Summarizing multiple columns with data.table

67
votes

I'm trying to use data.table to speed up processing of a large data.frame (300k x 60) made of several smaller merged data.frames. I'm new to data.table. The code so far is as follows

library(data.table)
a = data.table(index=1:5,a=rnorm(5,10),b=rnorm(5,10),z=rnorm(5,10))
b = data.table(index=6:10,a=rnorm(5,10),b=rnorm(5,10),c=rnorm(5,10),d=rnorm(5,10))
dt = merge(a,b,by=intersect(names(a),names(b)),all=T)
dt$category = sample(letters[1:3],10,replace=T)

and I wondered if there was a more efficient way than the following to summarize the data.

summ = dt[i=T,j=list(a=sum(a,na.rm=T),b=sum(b,na.rm=T),c=sum(c,na.rm=T),
                     d=sum(d,na.rm=T),z=sum(z,na.rm=T)),by=category]

I don't really want to type all 50 column calculations by hand and a eval(paste(...)) seems clunky somehow.

I had a look at the example below but it seems a bit complicated for my needs. thanks

how to summarize a data.table across multiple columns

1
rdata.table

1 Answers

113
votes

You can use a simple lapply statement with .SD

dt[, lapply(.SD, sum, na.rm=TRUE), by=category ]

   category index        a        b        z         c        d
1:        c    19 51.13289 48.49994 42.50884  9.535588 11.53253
2:        b     9 17.34860 20.35022 10.32514 11.764105 10.53127
3:        a    27 25.91616 31.12624  0.00000 29.197343 31.71285

If you only want to summarize over certain columns, you can add the .SDcols argument

#  note that .SDcols also allows reordering of the columns
dt[, lapply(.SD, sum, na.rm=TRUE), by=category, .SDcols=c("a", "c", "z") ] 

   category        a         c        z
1:        c 51.13289  9.535588 42.50884
2:        b 17.34860 11.764105 10.32514
3:        a 25.91616 29.197343  0.00000

This of course, is not limited to sum and you can use any function with lapply, including anonymous functions. (ie, it's a regular lapply statement).

Lastly, there is no need to use i=T and j= <..>. Personally, I think that makes the code less readable, but it is just a style preference.

EDIT: Documentation

You will find the documentation to .SDand several other special variables under the
help section of ?"[.data.table" (in the Arguments section, look under the info for by).

Also have a look at data.table FAQ 2.1

http://datatable.r-forge.r-project.org/datatable-faq.pdf