged r652, r657: cleaner output of summary.cca in unconstrained
+	models (PCA, CA).
+	
+Version 1.15-1 (released December 19, 2008)
+
 	* merged r644: \$ escape fix in Rd files.
 	
 	* added warning on permatswap, since the "swap" algorithm used