Re: [R] Debugging R's code: boxplot.stats
Duncan == Duncan Murdoch [EMAIL PROTECTED] on Sat, 28 Oct 2006 08:03:33 -0400 writes: [...] Duncan Not sure why boxplot.stats is in grDevices rather Duncan than graphics, but that's not really relevant to Duncan your problems. because it does computation for Graphics (capitalized on purpose) which should not at all be limited to old-style S graphics which is the topic of the graphics package. E.g. grid and grid-based graphics should use boxplot.stats (for consistency). For the same reason, color computations are in 'grDevices', [[and we have acknowledged a while ago that 'grDevices' has become a slight misnomer Martin Maechler __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
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 [EMAIL PROTECTED] http://stat.ethz.ch/people/maechler Seminar für Statistik, ETH Zürich LEO C16Leonhardstr. 27 CH-8092 Zurich, SWITZERLAND phone: +41-44-632-3408 fax: ...-1228 Matthew == Matthew Walker [EMAIL PROTECTED] 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@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. __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
Thank you Gabor for that explanation, I can now make a bit more sense of R's behaviour! When I edit boxplot.stats, a new version is copied to my local workspace. I have a few associated questions: 1. This has something to do with namespaces in R, and I know nothing about them. Can anyone point me to some online documentation that could step me through the important points? If that's not available (my searching failed to bring up anything) can anyone give me a quick list of functions that I could look up using help()? 2. This question follows on from question (1): given that I have two copies of boxplot.stats (in what I assume are different namespaces), how can I specify a specific one to the function debug()? 3. How can I edit the original version of boxplot.stats without creating a copy in my local workspace? 4. Is there a way that I can learn the status of the debug flag of a specific function? 5. Finally, the function traceback() lists the call-stack. How do I know which one of the two boxplot.stats functions was called? Thanks, Matthew On Fri, 2006-10-27 at 23:19 -0400, Gabor Grothendieck wrote: 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 [EMAIL PROTECTED] 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@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. __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On Sat, 2006-10-28 at 08:03 -0400, Duncan Murdoch wrote: 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 Duncan, Thanks for your reply. How do you know that (i) boxplot.stats lives in the grDevices namespace? and (ii) how do you know/change that boxplot will look in grDevices before it uses the local copy? I tried to do as you suggested and create a local copy of boxplot. I used the following commands: boxplot.stats - edit(boxplot.stats) # Made changes to line 14 boxplot - edit(boxplot) boxplot.default - edit(boxplot.default) # Added a call to cat() When I called boxplot() the local copy was executed (as I could see the output of my cat commands), however it appears that the local copy of boxplot.stats isn't the one being called from my version of boxplot. How do I fix this? Thanks again, Matthew __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On 10/29/2006 6:08 PM, Matthew Walker wrote: On Sat, 2006-10-28 at 08:03 -0400, Duncan Murdoch wrote: 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 Duncan, Thanks for your reply. How do you know that (i) boxplot.stats lives in the grDevices namespace? getAnywhere(boxplot.stats) starts out as getAnywhere(boxplot.stats) A single object matching 'boxplot.stats' was found It was found in the following places package:grDevices registered S3 method for boxplot from namespace grDevices namespace:grDevices and (ii) how do you know/change that boxplot will look in grDevices before it uses the local copy? That was actually a guess. But checking now: getAnywhere(boxplot) A single object matching 'boxplot' was found It was found in the following places package:graphics namespace:graphics with value function (x, ...) UseMethod(boxplot) environment: namespace:graphics so boxplot() is in the graphics package, and works in that namespace. The graphics namespace file starts out import(grDevices) so functions in that package will look in grDevices before they look elsewhere. I thought that meant that S3 methods would be found there before they're found anywhere else, but I didn't actually check this. So let's check: boxplot.stats - function(x, ...) stop(mine) x - 1 class(x) - stats boxplot(x) Error in boxplot.stats(x) : mine Whoops! Looks as though my local copy does get found first. Not sure if this is a bug... I tried to do as you suggested and create a local copy of boxplot. I used the following commands: boxplot.stats - edit(boxplot.stats) # Made changes to line 14 boxplot - edit(boxplot) boxplot.default - edit(boxplot.default) # Added a call to cat() When I called boxplot() the local copy was executed (as I could see the output of my cat commands), however it appears that the local copy of boxplot.stats isn't the one being called from my version of boxplot. How do I fix this? That's very strange. Which R version are you using? Are you sure the wrong version was being called? I was doing my tests in 2.4.0. Duncan Murdoch __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On 