From mtmorgan at fhcrc.org  Wed Nov 19 04:52:27 2008
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Tue, 18 Nov 2008 19:52:27 -0800
Subject: [Rd] more efficient small subsets from moderate vectors?
Message-ID: <6phk5b0cqys.fsf@gopher4.fhcrc.org>

This creates a named vector of length nx, then repeatedly draws a
single sample from it.

lkup <- function(nx, m=10000L) {
    tbl <- seq_len(nx)
    names(tbl) <- as.character(tbl)
    v <- sample(names(tbl), m, replace=TRUE)
    system.time(for(k in v) tbl[k], gcFirst=TRUE)
}

There is an abrupt performance degredation at nx=1000

> lkup(1000)
   user  system elapsed
  0.180   0.000   0.179
> lkup(1001)
   user  system elapsed
  2.444   0.016   2.462
          
This is because of the heuristic at stringSubscript.c:424, which
switches from a 'naive' nx * ns algorithm (ns is the number of
elements to be extracted, ns = 1 above) to a hash-based strategy when
nx * ns > 1.

It seems like the 'naive' algorithm takes nx * ns time, whereas the
hash-based algorithm takes C(nx) + ns, where C(nx) is the cost of
creating the hash. Guessing that the cost of building the hash is
about linear in nx, the results above suggest a new heuristic for
switching at ns of about 15.

(I don't quite follow the last sentence of the comment above
stringSubscript, so perhaps I misunderstand entirely).

Martin

> sessionInfo()
R version 2.9.0 Under development (unstable) (2008-11-15 r46953)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793



[Rd] more efficient small subsets from moderate vectors?
Martin Morgan