From noreply at r-forge.r-project.org  Thu Nov  5 15:02:12 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  5 Nov 2015 15:02:12 +0100 (CET)
Subject: [Vegan-commits] r2973 - pkg/vegan/R
Message-ID: <20151105140212.8E867187C61@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-05 15:02:11 +0100 (Thu, 05 Nov 2015)
New Revision: 2973

Modified:
   pkg/vegan/R/vegdist.R
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/R/vegdist.R
===================================================================
--- pkg/vegan/R/vegdist.R	2015-10-23 09:33:00 UTC (rev 2972)
+++ pkg/vegan/R/vegdist.R	2015-11-05 14:02:11 UTC (rev 2973)
@@ -15,10 +15,10 @@
         stop("invalid distance method")
     if (method == -1) 
         stop("ambiguous distance method")
-    if (method > 2 && any(rowSums(x, na.rm = TRUE) == 0)) 
+    if (!method %in% c(1,2,6,16) && any(rowSums(x, na.rm = TRUE) == 0))
         warning("you have empty rows: their dissimilarities may be meaningless in method ",
                 dQuote(inm))
-    if (method > 2 && any(x < 0, na.rm = TRUE)) 
+    if (!method %in% c(1,2,6,16) && any(x < 0, na.rm = TRUE))
         warning("results may be meaningless because data have negative entries in method ",
                 dQuote(inm))
     if (method == 11 && any(colSums(x) == 0)) 


From noreply at r-forge.r-project.org  Fri Nov 13 08:21:48 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 13 Nov 2015 08:21:48 +0100 (CET)
Subject: [Vegan-commits] r2974 - pkg/vegan/R
Message-ID: <20151113072148.D087F186D3D@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-13 08:21:48 +0100 (Fri, 13 Nov 2015)
New Revision: 2974

Modified:
   pkg/vegan/R/howHead.R
Log:
Squashed commit of the following:

commit 8587c83f846a91221a6cc9d24a533029e18425a0
Author: Gavin L. Simpson <ucfagls at gmail.com>
Date:   Thu Nov 12 16:09:43 2015 -0600

    fix a bug in determining the numbers of rows and columns in a within-plot grid design

    (cherry picked from commit 2fa990a8e23cfb0c56800155dac9c99127745218)

Modified: pkg/vegan/R/howHead.R
===================================================================
--- pkg/vegan/R/howHead.R	2015-11-05 14:02:11 UTC (rev 2973)
+++ pkg/vegan/R/howHead.R	2015-11-13 07:21:48 UTC (rev 2974)
@@ -39,8 +39,8 @@
             head <- paste0(head, " constant permutation within each Plot")
     }
     if (isTRUE(all.equal(type, "grid"))) {
-        nr <- getRow(x, which = "plots")
-        nc <- getCol(x, which = "plots")
+        nr <- getRow(x, which = "within")
+        nc <- getCol(x, which = "within")
         head <- paste0(head, sprintf(ngettext(nr, " %d row", " %d rows"),
                                     nr))
         head <- paste0(head, sprintf(ngettext(nc, " %d column",


From noreply at r-forge.r-project.org  Fri Nov 13 10:32:55 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 13 Nov 2015 10:32:55 +0100 (CET)
Subject: [Vegan-commits] r2975 - www
Message-ID: <20151113093256.0DF14187CFC@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-13 10:32:55 +0100 (Fri, 13 Nov 2015)
New Revision: 2975

Modified:
   www/NEWS.html
Log:
NEWS about 2.3-2


Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2015-11-13 07:21:48 UTC (rev 2974)
+++ www/NEWS.html	2015-11-13 09:32:55 UTC (rev 2975)
@@ -7,6 +7,51 @@
 
