From noreply at r-forge.r-project.org  Tue Feb 10 09:34:02 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 10 Feb 2015 09:34:02 +0100 (CET)
Subject: [Vegan-commits] r2932 - pkg/vegan/R
Message-ID: <20150210083402.BE1851864A2@r-forge.r-project.org>

Author: jarioksa
Date: 2015-02-10 09:34:02 +0100 (Tue, 10 Feb 2015)
New Revision: 2932

Modified:
   pkg/vegan/R/centroids.cca.R
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/R/centroids.cca.R
===================================================================
--- pkg/vegan/R/centroids.cca.R	2015-01-27 12:30:19 UTC (rev 2931)
+++ pkg/vegan/R/centroids.cca.R	2015-02-10 08:34:02 UTC (rev 2932)
@@ -17,13 +17,12 @@
     pnam <- labels(tmp)
     out <- NULL
     if (ncol(x) == 1) {
-        for(i in 1:length(tmp)) {
-            names(tmp[[i]]) <- paste(pnam[i], names(tmp[[i]]), sep="")
-            out <- c(out, tmp[[i]])
-            out <- matrix(out, nrow=1, dimnames = list(NULL, names(out)))
-        }  
+        nm <- unlist(sapply(pnam,
+                            function(nm) paste(nm, names(tmp[[nm]]), sep="")),
+                     use.names=FALSE)
+        out <- matrix(unlist(tmp), nrow=1, dimnames = list(NULL, nm))
     } else {
-        for (i in 1:length(tmp)) {
+        for (i in seq_along(tmp)) {
             colnames(tmp[[i]]) <- paste(pnam[i], colnames(tmp[[i]]), 
                                         sep = "")
             out <- cbind(out, tmp[[i]])


From noreply at r-forge.r-project.org  Mon Feb 23 09:41:47 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 23 Feb 2015 09:41:47 +0100 (CET)
Subject: [Vegan-commits] r2933 - in pkg/vegan: R man
Message-ID: <20150223084147.F14D6184220@r-forge.r-project.org>

Author: jarioksa
Date: 2015-02-23 09:41:47 +0100 (Mon, 23 Feb 2015)
New Revision: 2933

Modified:
   pkg/vegan/R/cca.default.R
   pkg/vegan/R/rda.default.R
   pkg/vegan/man/procrustes.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/R/cca.default.R
===================================================================
--- pkg/vegan/R/cca.default.R	2015-02-10 08:34:02 UTC (rev 2932)
+++ pkg/vegan/R/cca.default.R	2015-02-23 08:41:47 UTC (rev 2933)
@@ -12,6 +12,11 @@
         attr(x, "centre") <- w.c
         x
     }
+    ## Protect against grave misuse: some people have used
+    ## dissimilarities instead of data
+    if (inherits(X, "dist") || NCOL(X) == NROW(X) &&
+        isTRUE(all.equal(X, t(X))))
+        stop("function cannot be used with (dis)similarities")
     X <- as.matrix(X)
     if (any(rowSums(X) <= 0)) 
         stop("All row sums must be >0 in the community data matrix")

Modified: pkg/vegan/R/rda.default.R
===================================================================
--- pkg/vegan/R/rda.default.R	2015-02-10 08:34:02 UTC (rev 2932)
+++ pkg/vegan/R/rda.default.R	2015-02-23 08:41:47 UTC (rev 2933)
@@ -5,6 +5,11 @@
     CCA <- NULL
     pCCA <- NULL
     CA <- NULL
+    ## Protect against grave misuse: some people have used
+    ## dissimilarities instead of data
+    if (inherits(X, "dist") || NCOL(X) == NROW(X) &&
+        isTRUE(all.equal(X, t(X))))
+        stop("function cannot be used with (dis)similarities")
     X <- as.matrix(X)
     NR <- nrow(X) - 1
     Xbar <- scale(X, center = TRUE, scale = scale)

Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd	2015-02-10 08:34:02 UTC (rev 2932)
+++ pkg/vegan/man/procrustes.Rd	2015-02-23 08:41:47 UTC (rev 2933)
@@ -131,7 +131,7 @@
   function). Function \code{predict} can be used to add new rotated
   coordinates to the target. The \code{predict} function will always
   translate coordinates to the original non-centred matrix. The
-  function canot be used with \code{newdata} for \code{symmetric}
+  function cannot be used with \code{newdata} for \code{symmetric}
   analysis.
 
   Function \code{protest} performs symmetric Procrustes analysis