[Vegan-commits] r1500 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-02-20 12:26:09 +0100 (Sun, 20 Feb 2011)
New Revision: 1500

Modified:
   pkg/vegan/R/decorana.R
   pkg/vegan/inst/ChangeLog
Log:
computed zero decorana values are wrongly expanded to scores in rescaling and estimated eigenvalues based on those

Modified: pkg/vegan/R/decorana.R
===================================================================
--- pkg/vegan/R/decorana.R	2011-02-20 10:59:29 UTC (rev 1499)
+++ pkg/vegan/R/decorana.R	2011-02-20 11:26:09 UTC (rev 1500)
@@ -5,6 +5,7 @@
     Const1 <- 1e-10
     Const2 <- 5
     Const3 <- 1e-11
+    ZEROEIG <- 1e-7 # consider as zero eigenvalue
     veg <- as.matrix(veg)
     if (any(rowSums(veg) <= 0)) 
         stop("All row sums must be >0 in the community matrix: remove empty sites.")
@@ -147,6 +148,17 @@
         var.c <- diag(var.c$cov) * (1 - sum(var.c$wt^2))
         evals <- var.r/var.c
     }
+    ## Some decorana values may be zero, but they still get expanded
+    ## in rescaling and get estimates of shrinkage eigenvalues: zero
+    ## them.
+    zeroeigs <- evals.decorana < ZEROEIG
+    if (any(zeroeigs)) {
+        evals.decorana[zeroeigs] <- 0
+        evals[zeroeigs] <- 0
+        rproj[, zeroeigs] <- 0
+        cproj[, zeroeigs] <- 0
+        origin[zeroeigs] <- 0
+    }
     CA <- list(rproj = rproj, cproj = cproj, evals = evals, evals.decorana = evals.decorana, 
                origin = origin, v = v, fraction = v.fraction, adotj = adotj, 
                aidot = aidot, iweigh = iweigh, iresc = iresc, ira = ira, 

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-02-20 10:59:29 UTC (rev 1499)
+++ pkg/vegan/inst/ChangeLog	2011-02-20 11:26:09 UTC (rev 1500)
@@ -17,6 +17,15 @@
 
 	* prestonfit, as.preston: default now 'tiesplit = TRUE'.
 
+	* decorana: Cajo ter Braak notified about false expansion of
+	computed zero eigenvalues in rescaling to axis scors and in
+	estimating eigenvalues. They are now zeroed. Cajo's example was a
+	6x5 petrie matrix:
+	petrie <- matrix(0, 6, 5)
+	diag(petrie) <- 1
+	petrie[row(petrie) - 1 == col(petrie)] <- 1
+	decorana(petrie)
+
 	* FAQ updates: using 'select' in ordination text() and points(),
 	using 'xlim' to flip axes or zoom into ordination plot(), the
 	non-effects of 'strata' in adonis(). All these indeed are