R: Plot Group Means and Confidence Intervals

plotmeans {gplots} | R Documentation

## 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

`formula` | symbolic expression specifying the outcome (continuous) and grouping variable (factor). See lm() for details.
`data` | optional data frame containing the variables in the model.
`subset` | an optional vector specifying a subset of observations to be used in the fitting process.
`na.action` | a function which indicates what should happen when the data contain ‘NA’s. See lm() for details.
`bars` | a logical value indicating whether confidence interval bars should be plotted. Defaults to TRUE.
`p` | confidence level for error bars. Defaults to 0.95.
`minsd` | minumum permitted value for the standard deviation within each factor level. Any standard deviation estimates smaller than `minsd` will be replaced with `minsd`. Defaults to 0.
`minbar` | minumum allowed value for bar ends. If specified, values smaller than `minbar` will be replaced with `minbar`.
`maxbar` | maximum allowed value for bar ends. If specified, values larger than `maxbar` will be replaced with `maxbar`.
`xlab` | x-axis label.
`ylab` | y-axis label.
`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.
`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.
`n.label` | a logical value indicating whether text giving the number of observations in each group should should be added to the plot.
`text.n.label` | Prefix text for labeling observation counts. Defaults to "n=".
`digits` | number of significant digits to use when displaying mean or confidince limit values.
`col` | color of cicles marking group means. Default is "black".
`barwidth` | linewidth of interval bars and end marks. Default is 1.
`barcol` | color of interval bars and end marks. Default is "blue".
`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.
`ccol` | color of lines used to connect means. Defaults to the same color as "col".
`legends` | vector containing strings used to label groups along the x axis. Defaults to group names.
`xaxt` | A character which specifies the axis type. Specifying ‘"n"’ causes an axis to be set up, but not plotted.
`use.t` | a logical value indicating whether the t distribution should be used to compute confidence intervals. If `TRUE`, the default, a t distribution will the correct number of degrees of freedom for each group be used. If `FALSE`, the a normal distribution will be used.
`lwd` | Width of connecting lines
`...` | optional plotting parameters.

### Author(s)

Gregory R. Warnes greg@warnes.net

### See Also

`plotCI`, `boxplot`

### Examples

      # 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",
                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)

[Package gplots version 3.0.1 Index]