R help - Apr 2008 - Choice of notch size in R

Is there a way to modify the choice of notch size [1] in R's boxplot  
routine from outlining a 5% significance region, to say 1% or lower?

Thanks,
Alex

[1] McGill, Tukey, and Larsen. "Variations of Box Plots", The American
Statistician, Vol. 32, No. 1, 12-16.

Alex Reynolds wrote:
> Is there a way to modify the choice of notch size [1] in R's boxplot  
> routine from outlining a 5% significance region, to say 1% or lower?
>   
Not easily. If you look inside boxplots.stats you'll find the hardcoded 
constant 1.58, and the documentation has the following text:

     The notches (if requested) extend to '+/-1.58 IQR/sqrt(n)'. This
     seems to be based on 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.

Judging from the wording, either the theory is unclear, or the author of 
the help page was not up to speed. My bets are on the former, but as 
things stand, the best way forward is to reproduce the calculations 
leading up to 1.58 and substitute 0.05 by 0.01 in the appropriate
place.
> Thanks,
> Alex
>
> [1] McGill, Tukey, and Larsen. "Variations of Box Plots", The
American
> Statistician, Vol. 32, No. 1, 12-16.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
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>   

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Alex Reynolds <reynolda <at> u.washington.edu> writes:
 
> Is there a way to modify the choice of notch size [1] in R's boxplot  
> routine from outlining a 5% significance region, to say 1% or lower?
Not directly from boxplot, because it is hardwired to indirectly call fivenum,
not quantile. 

Check bxp instead, which is the workhorse for boxplot and is more flexible in
the parameters passed.

Dieter

> Is there a way to modify the choice of notch size [1] in R's boxplot 
> routine from outlining a 5% significance region, to say 1% or lower?
Yes, but it's not as simple as specifying the significance level. 
You'll
have to update the function boxplot.stats, specifically the line
conf <- if (do.conf)  stats[3] + c(-1.58, 1.58) * iqr/sqrt(n)

Then you either need to modify boxplot to find your version of 
boxplot.stats, or call bxp (the low-level plotting function that boxplot 
calls) directly.

Regards,
Richie.

Mathematical Sciences Unit
HSL


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