10/29/06, Matthew Walker [EMAIL PROTECTED] wrote: Thank you Gabor for that explanation, I can now make a bit more sense of R's behaviour! When I edit boxplot.stats, a new version is copied to my local workspace. I have a few associated questions: 1. This has something to do with namespaces in R, and I know nothing about them. Can anyone point me to some online documentation that could step me through the important points? If that's not available (my searching failed to bring up anything) can anyone give me a quick list of functions that I could look up using help()? Just issue the command: search() and you will get a list of environments through which R searches in the order ordered, at least if you typed the command into the console. Also see ?environment If the command was issued from a package with a namespace it normally will look there first or if its is a method of an S3 generic there is some info in ?UseMethod . In general, if f is called from g it will look at the functions defined in g, then the ones defined in g's lexical parent, i.e. the environment where g was defined not where it was called from, the grandparent and so on. 2. This question follows on from question (1): given that I have two copies of boxplot.stats (in what I assume are different namespaces), how can I specify a specific one to the function debug()? e.g. getAnywhere(boxplot.stats) # finds locations # choose a location debug(grDevices:::boxplot.stats) 3. How can I edit the original version of boxplot.stats without creating a copy in my local workspace? See ?assignInNamespace . Actually I think you are better off not to do that in the first place. Mucking around in the environments on the search path might get you into trouble. 4. Is there a way that I can learn the status of the debug flag of a specific function? Duncan posted code for that some time ago: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/27489.html 5. Finally, the function traceback() lists the call-stack. How do I know which one of the two boxplot.stats functions was called? I think you need to refer to the search list or your knowledge of how it works in other cases. Thanks, Matthew On Fri, 2006-10-27 at 23:19 -0400, Gabor Grothendieck wrote: 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 [EMAIL PROTECTED] 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, __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On 10/29/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 10/29/2006 6:08 PM, Matthew Walker wrote: On Sat, 2006-10-28 at 08:03 -0400, Duncan Murdoch wrote: 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 Duncan, Thanks for your reply. How do you know that (i) boxplot.stats lives in the grDevices namespace? getAnywhere(boxplot.stats) starts out as getAnywhere(boxplot.stats) A single object matching 'boxplot.stats' was found It was found in the following places package:grDevices registered S3 method for boxplot from namespace grDevices namespace:grDevices and (ii) how do you know/change that boxplot will look in grDevices before it uses the local copy? That was actually a guess. But checking now: getAnywhere(boxplot) A single object matching 'boxplot' was found It was found in the following places package:graphics namespace:graphics with value function (x, ...) UseMethod(boxplot) environment: namespace:graphics so boxplot() is in the graphics package, and works in that namespace. The graphics namespace file starts out import(grDevices) so functions in that package will look in grDevices before they look elsewhere. I thought that meant that S3 methods would be found there before they're found anywhere else, but I didn't actually check this. So let's check: boxplot.stats - function(x, ...) stop(mine) x - 1 class(x) - stats boxplot(x) Error in boxplot.stats(x) : mine Whoops! Looks as though my local copy does get found first. Not sure if this is a bug... I think UseMethod uses dynamic scoping whereas ordinary funtions use lexical scoping. From ?UseMethod Name spaces can register methods for generic functions. To support this, UseMethod and NextMethod search for methods in two places: first in the environment in which the generic function is called, and then in the registration data base for the environment in which the generic is defined (typically a name space). So methods for a generic function need to be available in the environment of the call to the generic, or they must be registered. (It does not matter whether they are visible in the environment in which the generic is defined.) __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On Sun, 2006-10-29 at 18:47 -0500, Duncan Murdoch wrote: [snip] Hi Duncan, Thanks for your reply. How do you know that (i) boxplot.stats lives in the grDevices namespace? getAnywhere(boxplot.stats) starts out as getAnywhere(boxplot.stats) A single object matching 'boxplot.stats' was found It was found in the following places package:grDevices registered S3 method for boxplot from namespace grDevices namespace:grDevices and (ii) how do you know/change that boxplot will look in grDevices before it uses the local copy? That was actually a guess. But checking now: getAnywhere(boxplot) A single object matching 'boxplot' was found It was found in the following places package:graphics namespace:graphics with value function (x, ...) UseMethod(boxplot) environment: namespace:graphics so boxplot() is in the graphics package, and works in that namespace. The