 <h2>vegan News</h2>
 
+<h3>Changes in version 2.3-2</h3>
+
+
+
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li><p> Display of gridded permutation results failed.
+</p>
+</li>
+<li> <p><code>ordicluster</code> joined the branches at wrong coordinates
+in some cases.
+</p>
+</li>
+<li> <p><code>ordiellipse</code> ignored weights when calculating standard
+errors (<code>kind = "se"</code>). This influenced plots of <code>cca</code>,
+and also influenced <code>ordiareatest</code>.
+</p>
+</li></ul>
+ 
+ 
+
+
+<h4>NEW FEATURES</h4>
+
+
+<ul>
+<li> <p><code>text</code>, <code>points</code> and <code>lines</code> functions for
+<code>procrustes</code> analysis gained new argument <code>truemean</code>
+which allows adding <code>procrustes</code> items to the plots of
+original analysis.
+</p>
+</li>
+<li> <p><code>rrarefy</code> returns observed non-rarefied communities
+(with a warning) when users request subsamples that are larger
+than the observed community instead of failing. Function
+<code>drarefy</code> has been similar and returned sampling
+probabilities of 1, but now it also issues a warning.
+</p>
+</li></ul>
+ 
+ 
+
+
 <h3>Changes in version 2.3-1</h3>
 
 


From noreply at r-forge.r-project.org  Fri Nov 13 13:05:33 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 13 Nov 2015 13:05:33 +0100 (CET)
Subject: [Vegan-commits] r2976 - pkg/vegan/inst
Message-ID: <20151113120533.E906D184BCD@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-13 13:05:33 +0100 (Fri, 13 Nov 2015)
New Revision: 2976

Modified:
   pkg/vegan/inst/NEWS.Rd
Log:
Squashed commit of the following:

commit 7024df2c2de9e54c23c97dc91b87b6d9b750b2b1
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Fri Nov 13 11:50:12 2015 +0200

    stop

commit 05da200d6df320d37e9ccf93b33f12004e1394ef
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Fri Nov 13 11:44:15 2015 +0200

    add ref to issue #144 in NEWS

commit 899bdb761317144fe616b00490111b6d8d4d1cf5
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Fri Nov 13 11:30:48 2015 +0200

    we probably have 2.3-2: write NEWS

commit 8587c83f846a91221a6cc9d24a533029e18425a0
Author: Gavin L. Simpson <ucfagls at gmail.com>
Date:   Thu Nov 12 16:09:43 2015 -0600

    fix a bug in determining the numbers of rows and columns in a within-plot grid design

    (cherry picked from commit 2fa990a8e23cfb0c56800155dac9c99127745218)

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2015-11-13 09:32:55 UTC (rev 2975)
+++ pkg/vegan/inst/NEWS.Rd	2015-11-13 12:05:33 UTC (rev 2976)
@@ -2,6 +2,43 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.3-2}{
+
+  \subsection{BUG FIXES}{
+    \itemize{
+
+      \item Display of gridded permutation results failed.
+
+      \item \code{ordicluster} joined the branches at wrong coordinates
+      in some cases.
+
+      \item \code{ordiellipse} ignored weights when calculating standard
+      errors (\code{kind = "se"}). This influenced plots of \code{cca},
+      and also influenced \code{ordiareatest}.
+
+    } % itemize
+  } % bug fixes
+
+  \subsection{NEW FEATURES}{
+    \itemize{
+
+      \item \code{text}, \code{points} and \code{lines} functions for
+      \code{procrustes} analysis gained new argument \code{truemean}
+      which allows adding \code{procrustes} items to the plots of
+      original analysis.
+
+      \item \code{rrarefy} returns observed non-rarefied communities
+      (with a warning) when users request subsamples that are larger
+      than the observed community instead of failing. Function
+      \code{drarefy} has been similar and returned sampling
+      probabilities of 1, but now it also issues a warning. Fixes issue
+      \href{https://github.com/vegandevs/vegan/issues/144}{#144} in
+      Github.
+
+    } % itemize
+  } % new features
+} %v2.3-2
+
 \section{Changes in version 2.3-1}{
 
