steffen steffen - 3 months ago 17
R Question

Is R's apply family more than syntactic sugar?

...regarding execution time and / or memory.

If this is not true, prove it with a code snippet. Note that speedup by vectorization does not count. The speedup must come from

apply
(
tapply
,
sapply
, ...) itself.

Answer

The apply functions in R don't provide improved performance over other looping functions (e.g. for). One exception to this is lapply which can be a little faster because it does more work in C code than in R (see this question for an example of this).

But in general, the rule is that you should use an apply function for clarity, not for performance.

I would add to this that apply functions have no side effects, which is an important distinction when it comes to functional programming with R. This can be overridden by using assign or <<-, but that can be very dangerous. Side effects also make a program harder to understand since a variable's state depends on the history.

Edit:

Just to emphasize this with a trivial example that recursively calculates the Fibonacci sequence; this could be run multiple times to get an accurate measure, but the point is that none of the methods have significantly different performance:

> fibo <- function(n) {
+   if ( n < 2 ) n
+   else fibo(n-1) + fibo(n-2)
+ }
> system.time(for(i in 0:26) fibo(i))
   user  system elapsed 
   7.48    0.00    7.52 
> system.time(sapply(0:26, fibo))
   user  system elapsed 
   7.50    0.00    7.54 
> system.time(lapply(0:26, fibo))
   user  system elapsed 
   7.48    0.04    7.54 
> library(plyr)
> system.time(ldply(0:26, fibo))
   user  system elapsed 
   7.52    0.00    7.58 

Edit 2:

Regarding the usage of parallel packages for R (e.g. rpvm, rmpi, snow), these do generally provide apply family functions (even the foreach package is essentially equivalent, despite the name). Here's a simple example of the sapply function in snow:

library(snow)
cl <- makeSOCKcluster(c("localhost","localhost"))
parSapply(cl, 1:20, get("+"), 3)

This example uses a socket cluster, for which no additional software needs to be installed; otherwise you will need something like PVM or MPI (see Tierney's clustering page). snow has the following apply functions:

parLapply(cl, x, fun, ...)
parSapply(cl, X, FUN, ..., simplify = TRUE, USE.NAMES = TRUE)
parApply(cl, X, MARGIN, FUN, ...)
parRapply(cl, x, fun, ...)
parCapply(cl, x, fun, ...)

It makes sense that apply functions should be used for parallel execution since they have no side effects. When you change a variable value within a for loop, it is globally set. On the other hand, all apply functions can safely be used in parallel because changes are local to the function call (unless you try to use assign or <<-, in which case you can introduce side effects). Needless to say, it's critical to be careful about local vs. global variables, especially when dealing with parallel execution.

Edit:

Here's a trivial example to demonstrate the difference between for and *apply so far as side effects are concerned:

> df <- 1:10
> # *apply example
> lapply(2:3, function(i) df <- df * i)
> df
 [1]  1  2  3  4  5  6  7  8  9 10
> # for loop example
> for(i in 2:3) df <- df * i
> df
 [1]  6 12 18 24 30 36 42 48 54 60

Note how the df in the parent environment is altered by for but not *apply.

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