[Vegan-commits] r511 - in pkg: . R inst man

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

Author: jarioksa
Date: 2008-09-30 14:36:44 +0200 (Tue, 30 Sep 2008)
New Revision: 511

Added:
   pkg/R/head.cca.R
Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
   pkg/man/plot.cca.Rd
Log:
head.cca & tail.cca for friendlier look in Sweave tutorials

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-09-30 07:04:55 UTC (rev 510)
+++ pkg/DESCRIPTION	2008-09-30 12:36:44 UTC (rev 511)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-0
-Date: September 26, 2008
+Version: 1.16-1
+Date: September 30, 2008
 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>

Added: pkg/R/head.cca.R
===================================================================
--- pkg/R/head.cca.R	                        (rev 0)
+++ pkg/R/head.cca.R	2008-09-30 12:36:44 UTC (rev 511)
@@ -0,0 +1,9 @@
+`head.cca` <-
+    function(x, n=6, tail = 0, ...) {
+        print(summary(x, ...), head=n, tail=tail)
+    }
+
+`tail.cca` <-
+    function(x, n=6, head = 0, ...) {
+        print(summary(x, ...), head=head, tail=n)
+    }

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-09-30 07:04:55 UTC (rev 510)
+++ pkg/inst/ChangeLog	2008-09-30 12:36:44 UTC (rev 511)
@@ -3,10 +3,17 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-0 (opened September 26, 2008)
+Versin 1.16-1 (opened September 30, 2008)
 
-	* New devel version after branching the release version 1.15-0.
+	* head.cca & tail.cca: shortcuts to print(summary(x, ...), head,
+	tail) for nicer Sweave tutorials.
 	
+Version 1.16-0 (closed on September 30, 2008)
+
+	* New devel version after branching the release version
+	1.15-0. Identical to the release version except that MOStest and
+	adipart functions were removed from 1.15-0.
+	
 Version 1.14-12 (closed September 26, 2008)
 
 	* add1.cca, drop1.cca: new functions that also implement

Modified: pkg/man/plot.cca.Rd
===================================================================
--- pkg/man/plot.cca.Rd	2008-09-30 07:04:55 UTC (rev 510)
+++ pkg/man/plot.cca.Rd	2008-09-30 12:36:44 UTC (rev 511)
@@ -7,6 +7,8 @@
 \alias{summary.cca}
 \alias{print.summary.cca}
 \alias{ade2vegancca}
+\alias{head.cca}
+\alias{tail.cca}
 
 \title{Plot or Extract Results of Constrained Correspondence Analysis
   or Redundancy Analysis}
@@ -28,6 +30,8 @@
 \method{summary}{cca}(object, scaling = 2, axes = 6, display = c("sp", "wa", 
     "lc", "bp", "cn"), digits = max(3, getOption("digits") - 3), ...)
 \method{print}{summary.cca}(x, digits = x$digits, head = NA, tail = head, ...)
+\method{head}{cca}(x, n = 6, tail = 0, ...)
+\method{tail}{cca}(x, n = 6, head = 0, ...)
 }
 
 \arguments{
@@ -69,9 +73,9 @@
     approximate original data.}
   \item{axes}{Number of axes in summaries.}
   \item{digits}{Number of digits in output.}
-  \item{head, tail}{Number of rows printed from the head and tail of
+  \item{n, head, tail}{Number of rows printed from the head and tail of
     species and site scores.  Default \code{NA} prints all.}
-  \item{...}{Other parameters for plotting functions.}
+  \item{...}{Parameters passed to other functions.}
 }
 
 \details{
@@ -117,7 +121,16 @@
   were little affected.  Therefore the \code{plot} function uses site
   scores (``WA scores'') as the default. This is consistent with the
   usage in statistics and other functions in \R
-  (\code{\link[MASS]{lda}}, \code{\link{cancor}}).
+  (\code{\link[MASS]{lda}}, \code{\link{cancor}}). The \code{summary}
+  output can be voluminous, but you can show only some lines of the
+  scores by setting \code{head} or \code{tail} arguments in
+  \code{print.summary.cca}, or by using functions \code{head} or
+  \code{tail}. Function \code{head} and \code{tail} are shortcuts to
+  \code{summary} with \code{head} or \code{tail} set in the
+  \code{print}. In general they only show \code{n} first or last rows of
+  the scores (and optionally also \code{head} or \code{tail}), but they
+  display all other results completely. They pass all arguments to
+  \code{summary}. 
 }
 \value{
   The \code{plot} function returns invisibly a plotting structure which
@@ -151,6 +164,8 @@
 text(mod, dis="cn")
 points(mod, pch=21, col="red", bg="yellow", cex=1.2)
 text(mod, "species", col="blue", cex=0.8)
+## Limited output of 'summary'
+head(mod, tail=2)
 }
 \keyword{hplot}
 \keyword{aplot}