\HeaderA{boxplot}{Box Plots}{boxplot}
\methaliasA{boxplot.default}{boxplot}{boxplot.default}
\methaliasA{boxplot.formula}{boxplot}{boxplot.formula}
\keyword{hplot}{boxplot}
\begin{Description}\relax
Produce box-and-whisker plot(s) of the given (grouped) values.
\end{Description}
\begin{Usage}
\begin{verbatim}
boxplot(x, ...)

## S3 method for class 'formula':
boxplot(formula, data = NULL, ..., subset, na.action = NULL)

## Default S3 method:
boxplot(x, ..., range = 1.5, width = NULL, varwidth = FALSE,
        notch = FALSE, outline = TRUE, names, plot = TRUE,
        border = par("fg"), col = NULL, log = "",
        pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5),
        horizontal = FALSE, add = FALSE, at = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{formula}] a formula, such as \code{y \textasciitilde{} grp}, where \code{y} is a
numeric vector of data values to be split into groups according to
the grouping variable \code{grp} (usually a factor).
\item[\code{data}] a data.frame (or list) from which the variables in
\code{formula} should be taken.
\item[\code{subset}] an optional vector specifying a subset of observations
to be used for plotting.
\item[\code{na.action}] a function which indicates what should happen
when the data contain \code{NA}s.  The default is to ignore missing
values in either the response or the group.
\item[\code{x}] for specifying data from which the boxplots are to be
produced. Either a numeric vector, or a single list containing such
vectors. Additional unnamed arguments specify further data
as separate vectors (each corresponding to a component boxplot).
\code{\LinkA{NA}{NA}}s are allowed in the data.
\item[\code{...}] For the \code{formula} method, named arguments to be passed to
the default method.

For the default method, unnamed arguments are additional data
vectors (unless \code{x} is a list when they are ignored),
and named arguments are arguments and graphical parameters to be
passed to \code{\LinkA{bxp}{bxp}} in addition to the ones
given by argument \code{pars} (and override those in \code{pars}).

\item[\code{range}] this determines how far the plot whiskers extend out
from the box.  If \code{range} is positive, the whiskers extend
to the most extreme data point which is no more than
\code{range} times the interquartile range from the box. A value
of zero causes the whiskers to extend to the data extremes.
\item[\code{width}] a vector giving the relative widths of the boxes making
up the plot.
\item[\code{varwidth}] if \code{varwidth} is \code{TRUE}, the boxes are
drawn with widths proportional to the square-roots of the number
of observations in the groups.
\item[\code{notch}] if \code{notch} is \code{TRUE}, a notch is drawn in
each side of the boxes.  If the notches of two plots do not
overlap this is \sQuote{strong evidence} that the two medians differ
(Chambers \emph{et al.}, 1983, p. 62).  See \code{\LinkA{boxplot.stats}{boxplot.stats}}
for the calculations used.
\item[\code{outline}] if \code{outline} is not true, the outliers are
not drawn (as points whereas S+ uses lines).
\item[\code{names}] group labels which will be printed under each boxplot.
Can be a character vector or an \LinkA{expression}{expression} (see
\LinkA{plotmath}{plotmath}).
\item[\code{boxwex}] a scale factor to be applied to all boxes.  When there
are only a few groups, the appearance of the plot can be improved
by making the boxes narrower.
\item[\code{staplewex}] staple line width expansion, proportional to box
width.
\item[\code{outwex}] outlier line width expansion, proportional to box
width.
\item[\code{plot}] if \code{TRUE} (the default) then a boxplot is
produced.  If not, the summaries which the boxplots are based on
are returned.
\item[\code{border}] an optional vector of colors for the outlines of the
boxplots.  The values in \code{border} are recycled if the
length of \code{border} is less than the number of plots.
\item[\code{col}] if \code{col} is non-null it is assumed to contain colors
to be used to colour the bodies of the box plots. By default they
are in the background colour.
\item[\code{log}] character indicating if x or y or both coordinates should
be plotted in log scale.
\item[\code{pars}] a list of (potentially many) more graphical parameters,
e.g., \code{boxwex} or \code{outpch}; these are passed to
\code{\LinkA{bxp}{bxp}} (if \code{plot} is true); for details, see there.
\item[\code{horizontal}] logical indicating if the boxplots should be
horizontal; default \code{FALSE} means vertical boxes.
\item[\code{add}] logical, if true \emph{add} boxplot to current plot.
\item[\code{at}] numeric vector giving the locations where the boxplots should
be drawn, particularly when \code{add = TRUE};
defaults to \code{1:n} where \code{n} is the number of boxes.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The generic function \code{boxplot} currently has a default method
(\code{boxplot.default}) and a formula interface (\code{boxplot.formula}).