graphics namespace file starts out import(grDevices) so functions in that package will look in grDevices before they look elsewhere. I thought that meant that S3 methods would be found there before they're found anywhere else, but I didn't actually check this. So let's check: boxplot.stats - function(x, ...) stop(mine) x - 1 class(x) - stats boxplot(x) Error in boxplot.stats(x) : mine Whoops! Looks as though my local copy does get found first. Not sure if this is a bug... That's an interesting way to check. If I enter boxplot.stats - function(x, ...) stop(mine) boxplot(1) I get a graph (i.e. no error) and so I concluded that the original boxplot is calling the original boxplot.stats. In other words, the original is ignoring my local copy. I tried to do as you suggested and create a local copy of boxplot. I used the following commands: boxplot.stats - edit(boxplot.stats) # Made changes to line 14 boxplot - edit(boxplot) boxplot.default - edit(boxplot.default) # Added a call to cat() When I called boxplot() the local copy was executed (as I could see the output of my cat commands), however it appears that the local copy of boxplot.stats isn't the one being called from my version of boxplot. How do I fix this? That's very strange. Which R version are you using? Are you sure the wrong version was being called? I was doing my tests in 2.4.0. I'm using 2.4.0 too (on Linux; sessionInfo() copied below) If I execute the following: boxplot.stats - function(x, ...) stop(mine) boxplot - edit(boxplot) # Added cat(local boxplot\n) boxplot.default - edit(boxplot.default) # Added cat(local boxplot.default\n) boxplot(1) I get a graph with the text local boxplot local boxplot.default Had boxplot.default called the local version of boxplot.stats, I would have expected the error mine. Is there a way I can avoid all this? Perhaps I can somehow edit the file that R loads when it reads the original boxplot.stats? Cheers, Matthew *** Output of sessionInfo(): *** R version 2.4.0 (2006-10-03) i686-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] methods stats graphics grDevices utils datasets [7] base __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On 10/29/06, Matthew Walker [EMAIL PROTECTED] wrote: On Sun, 2006-10-29 at 18:47 -0500, Duncan Murdoch wrote: [snip] Hi Duncan, Thanks for your reply. How do you know that (i) boxplot.stats lives in the grDevices namespace? getAnywhere(boxplot.stats) starts out as getAnywhere(boxplot.stats) A single object matching 'boxplot.stats' was found It was found in the following places package:grDevices registered S3 method for boxplot from namespace grDevices namespace:grDevices and (ii) how do you know/change that boxplot will look in grDevices before it uses the local copy? That was actually a guess. But checking now: getAnywhere(boxplot) A single object matching 'boxplot' was found It was found in the following places package:graphics namespace:graphics with value function (x, ...) UseMethod(boxplot) environment: namespace:graphics so boxplot() is in the graphics package, and works in that namespace. The graphics namespace file starts out import(grDevices) so functions in that package will look in grDevices before they look elsewhere. I thought that meant that S3 methods would be found there before they're found anywhere else, but I didn't actually check this. So let's check: boxplot.stats - function(x, ...) stop(mine) x - 1 class(x) - stats boxplot(x) Error in boxplot.stats(x) : mine Whoops! Looks as though my local copy does get found first. Not sure if this is a bug... That's an interesting way to check. If I enter boxplot.stats - function(x, ...) stop(mine) boxplot(1) I get a graph (i.e. no error) and so I concluded that the original boxplot is calling the original boxplot.stats. In other words, the original is ignoring my local copy. I tried to do as you suggested and create a local copy of boxplot. I used the following commands: boxplot.stats - edit(boxplot.stats) # Made changes to line 14 boxplot - edit(boxplot) boxplot.default - edit(boxplot.default) # Added a call to cat() When I called boxplot() the local copy was executed (as I could see the output of my cat commands), however it appears that the local copy of boxplot.stats isn't the one being called from my version of boxplot. How do I fix this? That's very strange. Which R version are you using? Are you sure the wrong version was being called? I was doing my tests in 2.4.0. I'm using 2.4.0 too (on Linux; sessionInfo() copied below) If I execute the following: boxplot.stats - function(x, ...) stop(mine) boxplot - edit(boxplot) # Added cat(local boxplot\n) boxplot.default - edit(boxplot.default) # Added cat(local boxplot.default\n) boxplot(1) I get a graph with the text local boxplot local boxplot.default Had boxplot.default called the local version of boxplot.stats, I would have expected the error mine. Is there a way I can avoid all this? Perhaps I can somehow edit the file that R loads when it reads the original boxplot.stats? Cheers, Matthew *** Output of sessionInfo(): *** R version 2.4.0 (2006-10-03) i686-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] methods stats graphics grDevices utils datasets [7] base The problem is that even though you have copied boxplot.default, its environment is still the graphics package so when boxplot.default looks for boxplot.stats it looks in the graphics package first so you need to reset the environment of boxplot.default like this: