From noreply at r-forge.r-project.org  Fri Apr 17 09:30:18 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 17 Apr 2015 09:30:18 +0200 (CEST)
Subject: [Vegan-commits] r2944 - in pkg/vegan: R man
Message-ID: <20150417073018.A3029183FEF@r-forge.r-project.org>

Author: jarioksa
Date: 2015-04-17 09:30:18 +0200 (Fri, 17 Apr 2015)
New Revision: 2944

Modified:
   pkg/vegan/R/print.oecosimu.R
   pkg/vegan/man/oecosimu.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/R/print.oecosimu.R
===================================================================
--- pkg/vegan/R/print.oecosimu.R	2015-03-24 08:53:00 UTC (rev 2943)
+++ pkg/vegan/R/print.oecosimu.R	2015-04-17 07:30:18 UTC (rev 2944)
@@ -32,7 +32,7 @@
                     less = c(0.05, 0.5))
     qu <- apply(x$oecosimu$simulated, 1, quantile, probs=probs, na.rm = TRUE)
     m <- cbind("statistic" = x$oecosimu$statistic,
-               "z" = x$oecosimu$z, "mean" = x$oecosimu$means, t(qu),
+               "SES" = x$oecosimu$z, "mean" = x$oecosimu$means, t(qu),
                "Pr(sim.)"=x$oecosimu$pval)
     printCoefmat(m, cs.ind = 3:(ncol(m)-1), ...)
     if (any(is.na(x$oecosimu$simulated))) {

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2015-03-24 08:53:00 UTC (rev 2943)
+++ pkg/vegan/man/oecosimu.Rd	2015-04-17 07:30:18 UTC (rev 2944)
@@ -177,8 +177,8 @@
   \item{statistic}{Observed values of the statistic.}
   \item{simulated}{Simulated values of the statistic.}
   \item{means}{Mean values of the statistic from simulations.}
-  \item{z}{\eqn{z}-values or the standardized effect sizes of the observed 
-     statistic based on simulations.}
+  \item{z}{Standardized effect sizes (SES, a.k.a. the \eqn{z}-values)
+     of the observed statistic based on simulations.}
   \item{pval}{The \eqn{P}-values of the statistic based on simulations.}
   \item{alternative}{The type of testing as given in argument \code{alternative}.}
   \item{method}{The \code{method} used in \code{\link{nullmodel}}.}


From noreply at r-forge.r-project.org  Mon Apr 20 08:46:45 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 20 Apr 2015 08:46:45 +0200 (CEST)
Subject: [Vegan-commits] r2945 - pkg/vegan/vignettes
Message-ID: <20150420064645.E600D183E26@r-forge.r-project.org>

Author: jarioksa
Date: 2015-04-20 08:46:45 +0200 (Mon, 20 Apr 2015)
New Revision: 2945

Modified:
   pkg/vegan/vignettes/FAQ-vegan.texi
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/vignettes/FAQ-vegan.texi
===================================================================
--- pkg/vegan/vignettes/FAQ-vegan.texi	2015-04-17 07:30:18 UTC (rev 2944)
+++ pkg/vegan/vignettes/FAQ-vegan.texi	2015-04-20 06:46:45 UTC (rev 2945)
@@ -704,8 +704,11 @@
 
 If there is a really high number of species or sites, the graphs often
 are congested and many labels are overwritten. It may be impossible to
-have complete readable graphics with some data sets. However, here are
-some tricks you can use:
+have complete readable graphics with some data sets. Below we give a
+brief overview of tricks you can use. Gavin Simpson's blog
+ at uref{http://www.fromthebottomoftheheap.net,, From the bottom of the
+heap} has a series of articles on ``decluttering ordination plots'' with
+more detailed discussion and examples.
 @itemize
 
 @item 
@@ -723,19 +726,25 @@
 Add labels using function @code{ordilabel} which uses non-transparent
 background to the text. The labels still shadow each other, but the
 uppermost labels are readable. Argument @code{priority} will help in
-displaying the most interesting labels.
+displaying the most interesting labels (see
+ at uref{http://www.fromthebottomoftheheap.net/2013/01/12/decluttering-ordination-plots-in-vegan-part-1-ordilabel/,,Decluttering
+blog, part 1}).
 
 @item 
 Use @code{orditorp} function that uses labels only if these can be
 added to a graph without overwriting other labels, and points otherwise,
 if you do not need to see all labels. You must first create an empty
 plot using  @code{plot(..., type="n")}, and then add labels or points
-with @code{orditorp}.  
+with @code{orditorp} (see
+ at uref{http://www.fromthebottomoftheheap.net/2013/01/13/decluttering-ordination-plots-in-vegan-part-2-orditorp/,,Decluttering
+blog}). 
 
 @item 
 Use @code{ordipointlabel} which uses points and text labels to the
 points, and tries to optimize the location of the text to minimize the
-overlap. 
+overlap (see
+ at uref{http://www.fromthebottomoftheheap.net/2013/06/27/decluttering-ordination-plots-in-vegan-part-3-ordipointlabel/,,
+Decluttering blog}).
 
 @item
 Ordination @code{text} and @code{points} functions have argument
@@ -745,7 +754,9 @@
 @item 
 Use interactive @code{orditkplot} function that lets you drag
 labels of points to better positions if you need to see all labels. Only
-one set of points can be used. 
+one set of points can be used (see
+ at uref{http://www.fromthebottomoftheheap.net/2013/12/31/decluttering-ordination-in-vegan-part-4-orditkplot/,,Decluttering
+blog}).
 
 @item 
 Most @code{plot} functions allow you to zoom to a part of the