[R] how to read in multiple files with unequal number of columns

[Tania Oh]

Thanks Ingmar,

but when I used merge in :

all <- merge(all, tmp),

I get an error:

Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
   invalid 'times' value

is  the error because of the  way I initialised 'all'?
what is the correct way of using merge in this case?

thanks
tania




On 22 Apr 2008, at 14:12, Ingmar Visser wrote:

> you may be looking for ?merge
> hth, Ingmar
>
> On 22 Apr 2008, at 15:05, Tania Oh wrote:
>
>> Dear all,
>>
>> I want to read in 1000 files which contain varying number of columns.
>> For example:
>>
>> file[1] contains 8 columns (mixture of characters and numbers)
>> file[2] contains 16 columns etc
>>
>> I'm reading everything into one big data frame and when I try  
>> rbind, R
>> returns an error of
>> "Error in rbind(deparse.level, ...) :
>>    numbers of columns of arguments do not match"
>>
>>
>> Below is my code:
>>
>> all <- NULL
>> all <- as.data.frame(all)
>>
>> ##read in the contents of the files
>> for (f in 1:length(fnames)){
>>
>>        tmp <- try(read.table(fnames[f], header=F, fill=T, sep="\t"),
>> TRUE)
>>
>>        if (class(tmp) == "try-error") {
>>                next ## skip this file if it's empty/non-existent
>>         }else{
>> 	       ## combine all the file contents into one big data frame
>>                 all <- rbind(all, tmp)
>>    }
>> }
>>
>>
>> Here is some example of what the data in the files:
>>
>> L3 <- LETTERS[1:3]
>> (d <- data.frame(cbind(x=1, y=1:10), fac=sample(L3, 10,  
>> replace=TRUE)))
>>
>>> str(d)
>> 'data.frame':	10 obs. of  3 variables:
>>   $ x  : num  1 1 1 1 1 1 1 1 1 1
>>   $ y  : num  1 2 3 4 5 6 7 8 9 10
>>   $ fac: Factor w/ 3 levels "A","B","C": 1 3 1 2 2 2 2 1 1 2
>>
>> my.fake.data <- data.frame(cbind(x=1, y=2))
>>> str(my.fake.data)
>> 'data.frame':	1 obs. of  2 variables:
>>   $ x: num 1
>>   $ y: num 2
>>
>>
>> all <- rbind(d, my.fake.data)
>>
>> Error in rbind(deparse.level, ...) :
>>    numbers of columns of arguments do not match
>>
>>
>> I've searched the R-site but couldn't find any relevant solution.I
>> might have used the wrong keywords to search, so if this question has
>> been answered already, I'd be very grateful if someone could point me
>> to the post. Else any help/suggestions would be greatly appreciated.
>>
>> Many thanks in advance,
>> tania
>>
>> D.Phil student
>> Department of Physiology, Anatomy and Genetics
>> University of Oxford
>>
>> ______________________________________________
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>> 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.
>
> Ingmar Visser
> Department of Psychology, University of Amsterdam
> Roetersstraat 15
> 1018 WB Amsterdam
> The Netherlands
> t: +31-20-5256723
>
>