Lattice barchart with error bars

The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be based on the same calculations as the formula with 1.57 in Chambers et al. (1983, p. 62), given in McGill et al. (1978, p. 16). They are based on asymptotic normality of the median and roughly equal sample sizes for the two medians being compared, and are said to be rather insensitive to the underlying distributions of the samples. The idea appears to be to give roughly a 95% confidence interval for the difference in two medians.

Be careful!

You are talking about 2 different varieties of apples here. As I read
it, the CI's in the  cancer data, which I know is just for example
purposes, are CI's for the **individual means**; the notches in
boxplots are nonparametric and for 2 groups with roughly equal sample
sizes, "The idea appears to be to give roughly a 95% confidence
interval for the **difference** in two medians." (from
?boxplot.stats). So I'm not sure which you want, but they are
certainly different (by a factor of around sqrt(2),right?), even if
both are for the mean or both are for the median.

Cheers,
Bert

On Fri, Jul 5, 2013 at 11:28 AM, David Winsemius <dwinsemius at comcast.net> wrote:

On Jul 5, 2013, at 11:15 AM, Shaun Jackman wrote:

Hi Bert, Dennis,

I'll agree that using a barchart was a poor choice. I was in fact using a
notched bwplot to show the median and confidence interval of the median. In
this case it's the median and confidence interval that I want to highlight,
and I find that the visual noise of the box and whiskers is detracting from
the focus, and those wee notches are not much to focus on. So, I'd like to
draw a stripplot with error bars, preferably in Lattice. Let's call this a
TIE fighter plot. Any suggestions?

I like the TIE fighter label. Try this:

library(latticeExtra)
data(USCancerRates)
segplot(reorder(factor(county), rate.male) ~ LCL95.male + UCL95.male,
        data = subset(USCancerRates, state == "Washington"),
        draw.bands = FALSE, centers = rate.male,
        segments.fun = panel.arrows, ends = "both",
        angle = 90, length = 1, unit = "mm")

It's what Sarkar has recommended in the past when this request has been posted.

--
David

Cheers,
Shaun

On 4 July 2013 18:00, Dennis Murphy <djmuser at gmail.com> wrote:

If you consult the lattice package help, you'll discover there is no
panel_errorbar() function, which would imply the package developers
have a distaste for that type of graphic. If you fish around the
R-help archives, though, you might be able to find someone who wrote a
function to do error bars in lattice. (Use a searchable archive such
as Nabble to hunt for it.)

Error bar plots are easier to do in the ggplot2 package, since there
is a specific function to generate the error bar 'geometry'
(geom_errorbar). See http://docs.ggplot2.org/current/ for an expanded
version of the package help pages, which include the graphs generated
by the code. I believe there's also a base graphics version that you
can get from the gplots package, but I don't know a lot about it.

Dennis

On Thu, Jul 4, 2013 at 2:53 PM, Shaun Jackman <sjackman at gmail.com> wrote:

Hi,

I'd like to draw a lattice barchart of means with error bars to show
the standard deviation. I have the barchart, how do I add the error
bars?

require(datasets)
require(lattice)
x <- aggregate(weight ~ Diet, ChickWeight, function(x) c(mean=mean(x),
sd=sd(x)))
barchart(weight[,'mean'] ~ Diet, x)

Thanks,
Shaun

      [[alternative HTML version deleted]]

David Winsemius
Alameda, CA, USA

--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm