[Vegan-commits] r303 - in pkg: R inst

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

Author: jarioksa
Date: 2008-04-06 19:33:12 +0200 (Sun, 06 Apr 2008)
New Revision: 303

Modified:
   pkg/R/print.summary.cca.R
   pkg/R/summary.cca.R
   pkg/inst/ChangeLog
Log:
I gave up and added more statististics on contributions to the total 'variance' in summary.cca (althouth I still think that this is stupid)

Modified: pkg/R/print.summary.cca.R
===================================================================
--- pkg/R/print.summary.cca.R	2008-04-06 14:46:33 UTC (rev 302)
+++ pkg/R/print.summary.cca.R	2008-04-06 17:33:12 UTC (rev 303)
@@ -22,9 +22,11 @@
         cat("after removing the contribution of conditiniong variables\n")
     }
     cat("\n")
-    out <- rbind(lambda = c(x$ev.con, x$ev.uncon), accounted = c(x$ev.con.account, 
-                                                   x$ev.uncon.account))
+    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$cca.acc, digits = digits, ...)
     cat("\nScaling", x$scaling, "for species and site scores\n")
     if (abs(x$scaling) == 2) {
         ev.ent <- "Species"
@@ -77,3 +79,4 @@
     cat("\n")
     invisible(x)
 }
+

Modified: pkg/R/summary.cca.R
===================================================================
--- pkg/R/summary.cca.R	2008-04-06 14:46:33 UTC (rev 302)
+++ pkg/R/summary.cca.R	2008-04-06 17:33:12 UTC (rev 303)
@@ -24,7 +24,9 @@
     if (!is.null(object$pCCA)) 
         ev.account <- ev.account - summ$partial.chi
     summ$ev.con.account <- cumsum(summ$ev.con)/ev.account
-    summ$ev.uncon.account <- cumsum(summ$ev.uncon)/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
     summ$ev.head <- c(summ$ev.con, summ$ev.uncon)[1:axes]
     summ$scaling <- scaling
     summ$digits <- digits

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-04-06 14:46:33 UTC (rev 302)
+++ pkg/inst/ChangeLog	2008-04-06 17:33:12 UTC (rev 303)
@@ -9,6 +9,10 @@
 	fitted vectors (in plot.envfit). Reversed axes 'xlim=c(1,-1)' work
 	now, and shifted origin 'at = c(1,1)' taken into account in
 	plot.envfit. 
+
+	* summary.cca: contributions of eigenvalues accumulated for
+	constrained and unconstrained axes, and separately (new) for
+	constrained axes. 
 	
 Version 1.12-8 (closed April 6, 2008)