[R] write.matrix row names vs sink vs capture.output

[Mark Ebbert]

Thank you, that's a good idea. I should have looked into that!

On Sep 19, 2011, at 8:42 AM, Paul Hiemstra wrote:

> Sorry, misread :). Consider my remark as retracted...however....
> 
> It looks like it would be relatively simple to rewrite write.matrix a
> little bit to include rownames...the cat statement in the while loop of
> write.matrix could be changed to include a row name. To get he source
> code of write.matrix:
> 
> library(MASS)
> write.matrix
> # without the ()!!
> 
> hope this helps more than my previous (useless) comment,
> Paul
> 
> On 09/19/2011 02:37 PM, Mark Ebbert wrote:
>> I'm afraid I don't understand your response. As I mentioned in the original question, write.table is way too slow and I need the row names in the file, so setting row.names to FALSE wouldn't accomplish my goal, anyway. And write.matrix doesn't have *any* options to include row names, which baffles me since row names are part of a matrix object. 
>> 
>> I need the row names because an external program, which requires row names, will be processing the files. I wound up using perl to fix the resultant file from write.matrix, but I would love to hear an explanation as to why write.matrix doesn't have an option to include row names, if you know. 
>> 
>> Anyway, thanks for taking the time to respond. 
>> 
>> On Sep 19, 2011, at 1:49 AM, "Paul Hiemstra" <paul.hiemstra at knmi.nl> wrote:
>> 
>>> What do you want with the row names? The help file for ?write.table
>>> lists a row.names argument which can be set to FALSE.
>>> 
>>> regards,
>>> Paul
>>> 
>>> On 09/06/2011 02:58 PM, Mark Ebbert wrote:
>>>> Thank you for your help.
>>>> 
>>>> The data is meant to be processed by a separate program that expects a simple matrix with row and column names in ascii format. "write.matrix" does exactly what I want except for the row names. It baffles me that this is not an option…
>>>> 
>>>> 
>>>> On Sep 6, 2011, at 8:22 AM, Paul Hiemstra wrote:
>>>> 
>>>>> On 09/06/2011 06:24 AM, Mark Ebbert wrote:
>>>>>> Dear R gurus,
>>>>>> 
>>>>>> I am trying to write several large matrices (~ 1GB) to separate files. I have learned that write.table is simply too slow for this task and was attempting to use write.matrix, but write.matrix does not have the ability to include row names in the output. Anyone know why that's the case? I've seen a thread stating that write.matrix is the way to go for large prints to files, but it doesn't do what I need it to. Since write.matrix wasn't working I tried both sink and capture.output, but then the output is printed to the file using the same 'width' restrictions as the general "options(width=)" limit.
>>>>>> 
>>>>>> Any ideas on how to print a large matrix with row names? I could write a perl script to modify the files after the fact, but I shouldn't have to do that.
>>>>>> 
>>>>>> Thanks for your help!
>>>>>> 
>>>>>> Mark T. W. Ebbert
>>>>>> ______________________________________________
>>>>>> 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.
>>>>> Hi,
>>>>> 
>>>>> What do you want with the data? If you want to store an R matrix on disk
>>>>> for later use in R, take a look at ?save. If it is for use in another
>>>>> programming language, I would write the matrix in binary format
>>>>> (?writebin). This saves a lot of space and prevents any (significant)
>>>>> rounding errors. It is probably also quite a bit faster. If you really
>>>>> need some more metadata (such as rownames), I would add a second text
>>>>> file which stores this information. Sort of a binary file plus a header,
>>>>> which is a quite common format for storing data. Maybe you can even find
>>>>> a standard binary format which you can use. But it is impossible to
>>>>> comment on this because you did not provide information as to what you
>>>>> want to do with the saved data.
>>>>> 
>>>>> good luck!
>>>>> Paul
>>>>> 
>>>>> -- 
>>>>> Paul Hiemstra, Ph.D.
>>>>> Global Climate Division
>>>>> Royal Netherlands Meteorological Institute (KNMI)
>>>>> Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
>>>>> P.O. Box 201 | 3730 AE | De Bilt
>>>>> tel: +31 30 2206 494
>>>>> 
>>>>> http://intamap.geo.uu.nl/~paul
>>>>> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>>>>> 
>>> 
>>> -- 
>>> Paul Hiemstra, Ph.D.
>>> Global Climate Division
>>> Royal Netherlands Meteorological Institute (KNMI)
>>> Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
>>> P.O. Box 201 | 3730 AE | De Bilt
>>> tel: +31 30 2206 494
>>> 
>>> http://intamap.geo.uu.nl/~paul
>>> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>>> 
> 
> 
> -- 
> Paul Hiemstra, Ph.D.
> Global Climate Division
> Royal Netherlands Meteorological Institute (KNMI)
> Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
> P.O. Box 201 | 3730 AE | De Bilt
> tel: +31 30 2206 494
> 
> http://intamap.geo.uu.nl/~paul
> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>