[Vegan-commits] r994 - in branches/1.15: . inst man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Sep 7 09:32:12 CEST 2009 

Author: jarioksa
Date: 2009-09-07 09:32:11 +0200 (Mon, 07 Sep 2009)
New Revision: 994

Modified:
   branches/1.15/DESCRIPTION
   branches/1.15/inst/ChangeLog
   branches/1.15/man/cca.Rd
   branches/1.15/man/decorana.Rd
   branches/1.15/man/humpfit.Rd
   branches/1.15/man/mantel.Rd
   branches/1.15/man/ordixyplot.Rd
   branches/1.15/man/rankindex.Rd
   branches/1.15/man/scores.Rd
Log:
merging CRAN 2.10 fixes to branches/1.15 to pass the release inspection (r889, 891)

Modified: branches/1.15/DESCRIPTION
===================================================================
--- branches/1.15/DESCRIPTION	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/DESCRIPTION	2009-09-07 07:32:11 UTC (rev 994)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
 Version: 1.15-4
-Date: September 1, 2009
+Date: September 7, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/inst/ChangeLog	2009-09-07 07:32:11 UTC (rev 994)
@@ -3,8 +3,13 @@
 
 VEGAN STABLE VERSIONS
 
-Version 1.15-4 (released September 1, 2009)
+Version 1.15-4 (released September 7, 2009)
 
+	* merged r889, 891: the package was submitted to CRAN on 1 Sep,
+	2009, but failed in R 2.10 (development version) tests due to
+	obsolete or wrong links in Rd files. These are fixed here, and the
+	package will be re-released.
+
 	* merged r874: rrarefy.
 
 	* merged r875,888: betadisper fix of removing zero eigenvalues.

Modified: branches/1.15/man/cca.Rd
===================================================================
--- branches/1.15/man/cca.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/cca.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -103,7 +103,7 @@
   as constraints.  However, such exploratory problems are better
   analysed with
   unconstrained methods such as correspondence analysis
-  (\code{\link{decorana}}, \code{\link[MASS]{ca}}) or non-metric
+  (\code{\link{decorana}}, \code{\link[MASS]{corresp}}) or non-metric
   multidimensional scaling (\code{\link[MASS]{isoMDS}}) and
   environmental interpretation after analysis
   (\code{\link{envfit}}, \code{\link{ordisurf}}).

Modified: branches/1.15/man/decorana.Rd
===================================================================
--- branches/1.15/man/decorana.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/decorana.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -169,9 +169,9 @@
   For unconstrained ordination, non-metric multidimensional scaling in
   \code{\link[MASS]{isoMDS}} may be more robust (see also
   \code{\link{metaMDS}}).  Constrained (or
-  `canonical') correspondence analysis can be made with
+  \sQuote{canonical}) correspondence analysis can be made with
   \code{\link{cca}}.  Orthogonal correspondence analysis can be
-  made with \code{\link[multiv]{ca}}, or with \code{decorana} or
+  made with \code{\link[MASS]{corresp}}, or with \code{decorana} or
   \code{\link{cca}}, but the scaling of results vary (and the one in
   \code{decorana} correspondes to \code{scaling = -1} in
   \code{\link{cca}}.).

Modified: branches/1.15/man/humpfit.Rd
===================================================================
--- branches/1.15/man/humpfit.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/humpfit.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -80,8 +80,8 @@
   fails with non-Poisson families, and function \code{profile} should be
   used to inspect the fitted models. If you have loaded \code{package}
   \pkg{MASS}, you can use functions
-  \code{\link[MASS]{plot.profile.glm}},
-  \code{\link[MASS]{pairs.profile.glm}} for graphical inspection of the
+  \code{\link[MASS]{plot.profile}},
+  \code{\link[MASS]{pairs.profile}} for graphical inspection of the
   profiles, and \code{\link[MASS]{confint.profile.glm}} for the profile
   based confidence intervals. 
 

Modified: branches/1.15/man/mantel.Rd
===================================================================
--- branches/1.15/man/mantel.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/mantel.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -52,7 +52,7 @@
   components: 
   \item{Call }{Function call.}
   \item{method }{Correlation method used, as returned by
-    \code{\link[ctest]{cor.test}}.}
+    \code{\link{cor.test}}.}
   \item{statistic}{The Mantel statistic.}
   \item{signif}{Empirical significance level from permutations.}
   \item{perm}{A vector of permuted values.}

Modified: branches/1.15/man/ordixyplot.Rd
===================================================================
--- branches/1.15/man/ordixyplot.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/ordixyplot.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -58,7 +58,7 @@
     line parameters are controlled by
     \code{\link[lattice]{trellis.par.set}} for \code{superpose.line},
     and the user can set \code{length}, \code{angle} and \code{ends}
-    parameters of \code{\link[trellis]{panel.arrows}}.}
+    parameters of \code{\link[lattice]{panel.arrows}}.}
   \item{\dots}{ Arguments passed to \code{\link{scores}} methods or
     \pkg{lattice} functions.}
 }

Modified: branches/1.15/man/rankindex.Rd
===================================================================
--- branches/1.15/man/rankindex.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/rankindex.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -29,7 +29,7 @@
   should have a high rank-order similarity with gradient separation.
   The function compares most indices in \code{\link{vegdist}} against
   gradient separation using rank correlation coefficients in
-  \code{\link[ctest]{cor.test}}.  The gradient separation between each
+  \code{\link{cor.test}}. The gradient separation between each
   point is assessed as Euclidean distance for continuous variables, and
   as Gower metric for mixed data using function
   \code{\link[cluster]{daisy}} when \code{grad} has factors.
@@ -47,7 +47,7 @@
   separation values are derived from just \eqn{n} observations.
   Due to floating point arithmetics, many tied values differ by
   machine epsilon and are arbitrarily ranked differently by
-  \code{\link{rank}} used in \code{\link[ctest]{cor.test}}.  Two indices
+  \code{\link{rank}} used in \code{\link{cor.test}}.  Two indices
   which are identical with certain
   transformation or standardization may differ slightly
   (magnitude \eqn{10^{-15}}) and this may lead into third or fourth decimal

Modified: branches/1.15/man/scores.Rd
===================================================================
--- branches/1.15/man/scores.Rd	2009-09-06 14:26:28 UTC (rev 993)
+++ branches/1.15/man/scores.Rd	2009-09-07 07:32:11 UTC (rev 994)
@@ -33,8 +33,7 @@
   columns of that matrix, ignoring whether species or sites were
   requested (do not regard this as a bug but as a feature, please).
   Currently the function seems to work at least for \code{\link[MASS]{isoMDS}},
-  \code{\link{prcomp}}, \code{\link{princomp}},
-  \code{\link[multiv]{ca}}, \code{\link[multiv]{pca}}.  It may work in
+  \code{\link{prcomp}}, \code{\link{princomp}}. It may work in
   other cases or fail mysteriously.
 }
 \value{

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