[Vegan-commits] r1378 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-11-21 18:45:48 +0100 (Sun, 21 Nov 2010)
New Revision: 1378

Modified:
   pkg/vegan/R/as.mlm.cca.R
   pkg/vegan/R/as.mlm.rda.R
   pkg/vegan/R/intersetcor.R
   pkg/vegan/inst/ChangeLog
Log:
circumvent bug with wrong column names in qr.X with pivoted qr

Modified: pkg/vegan/R/as.mlm.cca.R
===================================================================
--- pkg/vegan/R/as.mlm.cca.R	2010-11-18 07:51:23 UTC (rev 1377)
+++ pkg/vegan/R/as.mlm.cca.R	2010-11-21 17:45:48 UTC (rev 1378)
@@ -5,7 +5,10 @@
     wa <- x$CCA$wa
     wa <- sweep(wa, 1, sqrt(w), "*")
     X <- qr.X(x$CCA$QR)
-    colnames(X) <- colnames(X)[x$CCA$QR$pivot]
+    ## qr.X gives wrong column names now, and they are fixed here
+    ## (hopefully fixed in 2.12.1, but that's only a wish).
+    if (getRversion() <= "2.12.0")
+        colnames(X)[x$CCA$QR$pivot] <- colnames(X)
     lm(wa ~ . - 1, data = as.data.frame(X))
 }
 

Modified: pkg/vegan/R/as.mlm.rda.R
===================================================================
--- pkg/vegan/R/as.mlm.rda.R	2010-11-18 07:51:23 UTC (rev 1377)
+++ pkg/vegan/R/as.mlm.rda.R	2010-11-21 17:45:48 UTC (rev 1378)
@@ -2,7 +2,10 @@
     function (x) 
 {
     X <- qr.X(x$CCA$QR)
-    colnames(X) <- colnames(X)[x$CCA$QR$pivot]
+    ## We hope that column names will be fixed in R 2.12.1 (but
+    ## perhaps in vain).
+    if (getRversion() <= "2.12.0")
+        colnames(X)[x$CCA$QR$pivot] <- colnames(X)
     lm(x$CCA$wa ~ . - 1, data = as.data.frame(X))
 }
 

Modified: pkg/vegan/R/intersetcor.R
===================================================================
--- pkg/vegan/R/intersetcor.R	2010-11-18 07:51:23 UTC (rev 1377)
+++ pkg/vegan/R/intersetcor.R	2010-11-21 17:45:48 UTC (rev 1378)
@@ -7,5 +7,9 @@
         w <- object$rowsum
         wa <- sweep(object$CCA$wa, 1, sqrt(w), "*")
     }
-    cor(qr.X(object$CCA$QR), wa)
+    X <- qr.X(object$CCA$QR)
+    ## current R (2.12.0) uses wrong column names in pivoted qr.X()
+    if (getRversion() <= "2.12.0")
+        colnames(X)[object$CCA$QR$pivot] <- colnames(X)
+    cor(X, wa)
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-18 07:51:23 UTC (rev 1377)
+++ pkg/vegan/inst/ChangeLog	2010-11-21 17:45:48 UTC (rev 1378)
@@ -8,6 +8,10 @@
 	vegan. Mainly clean up and checking of functions intended for the
 	release. 
 
+	* as.mlm.cca/rda and intersector: should get the pivoting of names
+	in qr.X() correct both in the current buggy R and hopefully fixed
+	next version 2.12.1.
+
 	* vif.cca: aliased terms must be removed when calculating
 	VIFs. Test case vif.cca(cca(dune ~ Manure + Management, dune.env))
 	should give decent values all below <100 (used to give magnitude