Plot Group Means and Confidence Intervals

Plot group means and confidence intervals.

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

Gregory R. Warnes greg@warnes.net

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")
            )
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
#> Warning: zero-length arrow is of indeterminate angle and so skipped
  abline(v=c(6.5, 12.5, 18.5), lty=2)

Plot Group Means and Confidence Intervals

Arguments

Author

See also

Examples