[Vegan-commits] r2956 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2015-08-28 09:40:29 +0200 (Fri, 28 Aug 2015)
New Revision: 2956

Modified:
   pkg/vegan/R/metaMDS.R
   pkg/vegan/R/metaMDSdist.R
   pkg/vegan/inst/NEWS.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/R/metaMDS.R
===================================================================
--- pkg/vegan/R/metaMDS.R	2015-08-26 07:03:51 UTC (rev 2955)
+++ pkg/vegan/R/metaMDS.R	2015-08-28 07:40:29 UTC (rev 2956)
@@ -6,7 +6,13 @@
               plot = FALSE, previous.best,  ...) 
 {
     engine <- match.arg(engine)
-    commname <- deparse(substitute(comm))
+    ## This could be a character vector of length > 1L
+    commname <- deparse(substitute(comm), width.cutoff = 500L)
+    if (length(commname) > 1L) {
+        paste(commname, collapse = "", sep = "")
+        ## deparse can add more white space, so cull 2 or more spaces to a single space
+        commname <- gsub("[ ]{2,}", " ", commname)
+    }
     ## metaMDS was written for community data which should be all
     ## positive. Check this here, and set arguments so that they are
     ## suitable for non-negative data.
@@ -45,13 +51,14 @@
     points <- postMDS(out$points, dis, plot = max(0, plot - 1), ...)
     if (is.null(rownames(points))) 
         rownames(points) <- rownames(comm)
-    if (wascores) {
+    wa <- if (wascores) {
         ## transformed data
-        comm <- eval.parent(parse(text=attr(dis, "commname")))
-        wa <- wascores(points, comm, expand = expand)
+        ##comm <- eval.parent(parse(text=attr(dis, "commname")))
+        comm <- attr(dis, "comm")
+        wascores(points, comm, expand = expand)
+    } else {
+        NA
     }
-    else
-        wa <- NA
     out$points <- points
     out$species <- wa
     out$call <- match.call()

Modified: pkg/vegan/R/metaMDSdist.R
===================================================================
--- pkg/vegan/R/metaMDSdist.R	2015-08-26 07:03:51 UTC (rev 2955)
+++ pkg/vegan/R/metaMDSdist.R	2015-08-28 07:40:29 UTC (rev 2956)
@@ -64,6 +64,7 @@
     }
     attr(dis, "maxdis") <- maxdis
     attr(dis, "commname") <- commname
+    attr(dis, "comm") <- comm
     attr(dis, "function") <- distname
     dis
 }

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2015-08-26 07:03:51 UTC (rev 2955)
+++ pkg/vegan/inst/NEWS.Rd	2015-08-28 07:40:29 UTC (rev 2956)
@@ -2,6 +2,45 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.3-1}{
+
+  \subsection{BUG FIXES}{
+    \itemize{
+
+      \item Automated model building in constrained ordination
+      (\code{cca}, \code{rda}, \code{capscale}) with \code{step},
+      \code{ordistep} and \code{ordiR2step} could fail if there were
+      aliased candidate variables, or constraints that were completely
+      explained by other variables already in the model. This was a
+      regression introduced in \pkg{vegan} 2.2-0.
+
+      \item Constrained ordination methods \code{cca}, \code{rda} and
+      \code{capscale} treat character variables as factors in analysis,
+      but did not return their centroids for plotting.
+
+      \item Recovery of original data in \code{metaMDS} when computing
+      WA scores for species would fail if the expression supplied to
+      argument \code{comm} was long & got deparsed to multiple
+      strings. \code{metaMDSdist} now returns the (possibly modified)
+      data frame of community data \code{comm} as attribute
+      \code{"comm"} of the returned \code{dist} object. \code{metaMDS}
+      now uses this to compute the WA species scores for the NMDS. In
+      addition, the deparsed expression for \code{comm} is now robust to
+      long expressions.  Reported by Richard Telford.
+
+      \item Function \code{rarecurve} did not check its input and this
+      could cause confusing error messages. Now function checks that
+      input data are integers that can be interpreted as counts on
+      individuals and all sampling units have some species. Unchecked
+      bad inputs were the reason for problems reported in
+      \href{http://stackoverflow.com/questions/30856909/error-while-using-rarecurve-in-r}{Stackoverflow (Error while using rarecurve)}.
+
+    }
+
+  }
+
+}
+
 \section{Changes in version 2.3-0}{
 
   \subsection{BUG FIXES}{