Summarizing multiple columns with data.table

Question

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

Answer 1

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 

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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 

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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.

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Documentation

See ?.SD, ?data.table and its .SDcols argument, and the vignette Using .SD for Data Analysis.

Also have a look at data.table FAQ 2.1.