[R] formatting a list
Tomas Vaisar
tvaisar at u.washington.edu
Mon Oct 22 20:55:07 CEST 2007
Hi Chuck,
I am running the Windows version R-2.5.1. I will upgrade and will let
you know what the deal was. Your output definitely looks right.
Thanks,
Tomas
Charles C. Berry wrote:
>
> Tomas,
>
> Are you using R-2.6.0 ??
>
> Each method works for me producing as list of 7000 vectors.
>
> The file I used to test this is created by:
>
> for (i in 1:7000) cat( seq(from=i,by=1,length=19),"\n",
> sep='\t',file="tmp.tab",append=TRUE)
>
> The first line is:
>
>> scan("tmp.tab",nlines=1)
> Read 19 items
> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
>>
>
> The last line is
>
>> scan("tmp.tab",skip=6999,nlines=1)
> Read 19 items
> [1] 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012
> 7013 7014 7015 7016 7017 7018
>>
>
> and each method recapitulates this:
>
>> dat[[1]]
> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
>> dat[[7000]]
> [1] 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012
> 7013 7014 7015 7016 7017 7018
>>
>
> The second method threw lots of warnings because open connections must
> be closed. Those could be eliminated by explicitly opening and closing
> the connection. Before using the second method closeAllconnections()
> was sometimes needed, but the error it reported differs from the one
> you mention.
>
> I am using
>
>> version
> _
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major 2
> minor 6.0
> year 2007
> month 10
> day 03
> svn rev 43063
> language R
> version.string R version 2.6.0 (2007-10-03)
>>
>
>
> Chuck
>
> On Mon, 22 Oct 2007, Tomas Vaisar wrote:
>
>> Hi Chuck,
>>
>> thanks for your responses. I did not ignore your suggestions - I did
>> try them and they did not produce what I need.
>>
>> The first one produced table with the same format as a read.table would
>> generate, not not a list of lists.
>> Second one gave me an error after returning Read 19 items multiple times
>> : Error in textConnection(x) : all connections are in use
>> The last one gave me similar error on the first step - Error in
>> file(con, "r") : all connections are in use
>>
>> However, your last suggestion to make list of lists seems that it
>> works. I will have to test more.
>>
>> Cheers,
>>
>> Tomas
>>
>> Charles C. Berry wrote:
>>>
>>> Tomas,
>>>
>>> Three different ways to create a list of 7000 vectors from a file of
>>> 7000 rows and 19 columns are given here:
>>>
>>> http://article.gmane.org/gmane.comp.lang.r.general/97032
>>>
>>> which I think is what you are asking for.
>>>
>>> If you truly need a list of 7000 lists each of length 1 containing a
>>> vector of length 19, then do this:
>>>
>>> list.of.lists.of.one.vector.each <- lapply( list.of.vectors, list )
>>>
>>>
>>> BTW, as this thread appears in
>>>
>>> http://news.gmane.org/gmane.comp.lang.r.general
>>>
>>> the above article was the firt reply to your original query. I am
>>> puzzled as to why you did not simply implement one of the three
>>> methods shown there.
>>>
>>> Chuck
>>>
>>> On Mon, 22 Oct 2007, Tomas Vaisar wrote:
>>>
>>>> Hi Jim,
>>>>
>>>> I really appreciate your help.
>>>> From the input file I have - 19 columns, 7000 rows - the scan gives me
>>>> the desired format of a list consisting of 19 lists with 7000 values
>>>> each.
>>>> However I need a list of 7000 lists with 19 values each. (e.g. each
>>>> row
>>>> of my input file should be a separate list bound in a list of all
>>>> these
>>>> lists)
>>>> I use both commands you suggested -
>>>> x <- scan('temp.txt', what=c(rep(list(0), 19)))
>>>> followed by
>>>> x.matrix <- do.call('rbind', x) # gives 7000 x 19 matrix.
>>>>
>>>> Although this makes a matrix of the correct dimensions it is not the
>>>> "list of lists" the ROCR package expects as input. Can you convert
>>>> this
>>>> matrix into a "list of lists"? Or is there a simple way in R to
>>>> convert
>>>> a table into such a "list of lists"?
