From noreply at r-forge.r-project.org  Thu Mar 10 10:14:40 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 10 Mar 2016 10:14:40 +0100 (CET)
Subject: [Vegan-commits] r2996 - in pkg/vegan: . R man vignettes
Message-ID: <20160310091440.D4E5A187F69@r-forge.r-project.org>

Author: jarioksa
Date: 2016-03-10 10:14:40 +0100 (Thu, 10 Mar 2016)
New Revision: 2996

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/calibrate.cca.R
   pkg/vegan/man/cca.Rd
   pkg/vegan/man/plot.cca.Rd
   pkg/vegan/vignettes/decision-vegan.Rnw
   pkg/vegan/vignettes/partitioning.Rnw
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2016-02-26 11:05:24 UTC (rev 2995)
+++ pkg/vegan/DESCRIPTION	2016-03-10 09:14:40 UTC (rev 2996)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.3-4
-Date: 2016-02-26
+Version: 2.3-5
+Date: 2016-03-10
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 
    M. Henry H. Stevens, Helene Wagner  

Modified: pkg/vegan/R/calibrate.cca.R
===================================================================
--- pkg/vegan/R/calibrate.cca.R	2016-02-26 11:05:24 UTC (rev 2995)
+++ pkg/vegan/R/calibrate.cca.R	2016-03-10 09:14:40 UTC (rev 2996)
@@ -18,7 +18,7 @@
     qrank <- object$CCA$qrank
     b <- (coef(object))[object$CCA$QR$pivot[1:qrank], , drop=FALSE]
     b <- solve(b)
-    pred <- wa[ , 1:rank, drop=FALSE]  %*% b[1:qrank, , drop =FALSE]
+    pred <- wa[ , 1:rank, drop=FALSE]  %*% b[1:rank, , drop =FALSE]
     envcen <- object$CCA$envcentre[object$CCA$QR$pivot]
     envcen <- envcen[1:object$CCA$qrank]
     pred <- sweep(pred, 2, envcen, "+")

Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd	2016-02-26 11:05:24 UTC (rev 2995)
+++ pkg/vegan/man/cca.Rd	2016-03-10 09:14:40 UTC (rev 2996)
@@ -243,8 +243,8 @@
   several components (\code{\link{varpart}}).
 
   Design decisions are explained in \code{\link{vignette}}
-  \file{decision-vegan} which also can be accessed with
-  \code{\link{vegandocs}}.
+  on \dQuote{Design decisions} which can be accessed with
+  \code{browseVignettes("vegan")}.
 
   Package \pkg{ade4} provides alternative constrained ordination
   functions \code{\link[ade4]{cca}} and \code{\link[ade4]{pcaiv}}.

Modified: pkg/vegan/man/plot.cca.Rd
===================================================================
--- pkg/vegan/man/plot.cca.Rd	2016-02-26 11:05:24 UTC (rev 2995)
+++ pkg/vegan/man/plot.cca.Rd	2016-03-10 09:14:40 UTC (rev 2996)
@@ -182,9 +182,6 @@
 text(mod, "species", col="blue", cex=0.8)
 ## Limited output of 'summary'
 head(summary(mod), tail=2)
-## Read description of scaling in RDA in vegan:
-\dontrun{vegandocs("decision")}
-
 ## Scaling can be numeric or more user-friendly names
 ## e.g. Hill's scaling for (C)CA
 scrs <- scores(mod, scaling = "sites", hill = TRUE)

Modified: pkg/vegan/vignettes/decision-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/decision-vegan.Rnw	2016-02-26 11:05:24 UTC (rev 2995)
+++ pkg/vegan/vignettes/decision-vegan.Rnw	2016-03-10 09:14:40 UTC (rev 2996)
@@ -251,7 +251,6 @@
 r <- uniroot(cross, c(0,1), a = x+y, p = mod$p)$root
 arrows(x,y, r, f(r, mod$p), lwd=4)
 @
-\label{fig:nestedtemp}
 \caption{Matrix temperature for \emph{Falco subbuteo} on Sibbo
   Svartholmen (dot). The curve is the fill line, and in a cold
   matrix, all presences (red squares) should be in the upper left
@@ -260,6 +259,7 @@
   the fill line. The ``surprise'' for this point is $u = (d/D)^2$ and
   the matrix temperature is based on the sum of surprises: presences
   outside the fill line or absences within the fill line.}
+\label{fig:nestedtemp}
 \end{figure}
 The function can be implemented in many ways following the general
 principles.  \citet{RodGir06} have seen the original code and reveal

Modified: pkg/vegan/vignettes/partitioning.Rnw
===================================================================
--- pkg/vegan/vignettes/partitioning.Rnw	2016-02-26 11:05:24 UTC (rev 2995)
+++ pkg/vegan/vignettes/partitioning.Rnw	2016-03-10 09:14:40 UTC (rev 2996)
@@ -69,7 +69,7 @@
   
   [a] to [d] and subsets containing [a] to [d] can be tested for
   significance (5 canonical analyses per permutation to test [a] to
-  [d]). Fractions [e] to [o] cannot be tested for singly.}
+  [d]). Fractions [e] to [o] cannot be tested singly.}
 \label{fig:part4}
 \end{figure}
 \clearpage