Benchmarks : Grouping

• The input data is randomly ordered. No pre-sort, no indexes, no key.
• 5 simple queries are run similar to what a data analyst might do in practice; i.e., various ad hoc aggregations as the data is explored and investigated.
• Each package is tested separately in its own fresh R session.
• Each query is repeated once more, immediately. This is to isolate cache effects and confirm the first timing. The first and second times are displayed.
• The results are compared and checked allowing for numeric tolerance and column name differences.

Scroll to the bottom to find reproducible code and system info.

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Code to reproduce the timings above :

## data.table run
$ R --vanilla
require(data.table)
N=2e9; K=100
set.seed(1)
DT <- data.table(
  id1 = sample(sprintf("id%03d",1:K), N, TRUE),      # large groups (char)
  id2 = sample(sprintf("id%03d",1:K), N, TRUE),      # large groups (char)
  id3 = sample(sprintf("id%010d",1:(N/K)), N, TRUE), # small groups (char)
  id4 = sample(K, N, TRUE),                          # large groups (int)
  id5 = sample(K, N, TRUE),                          # large groups (int)
  id6 = sample(N/K, N, TRUE),                        # small groups (int)
  v1 =  sample(5, N, TRUE),                          # int in range [1,5]
  v2 =  sample(1e6, N, TRUE),                        # int in range [1,1e6]
  v3 =  sample(round(runif(100,max=100),4), N, TRUE) # numeric e.g. 23.5749
)
cat("GB =", round(sum(gc()[,2])/1024, 3), "\n")
system.time( DT[, sum(v1), keyby=id1] )
system.time( DT[, sum(v1), keyby=id1] )
system.time( DT[, sum(v1), keyby="id1,id2"] )
system.time( DT[, sum(v1), keyby="id1,id2"] )
system.time( DT[, list(sum(v1),mean(v3)), keyby=id3] )
system.time( DT[, list(sum(v1),mean(v3)), keyby=id3] )
system.time( DT[, lapply(.SD, mean), keyby=id4, .SDcols=7:9] )
system.time( DT[, lapply(.SD, mean), keyby=id4, .SDcols=7:9] )
system.time( DT[, lapply(.SD, sum), keyby=id6, .SDcols=7:9] )
system.time( DT[, lapply(.SD, sum), keyby=id6, .SDcols=7:9] )

## dplyr run
$ R --vanilla
require(dplyr)
N=2e9; K=100
set.seed(1)
DF <- data.frame(stringsAsFactors=FALSE,
  id1 = sample(sprintf("id%03d",1:K), N, TRUE),
  id2 = sample(sprintf("id%03d",1:K), N, TRUE),
  id3 = sample(sprintf("id%010d",1:(N/K)), N, TRUE),
  id4 = sample(K, N, TRUE),                          
  id5 = sample(K, N, TRUE),                         
  id6 = sample(N/K, N, TRUE),                       
  v1 =  sample(5, N, TRUE),                         
  v2 =  sample(1e6, N, TRUE),                       
  v3 =  sample(round(runif(100,max=100),4), N, TRUE)
)
cat("GB =", round(sum(gc()[,2])/1024, 3), "\n")
system.time( DF %>% group_by(id1) %>% summarise(sum(v1)) )
system.time( DF %>% group_by(id1) %>% summarise(sum(v1)) )
system.time( DF %>% group_by(id1,id2) %>% summarise(sum(v1)) )
system.time( DF %>% group_by(id1,id2) %>% summarise(sum(v1)) )
system.time( DF %>% group_by(id3) %>% summarise(sum(v1),mean(v3)) )
system.time( DF %>% group_by(id3) %>% summarise(sum(v1),mean(v3)) )
system.time( DF %>% group_by(id4) %>% summarise_each(funs(mean), vars=7:9) )
system.time( DF %>% group_by(id4) %>% summarise_each(funs(mean), vars=7:9) )
system.time( DF %>% group_by(id6) %>% summarise_each(funs(sum), vars=7:9) )
system.time( DF %>% group_by(id6) %>% summarise_each(funs(sum), vars=7:9) )

R info

$ R
# R version 3.1.1 (2014-07-10) -- "Sock it to Me"
# Copyright (C) 2014 The R Foundation for Statistical Computing
# Platform: x86_64-pc-linux-gnu (64-bit)

> sessionInfo()
# R version 3.1.1 (2014-07-10)
# Platform: x86_64-pc-linux-gnu (64-bit)
# 
# locale:
#  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
#  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
#  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
#  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
#  [9] LC_ADDRESS=C               LC_TELEPHONE=C
# [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods base

# other attached packages:
# [1] dplyr_0.2        data.table_1.9.2
# 
# loaded via a namespace (and not attached):
# [1] assertthat_0.1 parallel_3.1.1 plyr_1.8.1     Rcpp_0.11.2 reshape2_1.4
# [6] stringr_0.6.2  tools_3.1.1

System info

$ lsb_release -a
# No LSB modules are available.
# Distributor ID:    Ubuntu
# Description:    Ubuntu 14.04 LTS
# Release:    14.04
# Codename:    trusty

$ uname -a
# Linux ip-172-31-33-222 3.13.0-29-generic #53-Ubuntu SMP
# Wed Jun 4 21:00:20 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

$ lscpu
# Architecture:          x86_64
# CPU op-mode(s):        32-bit, 64-bit
# Byte Order:            Little Endian
# CPU(s):                32
# On-line CPU(s) list:   0-31
# Thread(s) per core:    2
# Core(s) per socket:    8
# Socket(s):             2
# NUMA node(s):          2
# Vendor ID:             GenuineIntel
# CPU family:            6
# Model:                 62
# Stepping:              4
# CPU MHz:               2494.090
# BogoMIPS:              5049.01
# Hypervisor vendor:     Xen
# Virtualization type:   full
# L1d cache:             32K
# L1i cache:             32K
# L2 cache:              256K
# L3 cache:              25600K
# NUMA node0 CPU(s):     0-7,16-23
# NUMA node1 CPU(s):     8-15,24-31

$ free -h
#              total       used       free     shared    buffers cached
# Mem:          240G       2.4G       237G       364K        60M 780M
# -/+ buffers/cache:       1.6G       238G
# Swap:           0B         0B         0B