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\name{plotmeans}
\alias{plotmeans}
\title{Plot Group Means and Confidence Intervals}
\description{Plot group means and confidence intervals.}
\usage{
plotmeans(formula, data=NULL, subset, na.action,
bars=TRUE, p=0.95, minsd=0, minbar, maxbar,
xlab=names(mf)[2], ylab=names(mf)[1], mean.labels=FALSE,
ci.label=FALSE, n.label=TRUE, text.n.label="n=",
digits=getOption("digits"), col="black", barwidth=1,
barcol="blue", connect=TRUE, ccol=
col, legends=names(means), xaxt, use.t=TRUE,
lwd=par("lwd"), ...)
}
\arguments{
\item{formula}{symbolic expression specifying the outcome (continuous)
and grouping variable (factor). See lm() for details.}
\item{data}{optional data frame containing the variables in the model.}
\item{subset}{an optional vector specifying a subset of observations to be
used in the fitting process.}
\item{na.action}{a function which indicates what should happen when the data
contain `NA's. See lm() for details. }
\item{bars}{a logical value indicating whether confidence interval
bars should be plotted. Defaults to TRUE.}
\item{p}{confidence level for error bars. Defaults to 0.95.}
\item{minsd}{minumum permitted value for the standard deviation within
each factor level. Any standard deviation estimates smaller than
\code{minsd} will be replaced with \code{minsd}. Defaults to 0.}
\item{minbar}{minumum allowed value for bar ends. If specified,
values smaller than \code{minbar} will be replaced with
\code{minbar}. }
\item{maxbar}{maximum allowed value for bar ends. If specified,
values larger than \code{maxbar} will be replaced with
\code{maxbar}. }
\item{xlab}{x-axis label.}
\item{ylab}{y-axis label.}
\item{mean.labels}{ either a logical value indicating whether the circles
representing the group means should be replaced with text giving the
actual mean values or a vector containing labels to use
instead. Defaults to FALSE.}
\item{ci.label}{ a logical value indicating whether text giving the
actual interval end values should be placed at the end of each
confidence interval bar. Defaults to FALSE.}
\item{n.label}{ a logical value indicating whether text giving the number of
observations in each group should should be added to the plot. }
\item{text.n.label}{Prefix text for labeling observation counts.
Defaults to "n=". }
\item{digits}{ number of significant digits to use when displaying
mean or confidince limit values.}
\item{col}{ color of cicles marking group means. Default is "black".}
\item{barwidth}{ linewidth of interval bars and end marks. Default is
1.}
\item{barcol}{ color of interval bars and end marks. Default is
"blue".}
\item{connect}{ either a logical value indicating whether the means of
each group should be connected by a line, or a list of vectors giving the
index of bars that should be connected by a line. Defaults to TRUE.}
\item{ccol}{ color of lines used to connect means. Defaults to the
same color as "col".}
\item{legends}{ vector containing strings used to label groups along
the x axis. Defaults to group names.}
\item{xaxt}{A character which specifies the axis type. Specifying `"n"'
causes an axis to be set up, but not plotted.}
\item{use.t}{ a logical value indicating whether the t distribution
should be used to compute confidence intervals. If \code{TRUE}, the
default, a t distribution will the correct number of degrees of
freedom for each group be used. If \code{FALSE}, the a normal
distribution will be used.}
\item{lwd}{Width of connecting lines }
\item{\dots}{ optional plotting parameters. }
}
%\details{
%
%
%}
\examples{
# library(gplots)
# show comparison with boxplot
data(state)
plotmeans(state.area ~ state.region)
# show some color and mean labels
plotmeans(state.area ~ state.region,
mean.labels=TRUE, digits=-3,
col="red", connect=FALSE)
# show how to specify which means should be connected
plotmeans(state.area ~ state.region, connect=list(1:2, 3:4),
ccol="red", pch=7 )
# more complicated example showing how to show an interaction
data(esoph)
par(las=2, # use perpendicular axis labels
mar=c(10.1,4.1,4.1,2.1), # create enough space for long x labels
mgp=c(8,1,0) # move x axis legend down to avoid overlap
)
plotmeans(ncases/ncontrols ~ interaction(agegp , alcgp, sep =" "),
connect=list(1:6,7:12,13:18,19:24),
barwidth=2,
col="dark green",
data=esoph,
xlab="Age Group and Alcohol Consumption",
ylab="# Cases / # Controls",
ylim = c(-.9,1.4),
main=c("Fraction of Cases for by Age and Alcohol Consumption",
"Ile-et-Vilaine Esophageal Cancer Study")
)
abline(v=c(6.5, 12.5, 18.5), lty=2)
}
\author{Gregory R. Warnes \email{greg@warnes.net}}
\seealso{\code{\link{plotCI}}, \code{\link{boxplot}}}
\keyword{hplot}
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