From noreply at r-forge.r-project.org  Mon Apr  4 09:26:57 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  4 Apr 2016 09:26:57 +0200 (CEST)
Subject: [Vegan-commits] r2997 - in pkg/vegan: . R inst man
Message-ID: <20160404072657.B90A3180506@r-forge.r-project.org>

Author: jarioksa
Date: 2016-04-04 09:26:57 +0200 (Mon, 04 Apr 2016)
New Revision: 2997

Modified:
   pkg/vegan/NAMESPACE
   pkg/vegan/R/add1.cca.R
   pkg/vegan/R/anova.cca.R
   pkg/vegan/R/anova.ccalist.R
   pkg/vegan/R/drop1.cca.R
   pkg/vegan/R/eigenvals.R
   pkg/vegan/R/ordiR2step.R
   pkg/vegan/R/ordistep.R
   pkg/vegan/inst/NEWS.Rd
   pkg/vegan/man/cca.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/NAMESPACE	2016-04-04 07:26:57 UTC (rev 2997)
@@ -388,6 +388,7 @@
 S3method(print, summary.clamtest)
 S3method(print, summary.decorana)
 S3method(print, summary.dispweight)
+S3method(print, summary.eigenvals)
 S3method(print, summary.humpfit)
 S3method(print, summary.isomap)
 S3method(print, summary.meandist)

Modified: pkg/vegan/R/add1.cca.R
===================================================================
--- pkg/vegan/R/add1.cca.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/add1.cca.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -4,6 +4,8 @@
 {
     if (inherits(object, "prc"))
         stop("'step'/'add1' cannot be used for 'prc' objects")
+    if (is.null(object$terms))
+        stop("ordination model must be fitted using formula")
     test <- match.arg(test)
     ## Default add1
     out <- NextMethod("add1", object, test = "none", ...)

Modified: pkg/vegan/R/anova.cca.R
===================================================================
--- pkg/vegan/R/anova.cca.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/anova.cca.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -38,6 +38,8 @@
     ## by cases
     if (!is.null(by)) {
         by <- match.arg(by, c("terms", "margin", "axis"))
+        if (is.null(object$terms))
+            stop("model must be fitted with formula interface")
         sol <- switch(by,
                       "terms" = anova.ccabyterm(object,
                       permutations = permutations,

Modified: pkg/vegan/R/anova.ccalist.R
===================================================================
--- pkg/vegan/R/anova.ccalist.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/anova.ccalist.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -14,17 +14,20 @@
         stop("same ordination method must be used in all models")
     else
         method <- method[1]
-    ## 2. Same response
+    ## 2. All models must be fitted with formula interface
+    if (any(sapply(object, function(x) is.null(x$terms))))
+        stop("all models must be fitted with formula interface")
+    ## 3. Same response
     resp <- sapply(object, function(z) deparse(formula(z)[[2]]))
     if (!all(resp == resp[1]))
         stop("response must be same in all models")
-    ## 3. Same no. of observations
+    ## 4. Same no. of observations
     N <- sapply(object, nobs)
     if (!all(N == N[1]))
         stop("number of observations must be same in all models")
     else
         N <- N[1]
-    ## 4. Terms must be nested
+    ## 5. Terms must be nested
     trms <- lapply(object, function(z) labels(terms(z)))
     o  <- order(sapply(trms, length))
     for (i in 2:nmodels) 

Modified: pkg/vegan/R/drop1.cca.R
===================================================================
--- pkg/vegan/R/drop1.cca.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/drop1.cca.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -4,6 +4,8 @@
 {
     if (inherits(object, "prc"))
         stop("'step'/'drop1' cannot be used for 'prc' objects")
+    if (is.null(object$terms))
+        stop("ordination model must be fitted using formula")
     test <- match.arg(test)
     out <- NextMethod("drop1", object, test="none", ...)
     cl <- class(out)

Modified: pkg/vegan/R/eigenvals.R
===================================================================
--- pkg/vegan/R/eigenvals.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/eigenvals.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -137,6 +137,17 @@
                         `Proportion Explained` = round(abs(vars), 5),
                         `Cumulative Proportion`= round(cumsum(abs(vars)), 5))
     out <- list(importance = importance)
-    class(out) <- c("summary.eigenvals", "summary.prcomp")
+    class(out) <- c("summary.eigenvals")
     out
 }
+
+## before R svn commit 70391 we used print.summary.prcomp, but now we
+## need our own version that is similar to pre-70391 R function
+
+`print.summary.eigenvals` <-
+    function(x, digits = max(3L, getOption("digits") - 3L), ...)
+{
+    cat("Importance of components:\n")
+    print(x$importance, digits = digits, ...)
+    invisible(x)
+}

