Quickly reading very large tables as dataframes

ghz 1years ago ⋅ 7295 views

Question

I have very large tables (30 million rows) that I would like to load as a dataframes in R. read.table() has a lot of convenient features, but it seems like there is a lot of logic in the implementation that would slow things down. In my case, I am assuming I know the types of the columns ahead of time, the table does not contain any column headers or row names, and does not have any pathological characters that I have to worry about.

I know that reading in a table as a list using scan() can be quite fast, e.g.:

datalist <- scan('myfile',sep='\t',list(url='',popularity=0,mintime=0,maxtime=0)))

But some of my attempts to convert this to a dataframe appear to decrease the performance of the above by a factor of 6:

df <- as.data.frame(scan('myfile',sep='\t',list(url='',popularity=0,mintime=0,maxtime=0))))

Is there a better way of doing this? Or quite possibly completely different approach to the problem?

Answer

An update, several years later

This answer is old, and R has moved on. Tweaking read.table to run a bit faster has precious little benefit. Your options are:

  1. Using vroom from the tidyverse package vroom for importing data from csv/tab-delimited files directly into an R tibble. See Hector's answer.

  2. Using fread in data.table for importing data from csv/tab-delimited files directly into R. See mnel's answer.

  3. Using read_table in readr (on CRAN from April 2015). This works much like fread above. The readme in the link explains the difference between the two functions (readr currently claims to be "1.5-2x slower" than data.table::fread).

  4. read.csv.raw from iotools provides a third option for quickly reading CSV files.

  5. Trying to store as much data as you can in databases rather than flat files. (As well as being a better permanent storage medium, data is passed to and from R in a binary format, which is faster.) read.csv.sql in the sqldf package, as described in JD Long's answer, imports data into a temporary SQLite database and then reads it into R. See also: the RODBC package, and the reverse depends section of the DBI package page. MonetDB.R gives you a data type that pretends to be a data frame but is really a MonetDB underneath, increasing performance. Import data with its monetdb.read.csv function. dplyr allows you to work directly with data stored in several types of database.

  6. Storing data in binary formats can also be useful for improving performance. Use saveRDS/readRDS (see below), the h5 or rhdf5 packages for HDF5 format, or write_fst/read_fst from the fst package.

The original answer

There are a couple of simple things to try, whether you use read.table or scan.

  1. Set nrows= the number of records in your data (nmax in scan).

  2. Make sure that comment.char="" to turn off interpretation of comments.

  3. Explicitly define the classes of each column using colClasses in read.table.

  4. Setting multi.line=FALSE may also improve performance in scan.

If none of these thing work, then use one of the profiling packages to determine which lines are slowing things down. Perhaps you can write a cut down version of read.table based on the results.

The other alternative is filtering your data before you read it into R.

Or, if the problem is that you have to read it in regularly, then use these methods to read the data in once, then save the data frame as a binary blob with ~~save~~ saveRDS, then next time you can retrieve it faster with ~~load~~ readRDS.

#r