This is not an R question. Read the references. Bert
Sent from my iPhone -- please excuse typos. On Jul 5, 2013, at 12:15 PM, Shaun Jackman <sjack...@gmail.com> wrote: > 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.
