Error bars in plots

A common irritation in making plots with R is the difficulty one has with superimposing error bars, or more precise, confidence intervals (c.i.'s) on plots. It can be actually quite simple to do, although you keep forgetting how if you don't often use it (like I do). It is most convenient to define the function superpose.eb which accepts the x and y coordinates of the points around which the confidence intervals should be marked, and a lower bound and upper bound which indicate how much lower/higher than y the lower/higher extreme of the c.i. reaches. By default a symmetric c.i. is assumed, so that the upper bound parameter is optional:

superpose.eb <-
function (x, y, ebl, ebu = ebl, length = 0.08, ...)
    arrows(x, y + ebu, x, y - ebl, angle = 90, code = 3,
    length = length, ...)

Its use is demonstrated in a barplot example (the RT data were kindly provided by Mariëtte Huizinga):

RT = matrix(c(814, 967, 500, 574, 424, 472, 394, 446), 2, 4) # data
colnames(RT) = c("7", "11", "15", "21")
rownames(RT) = c("repetition", "alternation")
eblb = matrix(c(14,21,12,18,12,18,13,19),2,4) # 1.96 * s.d. of data

x.abscis <- barplot(RT, beside=TRUE, col=0:1, ylim=c(0,1200),
    main="RT as a function of Age with 95%-confidance bars",
    xlab="Age (yrs)")
superpose.eb(x.abscis, RT, eblb, col="orange", lwd=2)

The function barplot returns the abscissa at which the bars are plotted, and these are used as the x coordinates passed to superpose.eb. The result lookes like this:

Farrel Buchinsky said... How does your function definition compare to the built in function, "errbar"

The function errbar is not realy built-in; its a function from the Hmisc package... I don't know all the differences, but one difference appears to be that in errbar you always have to fully compute the confidence interval by yourself, as in set.seed(1)
x <- 1:10
y <- x + rnorm(10)
delta <- runif(10)
errbar( x, y, y + delta, y - delta ) # you have to add and subtract delta from y by yourself
while superpose.eb can be called providing only means and associated s.d.'s (for asymptotic 68% c.i.'s), which is more intuitive for the people that ask me "how-to?" things like this (they apparently find it hard to think about how to calculate the locations for the lines to be drawn -- don't ask me why!). A more important difference is that errbar generates a plot if you do not set the add=TRUE parameter. Furthermore, superpose.eb has much much much less code than errbar (even if you would strip the optional plotting). Last but not least: setting col="orange" actually works in superpose.eb, as opposed to errbar.