   \subsection{BUG FIXES}{


From noreply at r-forge.r-project.org  Fri Nov 13 13:07:01 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 13 Nov 2015 13:07:01 +0100 (CET)
Subject: [Vegan-commits] r2977 - www
Message-ID: <20151113120701.2F919184BCD@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-13 13:07:00 +0100 (Fri, 13 Nov 2015)
New Revision: 2977

Modified:
   www/NEWS.html
Log:
update NEWS


Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2015-11-13 12:05:33 UTC (rev 2976)
+++ www/NEWS.html	2015-11-13 12:07:00 UTC (rev 2977)
@@ -45,7 +45,9 @@
 (with a warning) when users request subsamples that are larger
 than the observed community instead of failing. Function
 <code>drarefy</code> has been similar and returned sampling
-probabilities of 1, but now it also issues a warning.
+probabilities of 1, but now it also issues a warning. Fixes issue
+<a href="https://github.com/vegandevs/vegan/issues/144">#144</a> in
+Github.
 </p>
 </li></ul>
  


From noreply at r-forge.r-project.org  Thu Nov 19 09:21:24 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 19 Nov 2015 09:21:24 +0100 (CET)
Subject: [Vegan-commits] r2978 - in pkg/vegan: . R inst man
Message-ID: <20151119082125.130EB187060@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-19 09:21:24 +0100 (Thu, 19 Nov 2015)
New Revision: 2978

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/adonis.R
   pkg/vegan/R/capscale.R
   pkg/vegan/R/mso.R
   pkg/vegan/inst/NEWS.Rd
   pkg/vegan/man/clamtest.Rd
   pkg/vegan/man/mso.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/DESCRIPTION	2015-11-19 08:21:24 UTC (rev 2978)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
 Version: 2.3-2
-Date: 2015-09-25
+Date: 2015-11-19
 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/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/R/adonis.R	2015-11-19 08:21:24 UTC (rev 2978)
@@ -38,8 +38,11 @@
         if (any(lhs < -TOL))
             stop("dissimilarities must be non-negative")
         dmat <- as.matrix(lhs^2)
-    }
-    else {
+    } else if ((is.matrix(lhs) || is.data.frame(lhs)) &&
+               isSymmetric(unname(as.matrix(lhs)))) {
+        dmat <- as.matrix(lhs^2)
+        lhs <- as.dist(lhs) # crazy: need not to calculate beta.sites
+    } else {
         dist.lhs <- as.matrix(vegdist(lhs, method=method, ...))
         dmat <- dist.lhs^2
     }

Modified: pkg/vegan/R/capscale.R
===================================================================
--- pkg/vegan/R/capscale.R	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/R/capscale.R	2015-11-19 08:21:24 UTC (rev 2978)
@@ -18,6 +18,10 @@
     ## mysteriously at this point.
     X <- eval(formula[[2]], envir=environment(formula),
               enclos = globalenv())
+    ## see if user supplied dissimilarities as a matrix
+    if ((is.matrix(X) || is.data.frame(X)) &&
+        isSymmetric(unname(as.matrix(X))))
+        X <- as.dist(X)
     if (!inherits(X, "dist")) {
         comm <- X
         dfun <- match.fun(dfun)

Modified: pkg/vegan/R/mso.R
===================================================================
--- pkg/vegan/R/mso.R	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/R/mso.R	2015-11-19 08:21:24 UTC (rev 2978)
@@ -12,7 +12,14 @@
     N <- nrow(object$CA$Xbar)
     if (inherits(object, "rda")) 
         N <- 1
-    Dist <- dist(xy)
+    ## we expect xy are coordinates and calculate distances, but a
+    ## swift user may have supplied distances, and we use them.
+    ## However, we won't test for distances in square matrices, but
+    ## treat that as a user mistake and let it go.
+    if (inherits(xy, "dist"))
+        Dist <- xy
+    else
+        Dist <- dist(xy)
     object$grain <- grain
     if (round.up) 
         H <- ceiling(Dist/grain) * grain

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/inst/NEWS.Rd	2015-11-19 08:21:24 UTC (rev 2978)
@@ -7,7 +7,8 @@
   \subsection{BUG FIXES}{
     \itemize{
 
-      \item Display of gridded permutation results failed.
+      \item Printing details of a gridded permutation design would fail
+      when the grid was at the within-plot level.
 
