R help - Feb 2011 - 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


	[[alternative HTML version deleted]]

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


        [[alternative HTML version deleted]]

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