[Vegan-commits] r1001 - in pkg/vegan: . R inst

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

Author: jarioksa
Date: 2009-09-10 20:46:20 +0200 (Thu, 10 Sep 2009)
New Revision: 1001

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/capscale.R
   pkg/vegan/inst/ChangeLog
Log:
internal changes in capscale to introduce na.action later: user should see no difference

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-09-09 17:20:43 UTC (rev 1000)
+++ pkg/vegan/DESCRIPTION	2009-09-10 18:46:20 UTC (rev 1001)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-27
-Date: September 1, 2009
+Version: 1.16-28
+Date: September 10, 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: pkg/vegan/R/capscale.R
===================================================================
--- pkg/vegan/R/capscale.R	2009-09-09 17:20:43 UTC (rev 1000)
+++ pkg/vegan/R/capscale.R	2009-09-10 18:46:20 UTC (rev 1001)
@@ -49,6 +49,11 @@
         adjust <- sqrt(k)
     }
     nm <- attr(X, "Labels")
+    ## evaluate formula
+    fla <- update(formula, X ~ .)
+    environment(fla) <- environment()
+    d <- ordiParseFormula(fla, data, envdepth = 1)
+    X <- as.dist(d$X)
     ## cmdscale is only used if 'add = TRUE': it cannot properly
     ## handle negative eigenvalues and therefore we normally use
     ## wcmdscale. If we have 'add = TRUE' there will be no negative
@@ -64,10 +69,7 @@
         X$eig <- X$eig/k
     neig <- min(which(X$eig < 0) - 1, sum(X$eig > EPS))
     sol <- X$points[, 1:neig]
-    fla <- update(formula, sol ~ .)
-    environment(fla) <- environment()
-    d <- ordiParseFormula(fla, data, envdepth = 1)
-    sol <- rda.default(d$X, d$Y, d$Z, ...)
+    sol <- rda.default(sol, d$Y, d$Z, ...)
     if (!is.null(sol$CCA)) {
         colnames(sol$CCA$u) <- colnames(sol$CCA$biplot) <- names(sol$CCA$eig) <-
             colnames(sol$CCA$wa) <- colnames(sol$CCA$v) <-

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-09-09 17:20:43 UTC (rev 1000)
+++ pkg/vegan/inst/ChangeLog	2009-09-10 18:46:20 UTC (rev 1001)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-27 (opened September 1, 2009)
+Version 1.16-28 (opened September 10, 200)
 
+	* capscale: internal changes in the function to make it possible
+	to have na.action. The results should be identical to the previous
+	version, and the user should see no change (hope so).
+	
+Version 1.16-27 (closed September 10, 2009)
+
 	* cca & print.cca: no warning on removed species in cca.default,
 	but print information on their number.