       \item \code{ordicluster} joined the branches at wrong coordinates
       in some cases.
@@ -22,6 +23,17 @@
   \subsection{NEW FEATURES}{
     \itemize{
 
+      \item \code{adonis} and \code{capscale} functions recognize
+      symmetric square matrices as dissimilarities. Formerly
+      dissimilarities had to be given as \code{"dist"} objects such as
+      produced by \code{dist} or \code{vegdist} functions, and data
+      frames and matrices were regarded as observations x variables
+      data which could confuse users (e.g., issue
+      \href{https://github.com/vegandevs/vegan/issues/147}{#147}).
+
+      \item \code{mso} accepts \code{"dist"} objects for the distances
+      among locations as an alternative to coordinates of locations.
+
       \item \code{text}, \code{points} and \code{lines} functions for
       \code{procrustes} analysis gained new argument \code{truemean}
       which allows adding \code{procrustes} items to the plots of

Modified: pkg/vegan/man/clamtest.Rd
===================================================================
--- pkg/vegan/man/clamtest.Rd	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/man/clamtest.Rd	2015-11-19 08:21:24 UTC (rev 2978)
@@ -114,7 +114,7 @@
 }
 \note{
 The code was tested against standalone CLAM software provided
-on the website of Anne Chao (\url{http://chao.stat.nthu.edu.tw/softwarece.html});
+on the website of Anne Chao (\url{http://chao.stat.nthu.edu.tw/wordpress/});
 minor inconsistencies were found, especially for finding the
 threshold for 'too rare' species.
 These inconsistencies are probably due to numerical differences between the

Modified: pkg/vegan/man/mso.Rd
===================================================================
--- pkg/vegan/man/mso.Rd	2015-11-13 12:07:00 UTC (rev 2977)
+++ pkg/vegan/man/mso.Rd	2015-11-19 08:21:24 UTC (rev 2978)
@@ -18,12 +18,13 @@
 }
 \arguments{
   \item{object.cca}{ An object of class cca, created by the \code{\link{cca}} or
-    \code{\link{rda}} function.} 
-  \item{object.xy}{ A vector, matrix or data frame with the spatial
-    coordinates of the data represented by object.cca. Must have the
-    same number of rows as \code{object.cca$CA$Xbar} (see
-    \code{\link{cca.object}}). } 
-  \item{grain}{ Interval size for distance classes.}
+    \code{\link{rda}} function.}
+   \item{object.xy}{ A vector, matrix or data frame with the spatial
+    coordinates of the data represented by \code{object.cca}. The
+    number of rows must match the number of observations (as given by
+    \code{nobs}) in \code{cca.object}. Alternatively, interpoint
+    distances can be supplied as a \code{\link{dist}} object. }
+   \item{grain}{ Interval size for distance classes.}
   \item{round.up}{ Determines the choice of breaks. If false, distances
     are rounded to the nearest multiple of grain. If true, distances are
     rounded to the upper multiple of grain.} 


From noreply at r-forge.r-project.org  Thu Nov 19 09:27:00 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 19 Nov 2015 09:27:00 +0100 (CET)
Subject: [Vegan-commits] r2979 - www
Message-ID: <20151119082701.04190186F23@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-19 09:27:00 +0100 (Thu, 19 Nov 2015)
New Revision: 2979

Modified:
   www/NEWS.html
Log:
update NEWS


Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2015-11-19 08:21:24 UTC (rev 2978)
+++ www/NEWS.html	2015-11-19 08:27:00 UTC (rev 2979)
@@ -15,7 +15,8 @@
 
 
 <ul>
-<li><p> Display of gridded permutation results failed.
+<li><p> Printing details of a gridded permutation design would fail
+when the grid was at the within-plot level.
 </p>
 </li>
 <li> <p><code>ordicluster</code> joined the branches at wrong coordinates
@@ -35,6 +36,19 @@
 
