[Vegan-commits] r2356 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2013-01-09 16:08:57 +0100 (Wed, 09 Jan 2013)
New Revision: 2356

Modified:
   branches/2.0/R/capscale.R
   branches/2.0/R/multipart.default.R
   branches/2.0/inst/ChangeLog
Log:
merge r2349 (multipart bugfix) & r2350 (capscale species score scaling bugfix)

Modified: branches/2.0/R/capscale.R
===================================================================
--- branches/2.0/R/capscale.R	2013-01-09 13:08:16 UTC (rev 2355)
+++ branches/2.0/R/capscale.R	2013-01-09 15:08:57 UTC (rev 2356)
@@ -122,14 +122,12 @@
             comm <- qr.resid(sol$pCCA$QR, comm)
         if (!is.null(sol$CCA) && sol$CCA$rank > 0) {
             sol$CCA$v.eig <- t(comm) %*% sol$CCA$u/sqrt(k)
-            sol$CCA$v <- sweep(sol$CCA$v.eig, 2, sqrt(sol$CCA$eig), 
-                               "/")
+            sol$CCA$v <- decostand(sol$CCA$v.eig, "normalize", MARGIN = 2)
             comm <- qr.resid(sol$CCA$QR, comm)
         }
         if (!is.null(sol$CA) && sol$CA$rank > 0) {
             sol$CA$v.eig <- t(comm) %*% sol$CA$u/sqrt(k)
-            sol$CA$v <- sweep(sol$CA$v.eig, 2, sqrt(sol$CA$eig[1:poseig]), 
-                              "/")
+            sol$CA$v <- decostand(sol$CA$v.eig, "normalize", MARGIN = 2)
         }
     } else {
         ## input data were dissimilarities, and no 'comm' defined:

Modified: branches/2.0/R/multipart.default.R
===================================================================
--- branches/2.0/R/multipart.default.R	2013-01-09 13:08:16 UTC (rev 2355)
+++ branches/2.0/R/multipart.default.R	2013-01-09 15:08:57 UTC (rev 2356)
@@ -128,7 +128,7 @@
     attr(sim, "call") <- call
     attr(sim$oecosimu$simulated, "index") <- index
     attr(sim$oecosimu$simulated, "scales") <- scales
-    attr(sim$oecosimu$simulated, "global") <- TRUE
+    attr(sim$oecosimu$simulated, "global") <- global
     attr(sim, "n.levels") <- nlevs
     attr(sim, "terms") <- tlab
     attr(sim, "model") <- rhs

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-01-09 13:08:16 UTC (rev 2355)
+++ branches/2.0/inst/ChangeLog	2013-01-09 15:08:57 UTC (rev 2356)
@@ -4,6 +4,8 @@
 
 Version 2.0-6 (opened October 8, 2012)
 
+	* merge 2350: capscale species score scaling bug fix.
+	* merge 2349: multipart print bug fix.
 	* merge 2345: FAQ update (github, metric NMDS space).
 	* merge 2342: unused factor levels in envfit/factorfit.
 	* merge 2341 (partial): visible space in pdf of Rnw files.