| % File src/library/stats/man/TukeyHSD.Rd |
| % Part of the R package, https://www.R-project.org |
| % Copyright 1995-2015 R Core Team |
| % Distributed under GPL 2 or later |
| |
| \name{TukeyHSD} |
| \alias{TukeyHSD} |
| %\alias{TukeyHSD.aov} |
| %\alias{print.TukeyHSD} |
| %\alias{plot.TukeyHSD} |
| \title{Compute Tukey Honest Significant Differences} |
| \description{ |
| Create a set of confidence intervals on the differences between the |
| means of the levels of a factor with the specified family-wise |
| probability of coverage. The intervals are based on the Studentized |
| range statistic, Tukey's \sQuote{Honest Significant Difference} |
| method. |
| } |
| \usage{ |
| TukeyHSD(x, which, ordered = FALSE, conf.level = 0.95, \dots) |
| } |
| \arguments{ |
| \item{x}{A fitted model object, usually an \code{\link{aov}} fit.} |
| \item{which}{A character vector listing terms in the fitted model for |
| which the intervals should be calculated. Defaults to all the |
| terms.} |
| \item{ordered}{A logical value indicating if the levels of the factor |
| should be ordered according to increasing average in the sample |
| before taking differences. If \code{ordered} is true then |
| the calculated differences in the means will all be positive. The |
| significant differences will be those for which the \code{lwr} end |
| point is positive.} |
| \item{conf.level}{A numeric value between zero and one giving the |
| family-wise confidence level to use.} |
| \item{\dots}{Optional additional arguments. None are used at present.} |
| } |
| \details{ |
| This is a generic function: the description here applies to the method |
| for fits of class \code{"aov"}. |
| |
| When comparing the means for the levels of a factor in an analysis of |
| variance, a simple comparison using t-tests will inflate the |
| probability of declaring a significant difference when it is not in |
| fact present. This because the intervals are calculated with a |
| given coverage probability for each interval but the interpretation of |
| the coverage is usually with respect to the entire family of |
| intervals. |
| |
| John Tukey introduced intervals based on the range of the |
| sample means rather than the individual differences. The intervals |
| returned by this function are based on this Studentized range |
| statistics. |
| |
| The intervals constructed in this way would only apply exactly to |
| balanced designs where there are the same number of observations made |
| at each level of the factor. This function incorporates an adjustment |
| for sample size that produces sensible intervals for mildly unbalanced |
| designs. |
| |
| If \code{which} specifies non-factor terms these will be dropped with |
| a warning: if no terms are left this is an error. |
| } |
| \value{ |
| A list of class \code{c("multicomp", "TukeyHSD")}, |
| with one component for each term requested in \code{which}. |
| Each component is a matrix with columns \code{diff} giving the |
| difference in the observed means, \code{lwr} giving the lower |
| end point of the interval, \code{upr} giving the upper end point |
| and \code{p adj} giving the p-value after adjustment for the multiple |
| comparisons. |
| |
| There are \code{print} and \code{plot} methods for class |
| \code{"TukeyHSD"}. The \code{plot} method does not accept |
| \code{xlab}, \code{ylab} or \code{main} arguments and creates its own |
| values for each plot. |
| } |
| \references{ |
| Miller, R. G. (1981) |
| \emph{Simultaneous Statistical Inference}. Springer. |
| |
| Yandell, B. S. (1997) |
| \emph{Practical Data Analysis for Designed Experiments}. |
| Chapman & Hall. |
| } |
| \author{ |
| Douglas Bates |
| } |
| \seealso{ |
| \code{\link{aov}}, \code{\link{qtukey}}, \code{\link{model.tables}}, |
| \code{\link[multcomp]{glht}} in package \CRANpkg{multcomp}. |
| } |
| \examples{ |
| require(graphics) |
| |
| summary(fm1 <- aov(breaks ~ wool + tension, data = warpbreaks)) |
| TukeyHSD(fm1, "tension", ordered = TRUE) |
| plot(TukeyHSD(fm1, "tension")) |
| } |
| \keyword{models} |
| \keyword{design} |