Modified: pkg/vegan/R/ordiR2step.R
===================================================================
--- pkg/vegan/R/ordiR2step.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/ordiR2step.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -8,6 +8,8 @@
              trace = TRUE, ...)
 {
     direction <- match.arg(direction)
+    if (is.null(object$terms))
+        stop("ordination model must be fitted using formula")
     if (missing(scope))
         stop("needs scope")
     ## Works only for rda(): cca() does not have (yet) R2.adjusted

Modified: pkg/vegan/R/ordistep.R
===================================================================
--- pkg/vegan/R/ordistep.R	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/R/ordistep.R	2016-04-04 07:26:57 UTC (rev 2997)
@@ -5,6 +5,8 @@
 {
     if (!inherits(object, "cca"))
         stop("function can be only used with 'cca' and related objects")
+    if (is.null(object$terms))
+        stop("ordination model must be fitted using formula")
     ## handling 'direction' and 'scope' directly copied from
     ## stats::step()
     md <- missing(direction)

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/inst/NEWS.Rd	2016-04-04 07:26:57 UTC (rev 2997)
@@ -2,6 +2,22 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.3-5}{
+  \subsection{BUG FIXES}{
+    \itemize{
+
+      \item \code{eigenvals} fails with \code{prcomp} results in
+      \R-devel. The next version of \code{prcomp} will have an
+      argument to limit the number of eigenvalues shown
+      (\code{rank.}), and this breaks \code{eigenvals} in \pkg{vegan}.
+
+      \item \code{calibrate} failed for \code{cca} and friends if
+      \code{rank} was given.
+
+    } % itemise
+  } % bug fixes
+} % v2.3-5
+
 \section{Changes in version 2.3-4}{
 
   \subsection{BUG FIXES}{

Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd	2016-03-10 09:14:40 UTC (rev 2996)
+++ pkg/vegan/man/cca.Rd	2016-04-04 07:26:57 UTC (rev 2997)
@@ -34,7 +34,9 @@
     of the model formula.}
   \item{X}{ Community data matrix. }
   \item{Y}{ Constraining matrix, typically of environmental variables.
-    Can be missing. }
+    Can be missing. It is better to use \code{formula} instead of this
+    argument, and some further analyses only work when \code{formula}
+    was used.}
   \item{Z}{ Conditioning matrix, the effect of which is removed
     (`partialled out') before next step. Can be missing.}
   \item{scale}{Scale species to unit variance (like correlations).}
@@ -70,10 +72,13 @@
   algorithm of \pkg{vegan}. The algorithm of CCA is similar, but
   involves standardization by row and column weights.
 
-  The functions can be called either with matrix-like entries for community
-  data and constraints, or with formula interface.  In general, the
-  formula interface is preferred, because it allows a better control of
-  the model and allows factor constraints.
+  The functions can be called either with matrix-like entries for
+  community data and constraints, or with formula interface.  In
+  general, the formula interface is preferred, because it allows a
+  better control of the model and allows factor constraints. Some
+  analyses of ordination results are only possible if model was fitted
+  with formula (e.g., most cases of \code{\link{anova.cca}}, automatic
+  model building).
 
   In the following sections, \code{X}, \code{Y} and \code{Z}, although
   referred to as matrices, are more commonly data frames.


From noreply at r-forge.r-project.org  Mon Apr  4 09:28:16 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  4 Apr 2016 09:28:16 +0200 (CEST)
Subject: [Vegan-commits] r2998 - www
Message-ID: <20160404072816.AAE76180506@r-forge.r-project.org>

Author: jarioksa
Date: 2016-04-04 09:28:16 +0200 (Mon, 04 Apr 2016)
New Revision: 2998

Modified:
   www/NEWS.html
Log:
update NEWS for 2.3-5


Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2016-04-04 07:26:57 UTC (rev 2997)
+++ www/NEWS.html	2016-04-04 07:28:16 UTC (rev 2998)
@@ -7,6 +7,28 @@
 
 <h2>vegan News</h2>
 
+<h3>Changes in version 2.3-5</h3>
+
+
+
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li> <p><code>eigenvals</code> fails with <code>prcomp</code> results in
+<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>-devel. The next version of <code>prcomp</code> will have an
+argument to limit the number of eigenvalues shown
+(<code>rank.</code>), and this breaks <code>eigenvals</code> in <span class="pkg">vegan</span>.
+</p>
+</li>
+<li> <p><code>calibrate</code> failed for <code>cca</code> and friends if
+<code>rank</code> was given.
+</p>
+</li></ul>
+ 
+ 
+
+
 <h3>Changes in version 2.3-4</h3>