R help - Feb 2008 - Custom Plot - means, SD & 5th-95th% (Plotmeans or Boxplot)?

Any help with this problem would be greatly appreciated:

I need to produce a custom plot i haven't come across in R. Basically, I
want to show means, 1st standard deviation and 5th and 95th percentiles
visually, using something resembling a boxplot. Is it possible to completely
customize a boxplot so that it shows means as the bar (instead of, not as
well as medians), standard deviations at the hinges (instead of IQR) and 5th
& 95th percentiles at the brackets? The plotmeans function (ggplots) allows
means to be plotted, but it seems only with confidence intervals, not 5th
and 95th percentiles, and also without hinges (for standard deviations).
I've searched the forums and various books and have drawn a blank on this.
Thanks.

Steve

~~~~~~~~~~~~~~~~
Steve Worthington
Ph.D. Candidate
New York Consortium
in Evolutionary Primatology
-- 
View this message in context:
http://www.nabble.com/Custom-Plot---means%2C-SD---5th-95th--%28Plotmeans-or-Boxplot%29--tp15537706p15537706.html
Sent from the R help mailing list archive at Nabble.com.

It's fairly simple to set up something like this for ggplot2:

install.packages("ggplot2")
library(ggplot2)

library(ggplot2)

q5 <- function(data) {
 q <- function(p) unname(quantile(data$y, p))
 data.frame(min = q(0.05), max = q(0.95))
}

ggplot(diamonds, aes(x = cut, y = price)) +
stat_summary(fun="mean_sdl", geom="crossbar", mult=1) +
stat_summary(fun="q5", geom="linerange")

(see Hmisc::smean.sdl for more details on the first summary function).

Although from this example you can see that that choice of summary
statistics probably isn't the best.  You can read more about
stat_summary (and ggplot2 in general) at
http://had.co.nz/ggplot2/stat_summary.html.

Hadley

On 2/17/08, Stropharia <stevenworthington at hotmail.com>
wrote:
>
> Any help with this problem would be greatly appreciated:
>
> I need to produce a custom plot i haven't come across in R. Basically,
I
> want to show means, 1st standard deviation and 5th and 95th percentiles
> visually, using something resembling a boxplot. Is it possible to
completely
> customize a boxplot so that it shows means as the bar (instead of, not as
> well as medians), standard deviations at the hinges (instead of IQR) and
5th
> & 95th percentiles at the brackets? The plotmeans function (ggplots)
allows
> means to be plotted, but it seems only with confidence intervals, not 5th
> and 95th percentiles, and also without hinges (for standard deviations).
> I've searched the forums and various books and have drawn a blank on
this.
> Thanks.
>
> Steve
>
> ~~~~~~~~~~~~~~~~
> Steve Worthington
> Ph.D. Candidate
> New York Consortium
> in Evolutionary Primatology
> --
> View this message in context:
>
http://www.nabble.com/Custom-Plot---means%2C-SD---5th-95th--%28Plotmeans-or-Boxplot%29--tp15537706p15537706.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at 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.
>

-- 
http://had.co.nz/

Using builtin dataset stackloss try this:

f <- function(x) replace(quantile(x, c(5, 25, 50, 75, 95)/100), 3, mean(x))
bxp(list(stats = sapply(stackloss, f), n = stackloss, names = names(stackloss)))

and see ?bxp and ?boxplot

On Feb 17, 2008 9:17 PM, Stropharia <stevenworthington at hotmail.com>
wrote:
>
> Any help with this problem would be greatly appreciated:
>
> I need to produce a custom plot i haven't come across in R. Basically,
I
> want to show means, 1st standard deviation and 5th and 95th percentiles
> visually, using something resembling a boxplot. Is it possible to
completely
> customize a boxplot so that it shows means as the bar (instead of, not as
> well as medians), standard deviations at the hinges (instead of IQR) and
5th
> & 95th percentiles at the brackets? The plotmeans function (ggplots)
allows
> means to be plotted, but it seems only with confidence intervals, not 5th
> and 95th percentiles, and also without hinges (for standard deviations).
> I've searched the forums and various books and have drawn a blank on
this.
> Thanks.
>
> Steve
>
> ~~~~~~~~~~~~~~~~
> Steve Worthington
> Ph.D. Candidate
> New York Consortium
> in Evolutionary Primatology
> --
> View this message in context:
http://www.nabble.com/Custom-Plot---means%2C-SD---5th-95th--%28Plotmeans-or-Boxplot%29--tp15537706p15537706.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at 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.
>