[Vegan-commits] r1960 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2011-10-20 16:06:51 +0200 (Thu, 20 Oct 2011)
New Revision: 1960

Modified:
   branches/2.0/R/capscale.R
   branches/2.0/inst/ChangeLog
   branches/2.0/inst/NEWS.Rd
Log:
merge r1959 (capscale zero rank fix) + mark-up in NEWS

Modified: branches/2.0/R/capscale.R
===================================================================
--- branches/2.0/R/capscale.R	2011-10-20 09:55:57 UTC (rev 1959)
+++ branches/2.0/R/capscale.R	2011-10-20 14:06:51 UTC (rev 1960)
@@ -91,7 +91,7 @@
     if (adjust == 1)
         X$eig <- X$eig/k
     sol <- rda.default(X$points, d$Y, d$Z, ...)
-    if (!is.null(sol$CCA)) {
+    if (!is.null(sol$CCA) && sol$CCA$rank > 0) {
         colnames(sol$CCA$u) <- colnames(sol$CCA$biplot) <- names(sol$CCA$eig) <-
             colnames(sol$CCA$wa) <- colnames(sol$CCA$v) <-
                 paste("CAP", 1:ncol(sol$CCA$u), sep = "")
@@ -118,9 +118,9 @@
         ## NA action after 'subset'
         if (!is.null(d$na.action))
             comm <- comm[-d$na.action, , drop = FALSE]
-        if (!is.null(sol$pCCA)) 
+        if (!is.null(sol$pCCA) && sol$pCCA$rank > 0) 
             comm <- qr.resid(sol$pCCA$QR, comm)
-        if (!is.null(sol$CCA)) {
+        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$eig), 
                                "/")
@@ -139,7 +139,7 @@
             sol$CCA$v.eig[] <- sol$CCA$v[] <- NA
         sol$colsum <- NA
     }
-    if (!is.null(sol$CCA)) 
+    if (!is.null(sol$CCA) && sol$CCA$rank > 0) 
         sol$CCA$centroids <- centroids.cca(sol$CCA$wa, d$modelframe)
     if (!is.null(sol$CCA$alias)) 
         sol$CCA$centroids <- unique(sol$CCA$centroids)

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2011-10-20 09:55:57 UTC (rev 1959)
+++ branches/2.0/inst/ChangeLog	2011-10-20 14:06:51 UTC (rev 1960)
@@ -4,6 +4,8 @@
 
 Version 2.0-2 (opened October 20, 2011)
 
+	* merge r1959: capscale zero-rank constraints bug fix.
+
 Version 2.0-1 (released October 20, 2011)
 
 	* merge r1945: add plot & lines for as.preston & as.fisher.

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2011-10-20 09:55:57 UTC (rev 1959)
+++ branches/2.0/inst/NEWS.Rd	2011-10-20 14:06:51 UTC (rev 1960)
@@ -2,6 +2,24 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.0-2}{
+  \subsection{BUG FIXES}{
+
+   \itemize{
+
+     \item Function \code{capscale} failed if constrained component
+     had zero rank. This is most likely in partial models where the
+     conditions can alias constraints. This was manifest in
+     \code{anova(..., by ="margin")} which uses partial models to
+     analyses the marginal effects, and was raported in an email
+     message to
+     \href{https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html}{R-News
+     mailing list}.
+
+     }
+ }  % end bug fixes 		  
+} %end version 2.0-2
+
 \section{Changes in version 2.0-1}{
   \subsection{NEW FUNCTIONS}{
     \itemize{
@@ -27,8 +45,8 @@
       species and analytic equations. The new \code{raupcrick}
       function uses simulation with \code{oecosimu}. The function
       follows Chase et al. (2011) \emph{Ecosphere} 2:art24
-      [doi:10.1890/ES10-00117.1], and was developed with the
-      consultation of Brian Inouye.
+      [\href{http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1}{doi:10.1890/ES10-00117.1}],
+      and was developed with the consultation of Brian Inouye.
 
     }
   } % end NEW FUNCTIONS