Loading Big (ish) Data into R

November 24, 2009

(This article was first published on Cerebral Mastication » R, and kindly contributed to R-bloggers)

So for the rest of this conversation big data == 2 Gigs. Done. Don’t give me any of this ‘that’s not big, THIS is big’ shit. There now, on with the cool stuff:

This week on twitter Vince Buffalo asked about loading a 2 gig comma separated file (csv) into R (OK, he asked about tab delimited data, but I ignored that because I use mostly comma data and I wanted to test CSV. Sue me.)


I thought this was a dang good question. What I have always done in the past was load my data into SQL Server or Oracle using an ETL tool and then suck it from the database to R using either native database connections or the RODBC package. Matti Pastell (@mpastell) recommended using the sqldf (SQL to data frame) package to do the import. I’ve used sqldf before, but only to allow me to use SQL syntax to manipulate R data frames. I didn’t know it could import data, but that makes sense, given how sqldf works. How does it work? Well sqldf sets up an instance of the sqlite database server then shoves R data into the DB, does operations on the tables, and then spits out an R data frame of the results. What I didn’t realize is that we can call sqldf from within R and have it import a text file directly into sqlite and then return the data from sqlite directly into R using a pretty fast native connection. I did a little Googling and came up with this discussion on the R mailing list.

So enough background, here’s my setup: I have a Ubuntu virtual machine running with 2 cores and 10 gigs of memory. Here’s the code I ran to test:

bigdf <- data.frame(dim=sample(letters, replace=T, 4e7), fact1=rnorm(4e7), fact2=rnorm(4e7, 20, 50))
write.csv(bigdf, ‘bigdf.csv’, quote = F)

That code creates a data frame with 3 columns. I created a single letter text column, then two floating point columns. There are 40,000,000 records. When I run the write.csv step on my machine I get about 1.8GiB. That’s close enough to 2 gigs for me. I created the text file and then ran rm(list=ls()) to kill all objects. I then ran gc() and saw that I had hundreds of megs of something or other (I have not invested the brain cycles to understand the output that gc() gives). So I just killed and restarted R. I then ran the following:

f <- file(“bigdf.csv”)
system.time(bigdf <- sqldf(“select * from f”, dbname = tempfile(), file.format = list(header = T, row.names = F)))

That code loads the CSV into an sqlite DB then executes a select * query and returns the results to the R data frame bigdf. Pretty straightforward, ey? Well except for the dbname = tempfile() bit. In sqldf you can choose where it makes the sqlite db. If you don’t specify at all it makes it in memory which is what I first tried. I ran out of mem even on my 10GB box. So I read a little more and added the dbname = tempfile() which creates a temporary sqlite file on the disk. If I wanted to use an existing sqlite file I could have specified that instead.

So how long did it take to run? Just under 5 minutes.

So how long would the read.csv method take? Funny you should ask. I ran the following code to compare:

system.time(big.df <- read.csv(‘bigdf.csv’))

And I would love to tell you how long that took to run, but it’s been running for half an hour all night and I just don’t have that kind of patience.


To leave a comment for the author, please follow the link and comment on their blog: Cerebral Mastication » R.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Tags: , , ,

Comments are closed.

Search R-bloggers


Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)