| exp_links | Calculate expected number of links in a sample |
| falsediscoveryrate | Calculate false discovery rate of a sample |
| gen_dists | Calculate genetic distance distribution |
| gen_dist_sim | Simulations of the genetic distance distribution |
| get_optim_roc | Find optimal ROC threshold |
| obs_pairs_mtml | Expected number of observed pairs assuming multiple-transmission and multiple-linkage |
| obs_pairs_mtsl | Expected number of observed pairs assuming multiple-transmission and single-linkage |
| obs_pairs_stsl | Expected number of observed pairs assuming single-transmission and single-linkage |
| prob_trans_mtml | Probability of transmission assuming multiple-transmission and multiple-linkage |
| prob_trans_mtsl | Probability of transmission assuming multiple-transmission and single-linkage |
| prob_trans_stsl | Probability of transmission assuming single-transmission and single-linkage |
| samplesize | Calculate sample size |
| sens_spec_calc | Calculate sensitivity and specificity |
| sens_spec_roc | Make ROC from sensitivity and specificity |
| truediscoveryrate | Calculate true discovery rate of a sample |
| true_pairs | Calculate expected number of true transmission pairs |
| true_pairs_mtml | Expected number of true transmission pairs assuming multiple-transmission and multiple-linkage |
| true_pairs_mtsl | Expected number of true transmission pairs assuming multiple-transmission and single-linkage |
| true_pairs_stsl | Expected number of true transmission pairs assuming single-transmission and single-linkage |