PR #7690 points out that if the confidence intervals (+/-1.58
IQR/sqrt(n)) in a boxplot with notch=TRUE are larger than the
hinges -- which is most likely to happen for small n and asymmetric
distributions -- the resulting plot is ugly, e.g.:
set.seed(1001)
npts <- 5
X <- rnorm(2*npts,rep(3:4,each=npts),sd=1)
f <- factor(rep(1:2,each=npts))
boxplot(X~f)
boxplot(X~f,notch=TRUE)
I can imagine debate about what should be done in this case --
you could just say "don't do that", since the notches are based
on an asymptotic argument ... the diff below just truncates
the notches to the hinges, but produces a warning saying that the
notches have been truncated.
?? what should the behavior be ??
the diff is against the 11 Jan version of R 2.3.0
*** newboxplot.R 2006-01-23 14:32:12.000000000 -0500
--- oldboxplot.R 2006-01-23 14:29:29.000000000 -0500
***************
*** 84,98 ****
bplt <- function(x, wid, stats, out, conf, notch, xlog, i)
{
## Draw single box plot
- conf.ok <- TRUE
- if(!any(is.na(stats))) {
- ## check for overlap of notches and hinges
- if (notch && (stats[2]>conf[1] || stats[4]<conf[2])) {
- conf.ok <- FALSE
- conf[1] <- max(conf[1],stats[2])
- conf[2] <- min(conf[2],stats[4])
- }
## stats = +/- Inf: polygon & segments should handle
## Compute 'x + w' -- "correctly" in log-coord. case:
--- 84,91 ----
bplt <- function(x, wid, stats, out, conf, notch, xlog, i)
{
## Draw single box plot
+ if(!any(is.na(stats))) {
## stats = +/- Inf: polygon & segments should handle
## Compute 'x + w' -- "correctly" in log-coord. case:
***************
*** 148,154 ****
domain = NA)
}
}
- return(conf.ok)
} ## bplt
if(!is.list(z) || 0 == (n <- length(z$n)))
--- 141,146 ----
***************
*** 239,252 ****
xysegments <- segments
}
- conf.ok <- numeric(n)
for(i in 1:n)
! conf.ok[i] <- bplt(at[i], wid=width[i],
stats= z$stats[,i],
out = z$out[z$group==i],
conf = z$conf[,i],
notch= notch, xlog = xlog, i = i)
! if (any(!conf.ok)) warning("some confidence limits > hinges:
notches truncated")
axes <- is.null(pars$axes)
if(!axes) { axes <- pars$axes; pars$axes <- NULL }
if(axes) {
--- 231,243 ----
xysegments <- segments
}
for(i in 1:n)
! bplt(at[i], wid=width[i],
stats= z$stats[,i],
out = z$out[z$group==i],
conf = z$conf[,i],
notch= notch, xlog = xlog, i = i)
!
axes <- is.null(pars$axes)
if(!axes) { axes <- pars$axes; pars$axes <- NULL }
if(axes) {
--
620B Bartram Hall [EMAIL PROTECTED]
Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker
Box 118525 (ph) 352-392-5697
Gainesville, FL 32611-8525 (fax) 352-392-3704
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