[Rd] visualizing data flow and function calls
Hi All, I don't know if such a thing exists, but I am looking for a way to better keep track of where data is going, how it is being modified, and what functions are acting upon it when I give the data over to a function that calls many subfunctions (as happens in my current package I am working on), or in an R script I am using to do multiple processing steps on data. Currently I find it difficult to keep straight sometimes what a function has done to my data, or what output from another function is required now as input to my current internal function as I navigate through my software (or when I make changes six months later, and multiple objects are coming in). >From what I can tell, I want to generate sequence diagrams of my program (http://www.agilemodeling.com/artifacts/sequenceDiagram.htm). Is there any way to generate these kinds of things automatically in R, or to get the information easily from R? I know I could add code to each function to spit out that it has been called with what input, but I thought there might be a way to do it by calling the function within some kind of wrapper function that would tell me what other functions are being called. I have tried searching for such a beast, but if it exists I cannot seem to come up with the right search terms to find it. Thanks in advance, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.fli...@louisville.edu EM rfligh...@gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Suggestions for R-devel / R-help digest format
Hi Saravanan, You don't need a separate GMail account, as others suggested. I use GMail as my client, and I have FILTERS set up to catch any R-Help, etc (really anything that comes from a specific address), archive the message so I don't see it in my inbox (unless someone is replying directly to me in addition to sending to R-help), and then I can view the emails at my leisure. HTH, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.fli...@louisville.edu EM rfligh...@gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods. On Thu, Jul 7, 2011 at 15:26, Saravanan wrote: > Thanks Steve and Brian ! > > Probably, I will create a gmail account for mailing lists and let it take > care of the threading. > > Regards, > Saravanan > > On 07/07/2011 12:02 PM, Brian G. Peterson wrote: >> >> On Thu, 2011-07-07 at 11:44 -0500, Saravanan wrote: >>> >>> Hello, >>> >>> I am passive reader of both R-devel and R-help mailing lists. I am >>> sending the following comments to r-devel as it seemed more suitable. I >>> am aware that this list uses GNU mailman for the list management. I have >>> my options set that it sends a email digest. One thing I find is that >>> the digest consists of emails that ordered temporarlly. For eg lets say >>> there are two threads t1 and t2 and the emails arrive as e1 of t1, e2 of >>> t2, e3 of t3 . The digest lists them as e1,e2 and then e3. Is it >>> possible to somehow configure it as T1 : e1,e3 and then T2 : e2 ? >>> >>> This is the digest format that google groups uses which is incredibly >>> helpful as you can read all the messages in a thread. Additionally, it >>> also helpfully includes a header that lists all the threads in digest so >>> that you can jump to the one you are interested in. I checked the >>> mailman options but could not find any. >>> >>> Does anyone else have the same issue? It is not a big issue in R-devel >>> but R-help is a much more high traffic mailing list. I am interested in >>> hearing how you read/filter your digest mails in either R-help or other >>> high volume mailing lists. >> >> This really has nothing to do with R, but rather mailman. >> >> I use folders, filtered on the server using SIEVE and/or procmail. No >> digest required. I get the mails immediately, not later in the day or >> the next day, and can use all my various email clients easily to >> read/respond. >> >> mailman supports a MIME digest format that includes a table of contents >> with links to each MIME part. mailman does not support a threaded >> digest, to the best of my knowledge. >> >> Regards, >> >> - Brian >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] location of check.Renviron on Windows
Doing package development on a Windows 7 machine, and I want to tell R check not to worry about the "suggested" packages. I realize this can be done using the ~/.R/check.Renviron file, but what directory corresponds to "~"? Is that supposed to be the user directory? Or is it some other directory? I have this _R_CHECK_FORCE_SUGGESTS_=false (have also tried FALSE) in C:\Users\username\.R I have also tried putting the file in C:\Users\username Using r58183 Thanks, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.fli...@louisville.edu EM rfligh...@gmail.com robertmflight.blogspot.com bioinformatics.louisville.edu/lab The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac Asimov __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] location of check.Renviron on Windows
Thanks Simon, that did the ticket. Will remember that next time.
-Robert
Robert M. Flight, Ph.D.
University of Louisville Bioinformatics Laboratory
University of Louisville
Louisville, KY
PH 502-852-1809 (HSC)
PH 502-852-0467 (Belknap)
EM robert.fli...@louisville.edu
EM rfligh...@gmail.com
robertmflight.blogspot.com
bioinformatics.louisville.edu/lab
The most exciting phrase to hear in science, the one that heralds new
discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
Isaac Asimov
On Wed, Feb 1, 2012 at 14:52, Simon Urbanek wrote:
>
> On Feb 1, 2012, at 2:10 PM, Robert M. Flight wrote:
>
>> Doing package development on a Windows 7 machine, and I want to tell R
>> check not to worry about the "suggested" packages.
>>
>> I realize this can be done using the ~/.R/check.Renviron file, but
>> what directory corresponds to "~"? Is that supposed to be the user
>> directory? Or is it some other directory?
>>
>
> Ask R:
>
>> normalizePath("~")
> [1] "C:\\Users\\urbanek\\Documents"
>
> Cheers,
> S
>
>
>> I have this _R_CHECK_FORCE_SUGGESTS_=false (have also tried FALSE) in
>> C:\Users\username\.R
>>
>> I have also tried putting the file in C:\Users\username
>>
>> Using r58183
>>
>> Thanks,
>>
>> -Robert
>>
>> Robert M. Flight, Ph.D.
>> University of Louisville Bioinformatics Laboratory
>> University of Louisville
>> Louisville, KY
>>
>> PH 502-852-1809 (HSC)
>> PH 502-852-0467 (Belknap)
>> EM robert.fli...@louisville.edu
>> EM rfligh...@gmail.com
>> robertmflight.blogspot.com
>> bioinformatics.louisville.edu/lab
>>
>> The most exciting phrase to hear in science, the one that heralds new
>> discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
>> Isaac Asimov
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] add sessionInfo() option to "save"
Hi All, I was wondering if there would be any interest in adding an option to the "save" function in R that I think would be useful. I was thinking that it might be useful to have an option that would generate a ".sessionInfo" variable that contains the output of "sessionInfo()", and adds it to the list of objects to be saved. This way, whenever an RData object is loaded, all the information about the R version, and attached packages present would be available for query. I know I have been bitten by the problem of generating results using different versions of packages and different versions of R. I know that this is partly the idea behind Sweave (and other report generation measures), and perhaps I am at fault for not keeping better track of these types of things, but this seems like it would be useful to a lot of other people besides just me. Thoughts? -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.fli...@louisville.edu EM rfligh...@gmail.com robertmflight.blogspot.com bioinformatics.louisville.edu/lab github.com/rmflight/general/wiki The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac Asimov [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