 
 <ul>
+<li> <p><code>adonis</code> and <code>capscale</code> functions recognize
+symmetric square matrices as dissimilarities. Formerly
+dissimilarities had to be given as <code>"dist"</code> objects such as
+produced by <code>dist</code> or <code>vegdist</code> functions, and data
+frames and matrices were regarded as observations x variables
+data which could confuse users (e.g., issue
+<a href="https://github.com/vegandevs/vegan/issues/147">#147</a>).
+</p>
+</li>
+<li> <p><code>mso</code> accepts <code>"dist"</code> objects for the distances
+among locations as an alternative to coordinates of locations.
+</p>
+</li>
 <li> <p><code>text</code>, <code>points</code> and <code>lines</code> functions for
 <code>procrustes</code> analysis gained new argument <code>truemean</code>
 which allows adding <code>procrustes</code> items to the plots of


From noreply at r-forge.r-project.org  Thu Nov 26 10:14:59 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 26 Nov 2015 10:14:59 +0100 (CET)
Subject: [Vegan-commits] r2980 - in pkg/vegan: . R
Message-ID: <20151126091459.78165186E88@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-26 10:14:58 +0100 (Thu, 26 Nov 2015)
New Revision: 2980

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/anosim.R
   pkg/vegan/R/bioenv.default.R
   pkg/vegan/R/gdispweight.R
   pkg/vegan/R/mrpp.R
   pkg/vegan/R/rarefy.R
Log:
Squashed commit of the following:

commit 43e0233943ef8c6f56b6f1a716beb13a3b32ecfc
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Wed Nov 25 13:14:35 2015 +0200

    rarefy gave false warnings if data was a vector or dropped to vector

    also improved ordering of tests for warnings and errors

    (cherry picked from commit 223ec5fbfa800318428f689d2be7da89ef5d4316)

commit b73869871ed2ec227527c528e127ea5b42a4018d
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Wed Nov 25 12:11:30 2015 +0200

    community data cannot be a matrix, but it must be a data.frame

    (cherry picked from commit cd45945e36c2d5c6273b05910e95211e0a88f1d9)

commit 42738f74db28ffccd6000253ec10f490233bc779
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Thu Nov 19 19:54:39 2015 +0200

    cleaner test for symmetric matrices that also works for data frames

    (cherry picked from commit c10762873165c108e9591b1f0e38fbd5af13a87c)

commit c35d409d072f04dfd201f4cebaa0f83fc3c16f80
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Thu Nov 19 19:35:37 2015 +0200

    cleaner test for distances in symmetric matrices or data frames

    earlier failed with data.frames

    (cherry picked from commit dc815de504391a344264320cecfff0dfd6cabb84)

commit 4f5e2bb57baf3638cd7e9ce49199cc08898740a2
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Thu Nov 19 19:29:55 2015 +0200

    clean and correct test for distances in symmetric matrices

    as.dist() was not done after successful test for symmetric
    matrices and analysis failed later when it assumed data are
    no dist objects.

    (cherry picked from commit 96bb628b9833980d4d1b7bbb8ea33c6870c43283)

commit 670c79d5fe9f5101be4ec0b73fee2a4856e54d12
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Thu Nov 26 10:58:41 2015 +0200

    vegan 2.3-2 was released: update version

    version 2.3-3 may never be released, but head on towards 2.4-0.
    However, changes must go to a new number just in case.

