Hmm. Interesting point, Bert. I don't know whether the notches show the 95% confidence interval or the median, or the 95% confidence interval that two non-overlapping notches have different medians. You're saying it's the latter? Anyone know what the 95% confidence interval of the median would be?
Cheers, Shaun > 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. On 5 July 2013 11:48, Bert Gunter <gunter.ber...@gene.com> wrote: > 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 <dwinsem...@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 <djmu...@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 <sjack...@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 >>>>> >>>>> ______________________________________________ >>>>> R-help@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> >> 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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
