d4498d719f830e816aa383fa7d5b9c86f7f04a49,skbio/math/stats/evolve/hommola.py,,hommola_cospeciation,#Any#Any#Any#Any#,29

Before Change

    // Generate lists of host and symbiont edges, such that the index
    // of the lists represents an edge connecting the host to the parasite.
    s = 0
    while s < m:
        for i in range(interaction.shape[0]):
            for j in range(interaction.shape[1]):
                if interaction[i, j] == 1:
                    hosts[s] = j
                    pars[s] = i
                    s += 1

    // get a vector of pairwise distances for each interaction edge
    x = _get_dist(hosts, host_dist, range(interaction.shape[1]))
    y = _get_dist(pars, par_dist, range(interaction.shape[0]))

    // calculate the observed correlation coefficient for this host/symbionts

After Change

    // Generate lists of host and symbiont edges, such that the index
    // of the lists represents an edge connecting the host to the parasite.

    pars, hosts = np.nonzero(interaction)

    // print(hosts2, pars2)
    // get a vector of pairwise distances for each interaction edge
    x = _get_dist(hosts, host_dist, range(interaction.shape[1]))

Instances