R help - Apr 2011 - Box plot with 5th and 95th percentiles instead of 1.5 * IQR: problems implementing an existing solution...

Hi all,

I'm just getting started with R and I would appreciate some help. I'm
having
trouble creating a boxplot with whiskers at the 95th and 5th percentiles
instead of at 1.5 * IQR. I have read the relevant documentation, and checked
existing mails on this topic. I found a small modification that should work
: https://stat.ethz.ch/pipermail/r-help/2001-November/016817.html and tried
to implement it.

Basically, it says to replace boxplot.stats with:

myboxplot.stats <-  function (x, coef = NULL, do.conf = TRUE, do.out TRUE)
{
  nna <- !is.na(x)
  n <- sum(nna)
  stats <- quantile(x, c(.05,.25,.5,.75,.95), na.rm = TRUE)
  iqr <- diff(stats[c(2, 4)])
  out <- x < stats[1] | x > stats[5]
  conf <- if (do.conf)
    stats[3] + c(-1.58, 1.58) * diff(stats[c(2, 4)])/sqrt(n)
  list(stats = stats, n = n, conf = conf, out = x[out & nna])
}

I entered the new function, and used fix(boxplot.default) to modify
boxplot.default so that it references myboxplot.stats instead of the
original boxplot.stats function.

If I now type boxplot.default, I can see that the code has been modified as
expected. However, I get the exact same result as before when I create a
boxplot - it shows the whiskers at 1.5 * IQR. You can test this out by
creating a boxplot from the iris dataset supplied with R using
boxplot(iris$Sepal.Length ~ iris$Species). You see that the boxplot is the
same before and after the fix.  Does anybody know why this occurs, and how I
can get around this issue?

Thanks,
-- 
Regards,
Paul


====================Contact Details
====================Paul Raftery, BEng(Hons) (Mech), Fulbright Fellow, PhD
http://www.paulraftery.com/
 <http://www.paulraftery.com/>
Postdoctoral Research Engineer
Informatics Research Unit for Sustainable Engineering (IRUSE)
http://www.iruse.ie/

Department of Civil Engineering,
National University of Ireland, Galway,
University Road,
Galway,
Ireland.

Landline: +353 91 49 3086
Mobile: +353 85 124 7947
Skype: praftery

	[[alternative HTML version deleted]]

Try
require(Hmisc)
?panel.bpplot

This implements extended box plots that can show a variety of quantiles.
Frank


Paul Raftery wrote:
> 
> Hi all,
> 
> I'm just getting started with R and I would appreciate some help.
I'm
> having
> trouble creating a boxplot with whiskers at the 95th and 5th percentiles
> instead of at 1.5 * IQR. I have read the relevant documentation, and
> checked
> existing mails on this topic. I found a small modification that should
> work
> : https://stat.ethz.ch/pipermail/r-help/2001-November/016817.html and
> tried
> to implement it.
> 
> Basically, it says to replace boxplot.stats with:
> 
> myboxplot.stats <-  function (x, coef = NULL, do.conf = TRUE, do.out
> TRUE)
> {
>   nna <- !is.na(x)
>   n <- sum(nna)
>   stats <- quantile(x, c(.05,.25,.5,.75,.95), na.rm = TRUE)
>   iqr <- diff(stats[c(2, 4)])
>   out <- x < stats[1] | x > stats[5]
>   conf <- if (do.conf)
>     stats[3] + c(-1.58, 1.58) * diff(stats[c(2, 4)])/sqrt(n)
>   list(stats = stats, n = n, conf = conf, out = x[out & nna])
> }
> 
> I entered the new function, and used fix(boxplot.default) to modify
> boxplot.default so that it references myboxplot.stats instead of the
> original boxplot.stats function.
> 
> If I now type boxplot.default, I can see that the code has been modified
> as
> expected. However, I get the exact same result as before when I create a
> boxplot - it shows the whiskers at 1.5 * IQR. You can test this out by
> creating a boxplot from the iris dataset supplied with R using
> boxplot(iris$Sepal.Length ~ iris$Species). You see that the boxplot is the
> same before and after the fix.  Does anybody know why this occurs, and how
> I
> can get around this issue?
> 
> Thanks,
> -- 
> Regards,
> Paul
> 
> 
> ====================> Contact Details
> ====================> Paul Raftery, BEng(Hons) (Mech), Fulbright Fellow,
PhD
> http://www.paulraftery.com/
>  &lt;http://www.paulraftery.com/&gt;
> Postdoctoral Research Engineer
> Informatics Research Unit for Sustainable Engineering (IRUSE)
> http://www.iruse.ie/
> 
> Department of Civil Engineering,
> National University of Ireland, Galway,
> University Road,
> Galway,
> Ireland.
> 
> Landline: +353 91 49 3086
> Mobile: +353 85 124 7947
> Skype: praftery
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> 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.
> 

