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 |