[R] how to read CSV file in R?

Jens Oehlschlägel jens.oehlschlaegel at truecluster.com
Wed Jun 9 09:59:56 CEST 2010

If you have memory problems reading csv you can use read.csv.ffdf from package ff which reads in chunks.
The result is a ffdf object, say myffdf, from which binary subscripting [,] returns standard data.frames, such as 
myffdf[,]  # returns all data (if it fits into memory)
myffdf[somerows,] # returns a subset of data

Do read and understand the help concerning filename location and implications for finalizers and permanency.

Jens Oehlschlägel

-----Ursprüngliche Nachricht-----
Von: Joris Meys <jorismeys at gmail.com>
Gesendet: Jun 8, 2010 1:11:20 PM
An: dhanush <dhana.sa at gmail.com>
Betreff: Re: [R] how to read CSV file in R?

>That will be R 2.10.1 if I'm correct.
>For reading in csv files, there's a function read.csv who does just that:
>los <- read.csv("file.csv",header=T)
>But that is just a detail. You have problems with your memory, but
>that's not caused by the size of your dataframe. On my system, a
>matrix with 100,000 rows and 75 columns takes only 28 Mb. So I guess
>your workspace is cluttered with other stuff.
>Check following help pages :
>it generally doesn't make a difference, but sometimes using gc() can
>set some memory free again.
>If none of this information helps, please provide us with a bit more
>info regarding your system and the content of your current workspace.
>On Tue, Jun 8, 2010 at 8:46 AM, dhanush <dhana.sa at gmail.com> wrote:
>> I tried to read a CSV file in R. The file has about 100,000 records and 75
>> columns. When used read.delim, I got this error. I am using R ver 10.1.
>>> los<-read.delim("file.csv",header=T,sep=",")
>> Warning message:
>> In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>>  Reached total allocation of 1535Mb: see help(memory.size)
>> Thanks
>> --
>> View this message in context: http://r.789695.n4.nabble.com/how-to-read-CSV-file-in-R-tp2246930p2246930.html
>> Sent from the R help mailing list archive at Nabble.com.
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>Joris Meys
>Statistical consultant
>Ghent University
>Faculty of Bioscience Engineering
>Department of Applied mathematics, biometrics and process control
>tel : +32 9 264 59 87
>Joris.Meys at Ugent.be
>Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>R-help at r-project.org mailing list
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

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