-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
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On 17.04.2011 13:08, Paul Raftery wrote:
> Hi all,
>
> I'm just getting started with R and I would appreciate some help.
I'm having
> trouble creating a boxplot with whiskers at the 95th and 5th percentiles
> instead of at 1.5 * IQR. I have read the relevant documentation, and
checked
> existing mails on this topic. I found a small modification that should work
> : https://stat.ethz.ch/pipermail/r-help/2001-November/016817.html and tried
> to implement it.
>
> Basically, it says to replace boxplot.stats with:
>
> myboxplot.stats<-  function (x, coef = NULL, do.conf = TRUE, do.out >
TRUE)
> {
>    nna<- !is.na(x)
>    n<- sum(nna)
>    stats<- quantile(x, c(.05,.25,.5,.75,.95), na.rm = TRUE)
>    iqr<- diff(stats[c(2, 4)])
>    out<- x<  stats[1] | x>  stats[5]
>    conf<- if (do.conf)
>      stats[3] + c(-1.58, 1.58) * diff(stats[c(2, 4)])/sqrt(n)
>    list(stats = stats, n = n, conf = conf, out = x[out&  nna])
> }
>
> I entered the new function, and used fix(boxplot.default) to modify
> boxplot.default so that it references myboxplot.stats instead of the
> original boxplot.stats function.
>
> If I now type boxplot.default, I can see that the code has been modified as
> expected. However, I get the exact same result as before when I create a
> boxplot - it shows the whiskers at 1.5 * IQR. You can test this out by
> creating a boxplot from the iris dataset supplied with R using
> boxplot(iris$Sepal.Length ~ iris$Species). You see that the boxplot is the
> same before and after the fix.  Does anybody know why this occurs, and how
I
> can get around this issue?
Frank answered how to solve it using his functions. In order to do it 
your way, you need to change the boxplot.default function within its 
NAMESPACE, e.g. using fixInNamespace.

Otherwise you could also just call
   z <- boxplot(....)
then modify the relevant parts of the object z
and plot it using
   bxp(z)
afterwards.

Best,
Uwe




>
> Thanks,

Hello, 
you may just first change the boxplot.stats directly:

boxplot.stats <-  function (x, coef = NULL, do.conf = TRUE, do.out           
TRUE)
{
  nna <- !is.na(x)
  n <- sum(nna)
  stats <- quantile(x, c(.05,.25,.5,.75,.95), na.rm = TRUE)
  iqr <- diff(stats[c(2, 4)])
  out <- x < stats[1] | x > stats[5]
  conf <- if (do.conf)
    stats[3] + c(-1.58, 1.58) * diff(stats[c(2, 4)])/sqrt(n)
  list(stats = stats, n = n, conf = conf, out = x[out & nna])
} 


then use it plotting your data. 
And after that change them back :

boxplot.stats <- function (x, coef = 1.5, do.conf = TRUE, do.out = TRUE) 
{
  if (coef < 0) 
    stop("'coef' must not be negative")
  nna <- !is.na(x)
  n <- sum(nna)
  stats <- stats::fivenum(x, na.rm = TRUE)
  iqr <- diff(stats[c(2, 4)])
  if (coef == 0) 
    do.out <- FALSE
  else {
    out <- if (!is.na(iqr)) {
      x < (stats[2L] - coef * iqr) | x > (stats[4L] + coef * 
                                            iqr)
    }
    else !is.finite(x)
    if (any(out[nna], na.rm = TRUE)) 
      stats[c(1, 5)] <- range(x[!out], na.rm = TRUE)
  }
  conf <- if (do.conf) 
    stats[3L] + c(-1.58, 1.58) * iqr/sqrt(n)
  list(stats = stats, n = n, conf = conf, out = if (do.out) x[out & 
                                                                nna] else
numeric())
}


it works fine for me.





--
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