Re: [Rd] Very slow subsetting by name

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Thu, 15 Jul 2010 08:38:53 -0700

On 07/15/2010 01:12 AM, Hervé Pagès wrote:
> Hi,
>
> I'm subsetting a named vector using character indices.
> My vector of indices (or keys) is 10x longer than the vector
> I'm subsetting. All my keys are distinct and only 10% of them
> are valid (i.e. match a name of the vector being subsetted).
> It is surprisingly slow:
>
> x1 <- 1:1000
> names(x1) <- paste("a", x1, sep="")
> keys <- sample(c(names(x1), paste("b", 1:9000, sep="")))

>> system.time(y1 <- x1[keys])

> user system elapsed
> 0.410 0.000 0.416
>
> x2 <- 1:2000
> names(x2) <- paste("a", x2, sep="")
> keys <- sample(c(names(x2), paste("b", 1:18000, sep="")))
>> system.time(y2 <- x2[keys])

> user system elapsed
> 1.730 0.000 1.736

For what its worth, I think this comes about in the loop starting at subscript.c:538, which seems to be there to allow [<-,*,character to extend a vector with new named elements

> x=c(a=1)
> x["b"] = 2
> x

a b
1 2

It seems to be irrelevant (?) for sub-setting per se (though by analogy one might expect x["c"] to return a length-1 vector NA with name "c", whereas it returns a vector with names NA).

Seems like the O(n^2) loop through NonNullStringMatch could be replaced by look-ups into a hash, or an additional argument could be propagated to stringSubscript to exit early when names aren't required. Or the call to makeSubscript at subset.c:164 could instead be made to matchE in unique.c.

Martin

>
> x3 <- 1:4000
> names(x3) <- paste("a", x3, sep="")
> keys <- sample(c(names(x3), paste("b", 1:36000, sep="")))

>> system.time(y3 <- x3[keys])

> user system elapsed
> 8.900 0.010 9.227
>
> x4 <- 1:8000
> names(x4) <- paste("a", x4, sep="")
> keys <- sample(c(names(x4), paste("b", 1:72000, sep="")))
>> system.time(y4 <- x4[keys])

> user system elapsed
> 130.390 0.000 132.316
>
> And it's apparently worse than quadratic in time!
>
> I'm wondering why this subsetting by name is so slow since it
> seems it could be implemented with x4[match(keys, names(x4))],
> which is very fast: only 0.012s!
>
> This is with R-2.11.0 and R-2.12.0.
>
> Thanks,
> H.
>
>
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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