My code is slow!

Writing Efficient R Code

Colin Gillespie

Jumping Rivers & Newcastle University

Is my code really slow?

1 second?
1 minute?
1 hour?

Is my code really slow?

Benchmarking

We construct a function around the feature we wish to benchmark
We time the function under different scenarios, e.g., data set

Example: Sequence of numbers

$$ 1, 2, 3, \ldots, n $$

Option 1

1:n

Option 2

seq(1, n)

Option 3

seq(1, n, by = 1)

Function wrapping

colon <- function(n) 1:n
colon(5)

1 2 3 4 5

seq_default <- function(n) seq(1, n)
seq_by <- function(n) seq(1, n, by = 1)

Timing with system.time()

system.time(colon(1e8))

#   user  system elapsed
#  0.032   0.028   0.060

system.time(seq_default(1e8))

#   user  system elapsed
#  0.060   0.028   0.086

system.time(seq_by(1e8))

#   user  system elapsed
#  1.088   0.520   1.600

user time is the CPU time charged for the execution of user instructions.
- system time is the CPU time charged for execution by the system on behalf of the calling process.
- elapsed time is approximately the sum of user and system, this is the number we typically care about.

Storing the result

The trouble with

system.time(colon(1e8))

is we haven't stored the result. We need to rerun to code store the result

res <- colon(1e8)

The <- operator performs both:

Argument passing
Object assignment

system.time(res <- colon(1e8))

The = operator performs one of:

Argument passing
object assignment

# Raises an error
system.time(res = colon(1e8))

Relative time

Method	Absolute time (secs)	Relative time
`colon(n)`	0.060	$0.060/0.060 = 1.00$
`seq_default(n)`	0.086	$0.086/0.060 = 1.40$
`seq_by(n)`	1.607	$1.60/0.060 = 26.7$

Microbenchmark package

Compares functions
- Each function is run multiple times

library("microbenchmark")

n <- 1e8
microbenchmark(colon(n),
               seq_default(n),
               seq_by(n),
               times = 10) # Run each function 10 times

# Unit: milliseconds
#           expr  min   lq  mean  median   uq  max neval cld
#       colon(n)   59  130   220     202  341  391    10  a
# seq_default(n)   94  204   290     337  348  383    10  a
#      seq_by(n) 1945 2044  2260    2275 2359 2787    10   b

Let's practice!

Writing Efficient R Code