[R] speed up the code

[rex.dwyer at syngenta.com]

Yes, remove the call to intersect, and rely on the results of match to tell you whether there is an overlap.  If there are any matches,  all(is.na(index)) will be false.  Read help for match.

?match


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Hui Du
Sent: Wednesday, February 16, 2011 6:29 PM
To: r-help at r-project.org
Subject: [R] speed up the code


Hi All,

The following is a snippet of my code. It works fine but it is very slow. Is it possible to speed it up by using different data structure or better solution? For 40000 runs, it takes 8 minutes now. Thanks a lot



fun_activation = function(s_k, s_hat, x_k, s_hat_len)
{
    common = intersect(s_k, s_hat);
    if(length(common) != 0)
    {
        index  = match(common, s_k);
        round(sum(x_k[index]) * length(common) / (s_hat_len * length(s_k)), 3);
    }
    else
    {
        0;
    }

}

fun_x = function(a)
{
    round(runif(length(a), 0, 1), 2);
}

symbol_len = 50;
PHI_set = 1:symbol_len;

S = matrix(replicate(M * M, sort(sample(PHI_set, sample(symbol_len, 1)))), M, M);
X = matrix(mapply(fun_x, S), M, M);

S_hat = c(28, 34, 35)
S_hat_len = length(S_hat);

  S_hat_matrix = matrix(list(S_hat), M, M);

system.time(
for(I in 1:40000)
{
A = matrix(mapply(fun_activation, S, S_hat_matrix, X, S_hat_len), M, M);
}
)



HXD


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