Hi everyone, I think I have found a minor issue with the R function "boxplot.stats". But before I make such a rash comment, I'd like to check my facts by fixing what I think is the problem. However, why I try to do this, R does not behave as I expect. Can you tell me what I'm doing wrong? If I use the command: debug(boxplot.stats) I am allowed to step through the code as normal. I then want to edit the function, so I type: boxplot.stats <- edit(boxplot.stats) and I make my changes. I can check my changes have been made by typing: boxplot.stats and the updated version appears on screen. But now when I come to test my changes, the "debug" functionality has just up and disappeared; I can no longer step though the function as normal. Further to that, it appears that the change has somehow not been registered, as exactly the same error occurs---although I cannot be sure that it is occurring inside boxplot.stats. Does anyone have any tips, suggestions or comments? I'd love to be able to fix this. (For what it's worth I wish to change line 14 of boxplot.stats so that it reads "if (any(out[nna],na.rm=TRUE))".) Thank you for your thoughts, Matthew
The edit operations does not change the boxplot.stats that you
are debugging. It creates a new boxplot.stats (i.e. now there
are two) and the new one does not have debugging turned on.
Try
getAnywhere("boxplot.stats")
and it finds two. If you remove the one you just created using rm debugging
reappears since you are now accessing the original one for which
debugging is still on. If you like you can turn debugging on in the
new one.
On 10/27/06, Matthew Walker <m.g.walker at massey.ac.nz>
wrote:> Hi everyone,
>
> I think I have found a minor issue with the R function
"boxplot.stats".
> But before I make such a rash comment, I'd like to check my facts by
> fixing what I think is the problem. However, why I try to do this, R
> does not behave as I expect. Can you tell me what I'm doing wrong?
>
> If I use the command:
> debug(boxplot.stats)
> I am allowed to step through the code as normal.
>
> I then want to edit the function, so I type:
> boxplot.stats <- edit(boxplot.stats)
> and I make my changes.
>
> I can check my changes have been made by typing:
> boxplot.stats
> and the updated version appears on screen.
>
> But now when I come to test my changes, the "debug" functionality
has
> just up and disappeared; I can no longer step though the function as
> normal. Further to that, it appears that the change has somehow not
> been registered, as exactly the same error occurs---although I cannot be
> sure that it is occurring inside boxplot.stats.
>
> Does anyone have any tips, suggestions or comments? I'd love to be
able
> to fix this.
>
> (For what it's worth I wish to change line 14 of boxplot.stats so that
> it reads "if (any(out[nna],na.rm=TRUE))".)
>
>
> Thank you for your thoughts,
>
> Matthew
>
> ______________________________________________
> R-help at stat.math.ethz.ch 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.
>
On 10/27/2006 11:06 PM, Matthew Walker wrote:> Hi everyone, > > I think I have found a minor issue with the R function "boxplot.stats". > But before I make such a rash comment, I'd like to check my facts by > fixing what I think is the problem. However, why I try to do this, R > does not behave as I expect. Can you tell me what I'm doing wrong? > > If I use the command: > debug(boxplot.stats) > I am allowed to step through the code as normal. > > I then want to edit the function, so I type: > boxplot.stats <- edit(boxplot.stats) > and I make my changes. > > I can check my changes have been made by typing: > boxplot.stats > and the updated version appears on screen. > > But now when I come to test my changes, the "debug" functionality has > just up and disappeared; I can no longer step though the function as > normal. Further to that, it appears that the change has somehow not > been registered, as exactly the same error occurs---although I cannot be > sure that it is occurring inside boxplot.stats. > > Does anyone have any tips, suggestions or comments? I'd love to be able > to fix this. > > (For what it's worth I wish to change line 14 of boxplot.stats so that > it reads "if (any(out[nna],na.rm=TRUE))".)Besides what Gabor said, an issue here is that boxplot.stats lives in the grDevices namespace. If you call boxplot(), it will look there before it sees your locally modified copy. For testing, you can call boxplot.stats directly from the console, or also make a local copy of boxplot. Not sure why boxplot.stats is in grDevices rather than graphics, but that's not really relevant to your problems. Duncan Murdoch
Hi Martin, Sorry, I did intend to put some examples in but must have forgotten. This example is easy to understand: boxplot(c(1,Inf,Inf,Inf,Inf)) has lower bound: 1, lower quartile: Inf, median: Inf, upper quartile: Inf, upper bound: Inf. The command currently errors with the obscure message "Error in if (any(out[nna])) stats[c(1, 5)] <- range(x[!out], na.rm TRUE) : missing value where TRUE/FALSE needed" In this case I think boxplot should draw a (lower) whisker at 1 and nothing else. If my alteration is made, boxplot draws just that. The argument against this change is that the "range" argument (see ?boxplot) isn't able to be considered (but what is the value of the inter-quartile range anyway? Inf - Inf = NaN.) The smallest example to demonstrate this issue is: boxplot(c(1,Inf,Inf)) I hope that's helpful! Cheers, Matthew On Mon, 2006-10-30 at 15:53 +0100, Martin Maechler wrote:> Hi Matthew, > > I'm considering to apply your proposed change to the R sources > of boxplot.stats(). > > However, I'd like to see "interesting" examples where the new > and old version exhibit differences. > Since you've now spent so much time on this, > you will have a reproducible-code small example, will you? > > Thanks in advance! > Martin > > Martin <Maechler at stat.math.ethz.ch> http://stat.ethz.ch/people/maechler > Seminar f?r Statistik, ETH Z?rich LEO C16 Leonhardstr. 27 > CH-8092 Zurich, SWITZERLAND > phone: +41-44-632-3408 fax: ...-1228 <>< > > > >>>>> "Matthew" == Matthew Walker <m.g.walker at massey.ac.nz> > >>>>> on Mon, 30 Oct 2006 19:32:25 +1300 writes: > > Matthew> On Sun, 2006-10-29 at 20:18 -0500, Duncan Murdoch > Matthew> wrote: > >> If you're sure your change is a good idea then post a > >> patch here along with an explanation of why it's so good: > >> and it might make it into the next release. > > Matthew> Thank you to both Duncan and Gabor, your help was > Matthew> really appreciated. > > Matthew> My 10 character alteration did what I hoped it > Matthew> would. So I'd like to offer it to you or whoever > Matthew> else might be interested. > > Matthew> Boxplot does it's job well, it even mostly "works" > Matthew> with infinite values by not plotting certain lines. > Matthew> For example, if the upper bound is infinite, the > Matthew> upper whisker isn't plotted. > > Matthew> However boxplot doesn't work if the upper bound, > Matthew> upper quartile, median, and lower quartile are all > Matthew> infinite. Although there is sufficient data to > Matthew> plot a lower bound, boxplot.stats errors instead. > Matthew> This error also occurs when the lower bound through > Matthew> to the upper quartile are negative infinity. > > Matthew> This is not tricky to fix. All that needs to > Matthew> change is line 14 of boxplot.stats. It currently > Matthew> reads: "if (any(out[nna]))" Changing it to: "if > Matthew> (any(out[nna],na.rm=TRUE))" fixes these issues. > > Matthew> Cheers, > > Matthew> Matthew > > Matthew> ______________________________________________ > Matthew> R-help at stat.math.ethz.ch mailing list > Matthew> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE > Matthew> do read the posting guide > Matthew> http://www.R-project.org/posting-guide.html and > Matthew> provide commented, minimal, self-contained, > Matthew> reproducible code. >