Algorithm for sampling without replacement?

Question

I am trying to test the likelihood that a particular clustering of data has occurred by chance. A robust way to do this is Monte Carlo simulation, in which the associations between data and groups are randomly reassigned a large number of times (e.g. 10,000), and a metric of clustering is used to compare the actual data with the simulations to determine a p value.

I've got most of this working, with pointers mapping the grouping to the data elements, so I plan to randomly reassign pointers to data. THE QUESTION: what is a fast way to sample without replacement, so that every pointer is randomly reassigned in the replicate data sets?

For example (these data are just a simplified example):

Data (n=12 values) - Group A: 0.1, 0.2, 0.4 / Group B: 0.5, 0.6, 0.8 / Group C: 0.4, 0.5 / Group D: 0.2, 0.2, 0.3, 0.5

For each replicate data set, I would have the same cluster sizes (A=3, B=3, C=2, D=4) and data values, but would reassign the values to the clusters.

To do this, I could generate random numbers in the range 1-12, assign the first element of group A, then generate random numbers in the range 1-11 and assign the second element in group A, and so on. The pointer reassignment is fast, and I will have pre-allocated all data structures, but the sampling without replacement seems like a problem that might have been solved many times before.

Logic or pseudocode preferred.

Answer 1

Here's some code for sampling without replacement based on Algorithm 3.4.2S of Knuth's book Seminumeric Algorithms.

void SampleWithoutReplacement
(
    int populationSize,    // size of set sampling from
    int sampleSize,        // size of each sample
    vector<int> & samples  // output, zero-offset indicies to selected items
)
{
    // Use Knuth's variable names
    int& n = sampleSize;
    int& N = populationSize;

    int t = 0; // total input records dealt with
    int m = 0; // number of items selected so far
    double u;

    while (m < n)
    {
        u = GetUniform(); // call a uniform(0,1) random number generator

        if ( (N - t)*u >= n - m )
        {
            t++;
        }
        else
        {
            samples[m] = t;
            t++; m++;
        }
    }
}

There is a more efficient but more complex method by Jeffrey Scott Vitter in "An Efficient Algorithm for Sequential Random Sampling," ACM Transactions on Mathematical Software, 13(1), March 1987, 58-67.