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2015-11-19 08:27:00 UTC (rev 2979)
+++ pkg/vegan/DESCRIPTION	2015-11-26 09:14:58 UTC (rev 2980)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.3-2
-Date: 2015-11-19
+Version: 2.3-3
+Date: 2015-11-26
 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/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R	2015-11-19 08:27:00 UTC (rev 2979)
+++ pkg/vegan/R/anosim.R	2015-11-26 09:14:58 UTC (rev 2980)
@@ -5,12 +5,13 @@
     EPS <- sqrt(.Machine$double.eps)
     if (inherits(dat, "dist")) 
         x <- dat
-    else if (is.matrix(dat) && nrow(dat) == ncol(dat) && all(dat[lower.tri(dat)] == 
-        t(dat)[lower.tri(dat)])) {
-        x <- dat
+    else if ((is.matrix(dat) || is.data.frame(dat)) &&
+             isSymmetric(unname(as.matrix(dat)))) {
+        x <- as.dist(dat)
         attr(x, "method") <- "user supplied square matrix"
     }
-    else x <- vegdist(dat, method = distance)
+    else
+        x <- vegdist(dat, method = distance)
     if (any(x < -sqrt(.Machine$double.eps)))
         warning("some dissimilarities are negative -- is this intentional?")
     sol <- c(call = match.call())

Modified: pkg/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R	2015-11-19 08:27:00 UTC (rev 2979)
+++ pkg/vegan/R/bioenv.default.R	2015-11-26 09:14:58 UTC (rev 2980)
@@ -70,8 +70,8 @@
         index <- attr(comdis, "method")
         if (is.null(index))
             index <- "unspecified"
-    } else if (is.matrix(comm) && nrow(comm) == ncol(comm) &&
-             isTRUE(all.equal(comm, t(comm)))) {
+    } else if ((is.matrix(comm) || is.data.frame(comm)) &&
+               isSymmetric(unname(as.matrix(comm)))) {
         comdis <- as.dist(comm)
         index <- "supplied square matrix"
     } else {

Modified: pkg/vegan/R/gdispweight.R
===================================================================
--- pkg/vegan/R/gdispweight.R	2015-11-19 08:27:00 UTC (rev 2979)
+++ pkg/vegan/R/gdispweight.R	2015-11-26 09:14:58 UTC (rev 2980)
@@ -26,6 +26,7 @@
     family <- quasipoisson()
     V <- family$variance
     ## fit models to all species separately and extract results
+    comm <- as.data.frame(comm)
     mods <- lapply(comm, function(y) glm.fit(x, y, family = family))
     y <- sapply(mods, '[[', "y")
     mu <- sapply(mods, fitted)

Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R	2015-11-19 08:27:00 UTC (rev 2979)
+++ pkg/vegan/R/mrpp.R	2015-11-26 09:14:58 UTC (rev 2980)
@@ -14,8 +14,8 @@
     }
     if (inherits(dat, "dist")) 
         dmat <- dat
-    else if (is.matrix(dat) && nrow(dat) == ncol(dat) && all(dat[lower.tri(dat)] == 
-        t(dat)[lower.tri(dat)])) {
+    else if ((is.matrix(dat) || is.data.frame(dat)) &&
+               isSymmetric(unname(as.matrix(dat)))) {
         dmat <- dat
         attr(dmat, "method") <- "user supplied square matrix"
     }

Modified: pkg/vegan/R/rarefy.R
===================================================================
--- pkg/vegan/R/rarefy.R	2015-11-19 08:27:00 UTC (rev 2979)
+++ pkg/vegan/R/rarefy.R	2015-11-26 09:14:58 UTC (rev 2980)
@@ -2,22 +2,23 @@
     function (x, sample, se = FALSE, MARGIN = 1) 
 {
     x <- as.matrix(x)
-    minsample <- min(apply(x, MARGIN, sum))
-    if (any(sample > minsample))
-        warning(
-            gettextf("Requested 'sample' was larger than smallest site maximum (%d)",
-                     minsample))
     ## as.matrix changes an n-vector to a n x 1 matrix
     if (ncol(x) == 1 && MARGIN == 1)
         x <- t(x)
     if (!identical(all.equal(x, round(x)), TRUE))
         stop("function accepts only integers (counts)")
+    minsample <- min(apply(x, MARGIN, sum))
     if (missing(sample)) {
-        sample <- min(apply(x, MARGIN, sum))
-        info <- paste("The size of 'sample' must be given --\nHint: Smallest site maximum", 
-                      sample)
-        stop(info)
+        stop(
+            gettextf(
+                "The size of 'sample' must be given --\nHint: Smallest site maximum %d",
+                minsample))
     }
+    if (any(sample > minsample))
+        warning(
+            gettextf(
+                "Requested 'sample' was larger than smallest site maximum (%d)",
+                minsample))
     rarefun <- function(x, sample) {
         x <- x[x > 0]
         J <- sum(x)