>>>>
>>>> Thanks again,
>>>>
>>>> Tomas
>>>>
>>>>
>>>> jim holtman wrote:
>>>>> That is what I thought and that is the format that the 'scan'
>>>>> approach
>>>>> should provide. I was just confused when you said that you were
>>>>> going
>>>>> to have to transpose it, write it and then read it back in for some
>>>>> reason. I understand that Excel can not handle 7000 columns, but was
>>>>> wondering where that came into play.
>>>>>
>>>>> On 10/21/07, Tomas Vaisar <tvaisar at u.washington.edu> wrote:
>>>>>
>>>>>> The data I have is tab delimited file with 7000 lines of 19 values
>>>>>> each
>>>>>> (representing 7000 permutations on 19 variables). I want to get it
>>>>>> into
>>>>>> the ROCR package which expects the data to be in lists - single
>>>>>> list of
>>>>>> 19 values for each permutation, e.g. list of 7000 lists of 19
>>>>>> values each.
>>>>>>
>>>>>> I hope this is little clearer.
>>>>>>
>>>>>> Tomas
>>>>>>
>>>>>> jim holtman wrote:
>>>>>>
>>>>>>> What is it that you want to do? The 'scan' statement give you a
>>>>>>> list
>>>>>>> of length 7000 with 19 entries each. Do you want to create a
>>>>>>> matrix
>>>>>>> that has 7000 rows by 19 columns? If so, then you just have to
>>>>>>> take
>>>>>>> the output of the 'scan' and do:
>>>>>>>
>>>>>>> x.matrix <- do.call('rbind', x) # gives 7000 x 19 matrix.
>>>>>>>
>>>>>>> So I am still not sure exactly what your input is and what you
>>>>>>> want to
>>>>>>> do with it.
>>>>>>>
>>>>>>> On 10/21/07, Tomas Vaisar <tvaisar at u.washington.edu> wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi Jim,
>>>>>>>>
>>>>>>>> thanks a lot. It works, however - my other problem is that I
>>>>>>>> need to
>>>>>>>> transpose the original table before reading it into the list
>>>>>>>> because the
>>>>>>>> data come from Excel and it can't handle 7000 columns. I could
>>>>>>>> read it
>>>>>>>> in R transpose end write into a new tab delim file and then read
>>>>>>>> it back
>>>>>>>> in, but I would think that there might be a way in R to do both.
>>>>>>>> Would you know about the way?
>>>>>>>>
>>>>>>>> Tomas
>>>>>>>>
>>>>>>>> jim holtman wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> another choice is:
>>>>>>>>>
>>>>>>>>> x <- scan('temp.txt', what=c(rep(list(0), 19)))
>>>>>>>>>
>>>>>>>>> On 10/20/07, Tomas Vaisar <tvaisar at u.washington.edu> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I am new to R and need to read in a file with 19 columns and
>>>>>>>>>> 7000 rows
>>>>>>>>>> and make it into a list of 7000 lists with 19 items each. For a
>>>>>>>>>> simpler case of 10 by 10 table I used x <-scan("file",
>>>>>>>>>> list(0,0,0,0,0,0,0,0,0,0)), perhaps clumsy, but it did the job.
>>>>>>>>>> However with the large 19x7000 (which needs to be transposed) I
>>>>>>>>>> am not
>>>>>>>>>> sure how to go about it.
>>>>>>>>>>
>>>>>>>>>> Coudl somebody suggest a way?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Tomas
>>>>>>>>>>
>>>>>>>>>> ______________________________________________
>>>>>>>>>> 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.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> ______________________________________________
>>>> 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.
>>>>
>>>
>>> Charles C. Berry (858) 534-2098
>>> Dept of Family/Preventive
>>> Medicine
>>> E mailto:cberry at tajo.ucsd.edu UC San Diego
>>> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
>>> 92093-0901
>>>
>>>
>>
>> ______________________________________________
>> 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.
>>
>
> Charles C. Berry (858) 534-2098
> Dept of Family/Preventive
> Medicine
> E mailto:cberry at tajo.ucsd.edu UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
> 92093-0901
>
>
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