[Vegan-commits] r287 - in pkg: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 25 17:34:33 CET 2008
Author: gsimpson
Date: 2008-03-25 17:34:33 +0100 (Tue, 25 Mar 2008)
New Revision: 287
Removed:
pkg/man/TukeyHSD.betadisper.Rd
Modified:
pkg/inst/ChangeLog
pkg/man/betadisper.Rd
Log:
Merging TukeyHSD.betadisper doc with that for betadisper to reduce number of help files
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2008-03-25 15:58:32 UTC (rev 286)
+++ pkg/inst/ChangeLog 2008-03-25 16:34:33 UTC (rev 287)
@@ -9,6 +9,8 @@
* permDisper: This function has been renamed to permutest.betadisper
and documentation updated.
+
+ * TukeyHSD.betadisper: Function is now documented with betadisper.
Version 1.12-6 (closed Mar 25, 2008)
Deleted: pkg/man/TukeyHSD.betadisper.Rd
===================================================================
--- pkg/man/TukeyHSD.betadisper.Rd 2008-03-25 15:58:32 UTC (rev 286)
+++ pkg/man/TukeyHSD.betadisper.Rd 2008-03-25 16:34:33 UTC (rev 287)
@@ -1,51 +0,0 @@
-\name{TukeyHSD.betadisper}
-\alias{TukeyHSD.betadisper}
-\title{Compute Tukey Honest Significant Differences}
-
-\description{
- Create a set of confidence intervals on the differences between
- the means of the levels of the grouping factor with the specified
- family-wise probability of coverage. The intervals are based on the
- Studentized range statistic, Tukey's 'Honest Significant
- Difference' method.
-}
-\usage{
-\method{TukeyHSD}{betadisper}(x, which = "group", ordered = FALSE,
- conf.level = 0.95, \ldots)
-}
-\arguments{
- \item{x}{A fitted model object of class \code{\link{betadisper}}.}
- \item{which}{A character vector listing terms in the fitted model for
- which the intervals should be calculated. Defaults to the grouping
- factor.}
- \item{ordered}{Logical; see \code{\link{TukeyHSD}}.}
- \item{conf.level}{A numeric value between zero and one giving the
- family-wise confidence level to use.}
- \item{\ldots}{Additional arguments passed to \code{\link{TukeyHSD}}.}
-}
-\details{
- This is a simple wrapper to \code{\link{TukeyHSD.aov}}. The user is
- directed to read the help file for \code{\link{TukeyHSD}} before using
- this function.
-
- In particular, note the statement about using the function with
- unbalanced designs.
-}
-\author{
- Gavin L. Simpson
-}
-\seealso{
- \code{\link{betadisper}}, \code{\link{permutest.betadisper}},
- \code{\link{aov}}. The fitting function itself is
- \code{\link{TukeyHSD}}.
-}
-\examples{
-## continue the example from ?betadisper
-example(betadisper)
-
-mod.hsd <- TukeyHSD(mod)
-plot(mod.hsd)
-
-}
-\keyword{models}
-\keyword{design}
\ No newline at end of file
Modified: pkg/man/betadisper.Rd
===================================================================
--- pkg/man/betadisper.Rd 2008-03-25 15:58:32 UTC (rev 286)
+++ pkg/man/betadisper.Rd 2008-03-25 16:34:33 UTC (rev 287)
@@ -5,6 +5,8 @@
\alias{plot.betadisper}
\alias{boxplot.betadisper}
\alias{print.betadisper}
+\alias{TukeyHSD.betadisper}
+
\title{Multivariate homogeneity of groups dispersions (variances)}
\description{
Implements Marti Anderson's PERMDISP2 procedure for the analysis of
@@ -13,7 +15,14 @@
homogeneity of variances. Non-euclidean distances between objects and
group centroids are handled by reducing the original distances to
principal coordinates. This procedure has latterly been used as a
- means of assessing beta diversity.
+ means of assessing beta diversity. There are \code{anova},
+ \code{scores}, \code{plot} and \code{boxplot} methods.
+
+ \code{TukeyHSD.betadisper} creates a set of confidence intervals on
+ the differences between the mean distance-to-centroid of the levels of
+ the grouping factor with the specified family-wise probability of
+ coverage. The intervals are based on the Studentized range statistic,
+ Tukey's 'Honest Significant Difference' method.
}
\usage{
betadisper(d, group, type = c("centroid", "median"))
@@ -27,6 +36,9 @@
ylab, xlab, main, sub, \dots)
\method{boxplot}{betadisper}(x, ylab = "Distance to centroid", ...)
+
+\method{TukeyHSD}{betadisper}(x, which = "group", ordered = FALSE,
+ conf.level = 0.95, \ldots)
}
\arguments{
@@ -46,7 +58,14 @@
\item{hull}{logical; should the convex hull for each group be plotted?}
\item{cex, ylab, xlab, main, sub}{graphical parameters. For details,
see \code{\link{plot.default}}.}
- \item{\dots}{arguments, including graphical parameters, passed to
+ \item{which}{A character vector listing terms in the fitted model for
+ which the intervals should be calculated. Defaults to the grouping
+ factor.}
+ \item{ordered}{Logical; see \code{\link{TukeyHSD}}.}
+ \item{conf.level}{A numeric value between zero and one giving the
+ family-wise confidence level to use.}
+ \item{\dots}{arguments, including graphical parameters (for
+ \code{plot.betadisper} and \code{boxplot.betadisper}), passed to
other methods.}
}
\details{
@@ -84,7 +103,11 @@
using \code{\link{permutest.betadisper}}. An alternative to the classical
comparison of group dispersions, is to calculate Tukey's Honest
Significant Differences between groups, via
- \code{\link{TukeyHSD.betadisper}}.
+ \code{TukeyHSD.betadisper}. This is a simple wrapper to
+ \code{\link{TukeyHSD.aov}}. The user is directed to read the help file
+ for \code{\link{TukeyHSD}} before using this function. In particular,
+ note the statement about using the function with
+ unbalanced designs.
The results of the analysis can be visualised using the \code{plot}
and \code{boxplot} methods.
@@ -108,6 +131,9 @@
The \code{boxplot} function invisibly returns a list whose components
are documented in \code{\link[graphics]{boxplot}}.
+ \code{TukeyHSD.betadisper} returns a list. See \code{\link{TukeyHSD}}
+ for further details.
+
\code{betadisper} returns a list of class \code{"betadisper"} with the
following components:
@@ -134,7 +160,7 @@
\author{Gavin L. Simpson}
\seealso{\code{\link{permutest.betadisper}}, \code{\link[stats]{anova.lm}},
\code{\link{scores}}, \code{\link[graphics]{boxplot}},
- \code{\link{TukeyHSD.betadisper}}. Further measure of beta diversity
+ \code{\link{TukeyHSD}}. Further measure of beta diversity
can be found in \code{\link{betadiver}}.}
\examples{
data(varespec)
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