From noreply at r-forge.r-project.org  Mon Nov 30 08:46:30 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 30 Nov 2015 08:46:30 +0100 (CET)
Subject: [Vegan-commits] r2981 - pkg/vegan/R
Message-ID: <20151130074631.048C2187AF9@r-forge.r-project.org>

Author: jarioksa
Date: 2015-11-30 08:46:30 +0100 (Mon, 30 Nov 2015)
New Revision: 2981

Modified:
   pkg/vegan/R/treedist.R
   pkg/vegan/R/treedive.R
   pkg/vegan/R/treeheight.R
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/R/treedist.R
===================================================================
--- pkg/vegan/R/treedist.R	2015-11-26 09:14:58 UTC (rev 2980)
+++ pkg/vegan/R/treedist.R	2015-11-30 07:46:30 UTC (rev 2981)
@@ -1,6 +1,11 @@
 `treedist` <-
     function(x, tree, relative = TRUE,  match.force = TRUE, ...)
 {
+    ## we cannot reconstruct tree with reversals from cophenetic
+    tree <- as.hclust(tree)
+    if (any(diff(tree$height) < -sqrt(.Machine$double.eps)))
+        stop("tree with reversals cannot be handled")
+    x <- as.matrix(x)
     n <- nrow(x)
     ABJ <- matrix(0, n , n)
     dmat <- as.matrix(cophenetic(tree))

Modified: pkg/vegan/R/treedive.R
===================================================================
--- pkg/vegan/R/treedive.R	2015-11-26 09:14:58 UTC (rev 2980)
+++ pkg/vegan/R/treedive.R	2015-11-30 07:46:30 UTC (rev 2981)
@@ -1,8 +1,12 @@
 `treedive` <-
     function(comm, tree, match.force = TRUE, verbose = TRUE)
 {
+    EPS <- sqrt(.Machine$double.eps)
+    comm <- as.matrix(comm)
     if (!inherits(tree, c("hclust", "spantree")))
-        stop("'clus' must be an 'hclust' or 'spantree' result object")
+        stop("'tree' must be an 'hclust' or 'spantree' result object")
+    if (inherits(tree, "hclust") && any(diff(tree$height) < -EPS))
+        stop("tree with reversals cannot be handled")
     m <- as.matrix(cophenetic(tree))
     ## Check tree/comm match by names
     if (match.force || ncol(comm) != ncol(m)) {

Modified: pkg/vegan/R/treeheight.R
===================================================================
--- pkg/vegan/R/treeheight.R	2015-11-26 09:14:58 UTC (rev 2980)
+++ pkg/vegan/R/treeheight.R	2015-11-30 07:46:30 UTC (rev 2981)
@@ -4,6 +4,27 @@
     if (inherits(tree, "spantree"))
         return(sum(tree$dist))
     tree <- as.hclust(tree)
-    sum(tree$height) + max(tree$height)
+    ## nodes should start from 0 -- if there are negative heights,
+    ## tree is too pathological to be measured.
+    if (any(tree$height < 0))
+        stop("negative heights: tree cannot be measured")
+    ## can be done really fast if there are no reversals, but we need
+    ## to traverse the tree with reversals
+    if (is.unsorted(tree$height)) { # slow
+        h <- tree$height
+        m <- tree$merge
+        height <- 0
+        for (i in 1:nrow(m)) {
+            for (j in 1:2) {
+                if (m[i,j] < 0)
+                    height <- height + h[i]
+                else
+                    height <- height + abs(h[i] - h[m[i,j]])
+            }
+        }
+        height
+    }
+    else    # fast
+        sum(tree$height) + max(tree$height)
 }