If multiple groups are supplied either as multiple arguments or via a
formula, parallel boxplots will be plotted, in the order of the
arguments or the order of the levels of the factor (see
\code{\LinkA{factor}{factor}}).

Missing values are ignored when forming boxplots.
\end{Details}
\begin{Value}
List with the following components:
\begin{ldescription}
\item[\code{stats}] a matrix, each column contains the extreme of the lower
whisker, the lower hinge, the median, the upper hinge and the
extreme of the upper whisker for one group/plot.  If all the inputs
have the same class attribute, so will this component.
\item[\code{n}] a vector with the number of observations in each group.
\item[\code{conf}] a matrix where each column contains the lower and upper
extremes of the notch.
\item[\code{out}] the values of any data points which lie beyond the
extremes of the whiskers.
\item[\code{group}] a vector of the same length as \code{out} whose elements
indicate to which group the outlier belongs.
\item[\code{names}] a vector of names for the groups.
\end{ldescription}
\end{Value}
\begin{References}\relax
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
\emph{The New S Language}.
Wadsworth \& Brooks/Cole.

Chambers, J. M., Cleveland, W. S., Kleiner, B. and Tukey, P. A. (1983)
\emph{Graphical Methods for Data Analysis.}  Wadsworth \& Brooks/Cole.

Murrell, P. (2005) \emph{R Graphics}. Chapman \& Hall/CRC Press.

See also \code{\LinkA{boxplot.stats}{boxplot.stats}}.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{boxplot.stats}{boxplot.stats}} which does the computation,
\code{\LinkA{bxp}{bxp}} for the plotting and more examples;
and \code{\LinkA{stripchart}{stripchart}} for an alternative (with small data
sets).
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## boxplot on a formula:
boxplot(count ~ spray, data = InsectSprays, col = "lightgray")
# *add* notches (somewhat funny here):
boxplot(count ~ spray, data = InsectSprays,
        notch = TRUE, add = TRUE, col = "blue")

boxplot(decrease ~ treatment, data = OrchardSprays,
        log = "y", col = "bisque")

rb <- boxplot(decrease ~ treatment, data = OrchardSprays, col="bisque")
title("Comparing boxplot()s and non-robust mean +/- SD")

mn.t <- tapply(OrchardSprays$decrease, OrchardSprays$treatment, mean)
sd.t <- tapply(OrchardSprays$decrease, OrchardSprays$treatment, sd)
xi <- 0.3 + seq(rb$n)
points(xi, mn.t, col = "orange", pch = 18)
arrows(xi, mn.t - sd.t, xi, mn.t + sd.t,
       code = 3, col = "pink", angle = 75, length = .1)

## boxplot on a matrix:
mat <- cbind(Uni05 = (1:100)/21, Norm = rnorm(100),
             `5T` = rt(100, df = 5), Gam2 = rgamma(100, shape = 2))
boxplot(as.data.frame(mat),
        main = "boxplot(as.data.frame(mat), main = ...)")
par(las=1)# all axis labels horizontal
boxplot(as.data.frame(mat), main = "boxplot(*, horizontal = TRUE)",
        horizontal = TRUE)

## Using 'at = ' and adding boxplots -- example idea by Roger Bivand :

boxplot(len ~ dose, data = ToothGrowth,
        boxwex = 0.25, at = 1:3 - 0.2,
        subset = supp == "VC", col = "yellow",
        main = "Guinea Pigs' Tooth Growth",
        xlab = "Vitamin C dose mg",
        ylab = "tooth length",
        xlim = c(0.5, 3.5), ylim = c(0, 35), yaxs = "i")
boxplot(len ~ dose, data = ToothGrowth, add = TRUE,
        boxwex = 0.25, at = 1:3 + 0.2,
        subset = supp == "OJ", col = "orange")
legend(2, 9, c("Ascorbic acid", "Orange juice"),
       fill = c("yellow", "orange"))

## more examples in  help(bxp)
\end{ExampleCode}
\end{Examples}

