Dear r-helpers,
I have been bitten by a cryptic comment in the help page for xYplot().
Here is some code from Madeline Bauer, one of the authors, which is
essentailly the code on the help page for xYplot():
# This example uses the summarize function in Hmisc to
# compute the median and outer quartiles. The outer quartiles are
# displayed using "filled bands"
set.seed(111)
dfr <- expand.grid(month=1:12, year=c(1997,1998), reps=1:100)
month <- dfr$month; year <- dfr$year
y <- abs(month-6.5) + 2*runif(length(month)) + year-1997
s <- summarize(y, llist(month,year), smedian.hilow, conf.int=.5)
# filled bands: default fill = pastel colors matching solid colors
# in superpose.line (this works differently in R)
xYplot ( Cbind ( y, Lower, Upper ) ~ month, groups=year,
method="filled bands" , data=s, type="l")
The comment "this works differently in R" should be ammended to a
more explicit danger sign (otherwise users like myself might find
themselves wasting a great deal of time). There appear to be two
differences between S+ and R here: (1) the default colors of the
bands are not as expected (but they can be changed at will, so that's
not a serious problem); (2) I have not been able get rid of the
outline around the filled bands or change their colors to match the
fill.
I would have thought that ...
xYplot ( Cbind ( y, Lower, Upper ) ~ month, groups=year,
method="filled bands" , data=s, type="l", lwd.bands = 0,
lty.bands = 0, col.bands = 'white')
... would do the trick.
I even tried to fix the problem in the code of xYplot:
> panel.XYplot
function (x, y, subscripts, groups = NULL, type = if (is.function
(method) ||
...
if (method == "filled bands") {
if (.R.)
grid.polygon(x = c(x, rev(x)), y = c(lower, rev(upper)),
gp = gpar(fill = col.fill, col = col.bands,
lty = lty.bands, lwd = lwd.bands),
default.units = "native")
else polygon(x = c(x, rev(x)), y = c(lower, rev(upper)),
col = col.fill)
}
...
}
Obviously I don't know grid well enough to fix the problem. Help
would be much appreciated, as well as a more explicit warning on the
xYplot() help page.
There is, of course, the possibility that there's something wrong
with my version of R or my OS or my machine. In that case a
replication or non-replication of this problem on a different OS
might alert me to this.
R version 2.5.0 RC (2007-04-21 r41269)
i386-apple-darwin8.9.1
locale:
C
attached base packages:
[1] "grDevices" "datasets" "grid" "graphics" "stats" "utils"
[7] "methods" "base"
other attached packages:
coda lme4 Matrix car
cacheSweave stashR
"0.10-7" "0.9975-13" "0.9975-11" "1.2-1"
"0.3" "0.2-1"
filehash digest circular boot gmodels
multcompView
"0.9-4" "0.2.3" "0.3-6" "1.2-27"
"2.13.2" "0.1-0"
reshape vcd colorspace effects
Hmisc acepack
"0.7.2" "1.0-3" "0.95" "1.0-10" "3.3-1"
"1.3-2.2"
HH multcomp mvtnorm JGR
iplots JavaGD
"1.18-3" "0.991-9" "0.7-5" "1.4-15"
"1.0-7" "0.3-6"
MASS gridBase lattice latticeExtra
rJava xtable
"7.2-33" "0.4-3" "0.15-4" "0.1-6"
"0.4-15" "1.4-3"
Thanks,
Michael Kubovy
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