Type this into a fresh R session: environment(boxplot.default) - .GlobalEnv # this will also copy it boxplot.stats - edit(boxplot.stats) # add cat(boxplot.stats\n) boxplot(1:10) __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On 10/29/2006 8:01 PM, Matthew Walker wrote: On Sun, 2006-10-29 at 18:47 -0500, Duncan Murdoch wrote: [snip] Hi Duncan, Thanks for your reply. How do you know that (i) boxplot.stats lives in the grDevices namespace? getAnywhere(boxplot.stats) starts out as getAnywhere(boxplot.stats) A single object matching 'boxplot.stats' was found It was found in the following places package:grDevices registered S3 method for boxplot from namespace grDevices namespace:grDevices and (ii) how do you know/change that boxplot will look in grDevices before it uses the local copy? That was actually a guess. But checking now: getAnywhere(boxplot) A single object matching 'boxplot' was found It was found in the following places package:graphics namespace:graphics with value function (x, ...) UseMethod(boxplot) environment: namespace:graphics so boxplot() is in the graphics package, and works in that namespace. The graphics namespace file starts out import(grDevices) so functions in that package will look in grDevices before they look elsewhere. I thought that meant that S3 methods would be found there before they're found anywhere else, but I didn't actually check this. So let's check: boxplot.stats - function(x, ...) stop(mine) x - 1 class(x) - stats boxplot(x) Error in boxplot.stats(x) : mine Whoops! Looks as though my local copy does get found first. Not sure if this is a bug... That's an interesting way to check. If I enter boxplot.stats - function(x, ...) stop(mine) boxplot(1) I get a graph (i.e. no error) and so I concluded that the original boxplot is calling the original boxplot.stats. In other words, the original is ignoring my local copy. I tried to do as you suggested and create a local copy of boxplot. I used the following commands: boxplot.stats - edit(boxplot.stats) # Made changes to line 14 boxplot - edit(boxplot) boxplot.default - edit(boxplot.default) # Added a call to cat() When I called boxplot() the local copy was executed (as I could see the output of my cat commands), however it appears that the local copy of boxplot.stats isn't the one being called from my version of boxplot. How do I fix this? That's very strange. Which R version are you using? Are you sure the wrong version was being called? I was doing my tests in 2.4.0. I'm using 2.4.0 too (on Linux; sessionInfo() copied below) If I execute the following: boxplot.stats - function(x, ...) stop(mine) boxplot - edit(boxplot) # Added cat(local boxplot\n) boxplot.default - edit(boxplot.default) # Added cat(local boxplot.default\n) boxplot(1) I get a graph with the text local boxplot local boxplot.default Had boxplot.default called the local version of boxplot.stats, I would have expected the error mine. Sorry, I didn't realize that boxplot.default was calling boxplot.stats. To get boxplot.default to call your local copy of boxplot.stats, you need to make a local copy of it, and (the part I left out before) set its environment to globalenv(). For example: boxplot.default - boxplot.default environment(boxplot.default) - globalenv() The environment is where it goes to look for names that aren't defined locally within it. Is there a way I can avoid all this? Perhaps I can somehow edit the file that R loads when it reads the original boxplot.stats? Well, you can edit the source to R, but it's not usually advisable: when the next release comes out, you'll have to worry about merging your changes in. It's better to write your own function with a different name to do what you want. 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. Duncan Murdoch __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
On Sun, 2006-10-29 at 20:18 -0500, Duncan Murdoch 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. Thank you to both Duncan and Gabor, your help was really appreciated. My 10 character alteration did what I hoped it would. So I'd like to offer it to you or whoever else might be interested. Boxplot does it's job well, it even mostly works with infinite values by not plotting certain lines. For example, if the upper bound is infinite, the upper whisker isn't plotted. However boxplot doesn't work if the upper bound, upper quartile, median, and lower quartile are all infinite. Although there is sufficient data to plot a lower bound, boxplot.stats errors instead. This error also occurs when the lower bound through to the upper quartile are negative infinity. This is not tricky to fix. All that needs to change is line 14 of boxplot.stats. It currently reads: if (any(out[nna])) Changing it to: if (any(out[nna],na.rm=TRUE)) fixes these issues. Cheers, Matthew __ R-help@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.
Re: [R] Debugging R's code: boxplot.stats
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 __ R-help@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.
[R] Debugging R's code: boxplot.stats
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@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.
Re: [R] Debugging R's code: boxplot.stats
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 [EMAIL PROTECTED] 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@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. __ R-help@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.
