[R] large dataset

Thomas Lumley tlumley at u.washington.edu
Tue Mar 30 19:04:51 CEST 2010


If you're arguing that there should be more documentation and examples explaining how to use very large data sets with R, then I agree. Feel free to write some.

I've been giving tutorials on this for years now.  I wrote the first netCDF interface package for R because I needed to use data that wouldn't fit on a 64Mb system. I wrote the biglm package to handle out-of-core regression. My presentation at the last useR meeting was on how to automatically load variables on demand from a SQL connection.

It's still true that you can't treat large data sets and small data sets the same way, and I still think that it's even more important to point out that nearly everyone doesn't have large data and doesn't need to worry about these issues.


On Mon, 29 Mar 2010, kMan wrote:

> Dear Thomas,
> While it may be true that "R (and S) are *accused* of being slow,
> memory-hungry, and able to handle only
> small data sets" (emphasis added), the accusation is  false, rendering the
> *accusers* misinformed. Transparency is another, perhaps more interesting
> matter. R-users can *experience* R as limited in the ways described above (a
> functional limitation) while making a false technical assertion, without
> generating a dichotomy. It is a bit like a cell phone example from
> human-computer interaction circles in the 90s. The phone could technically
> work, provided one is an engineer so as to make sense out of its interface,
> while for most people, it may *functionally* be nothing more than a
> paperweight. R is not "technically" limited in the way the accusation reads
> (the point I was making), though many users are functionally limited so (the
> point you seem to have made or at least passed along).
> An R user can get far more data into memory as single objects with R than
> with other stats packages; including matlab, JMP, and, obviously, excel.
> This is just a simple comparison of the programs' documented environment
> size and object limits. The difference in the same read/scan operation
> between R and JMP on 600 Mb of data could easily be 25+ minutes (R perhaps
> taking 5-7 minutes, with JMP taking 30+ minutes, assuming 1.8GHz & 3GB RAM I
> used back when I made the comparison that sold me on R). R can do formal
> operations with all that data in memory, assuming the environment is given
> enough space to work with, while JMP will do the same operation in several
> smaller chunks, reference the disk several times, AND on windows machines,
> cause the OS to page. In that case, the differences can be upwards of a day.
> With the ability to handle larger chunks at once, and direct control over
> preventing one's OS from paging, R users should be able to crank out
> analyses on very large datasets faster than other programs.
> I am perfectly willing to accept that consumers of statistical software may
> *experience* R as more limiting, in keeping with the accusations, that the
> effect may be larger for newcomers, and even larger for newcomers after
> controlling for transparency. I'd expect the effect  to reverse at around 3
> years of experience, controlling for transparency or not. Large scale data
> may present technical problems many users choose simply to avoid using R
> for, so the effect may not reverse for these issues. Even when R is more
> than capable of outperforming other programs, its usability (or access to
> suitable documentation/training material) apparently isn't currently up to
> the challenge. This is something the R community should be gnawing at the
> bit to address.
> I'd think a consortium of sorts showcasing large-scale data support in R
> would be a stellar contribution, and perhaps an issue of R-journal devoted
> to the topic, say, of near worst-case scenario - 10Gb of data containing
> different data types (categorical, numeric, & embedded matrices), in a .csv
> file, header information somewhere else. Now how do the authors explain to
> the beginner (say, <1 year experience with I/O) how to tackle getting the
> data into a more suitable format, and then how did they analyze it 300Mb at
> a time, all using R, in a non-cluster/single user environment, 32 bit, while
> controlling for the environment size, missing data, and preventing paging?
> How was their solution different when moving to 64 bit? Moving to a cluster?
> One of the demos would certainly have to use scan() exclusively for I/O,
> perhaps also demonstrating why the 'bad practice' part of working with raw
> text files is something more than mere prescription.
> Sincerely,
> KeithC.
> -----Original Message-----
> From: Thomas Lumley [mailto:tlumley at u.washington.edu]
> Sent: Monday, March 29, 2010 2:56 PM
> To: Gabor Grothendieck
> Cc: kMan; r-help; n.vialma at libero.it
> Subject: Re: [R] large dataset
> On Mon, 29 Mar 2010, Gabor Grothendieck wrote:
>> On Mon, Mar 29, 2010 at 4:12 PM, Thomas Lumley <tlumley at u.washington.edu>
> wrote:
>>> On Sun, 28 Mar 2010, kMan wrote:
>>>>> This was *very* useful for me when I dealt with a 1.5Gb text file
> http://www.csc.fi/sivut/atcsc/arkisto/atcsc3_2007/ohjelmistot_html/R_and_la
>>>> rge_data/
>>>> Two hours is a *very* long time to transfer a csv file to a db. The
> author
>>>> of the linked article has not documented how to use scan() arguments
>>>> appropriately for the task. I take particular issue with the authors
>>>> statement that "R is said to be slow, memory hungry and only capable of
>>>> handling small datasets," indicating he/she has crummy informants and
> not
>>>> challenged the notion him/herself.
>>> Ahem.
>>> I believe that *I* am the author of the particular statement you take
> issue
>>> with (although not the of the rest of the page).
>>> However, when I wrote it, it continued:
>>> ---------
>>> "R (and S) are accused of being slow, memory-hungry, and able to handle
> only
>>> small data sets.
>>> This is completely true.
>>> Fortunately, computers are fast and have lots of memory. Data sets with
>  a
>>> few tens of thousands of observations can be handled in 256Mb of memory,
> and
>>> quite large data sets with 1Gb of memory.  Workstations with 32Gb or more
> to
>>> handle millions of observations are still expensive (but in a few years
>>> Moore's Law should catch up).
>>> Tools for interfacing R with databases allow very large data sets, but
> this
>>> isn't transparent to the user."
>> I don`t think the last sentence is true if you use sqldf.   Assuming
>> the standard type of csv file accepted by sqldf:
>> install.packages("sqldf")
>> library(sqldf)
>> DF <- read.csv.sql("myfile.csv")
>> is all you need.  The install.packages statement downloads and
>> installs sqldf, DBI and RSQLite (which in turn installs SQLite
>> itself), and then read.csv.sql sets up the database and table layouts,
>> reads the file into the database, reads the data from the database
>> into R (bypassing R's read routines) and then destroys the database
>> all transparently.
> It's not the data reading that's the problem. As you say, sqldf handles that
> nicely.  It's using a data set larger than memory that is not transparent --
> you need special packages and can still only do a quite limited set of
> operations.
>      -thomas
> Thomas Lumley			Assoc. Professor, Biostatistics
> tlumley at u.washington.edu	University of Washington, Seattle
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Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

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