Calculate the transmission probability in a sample
truediscoveryrate()
Calculate true discovery rate of a sample
falsediscoveryrate()
Calculate false discovery rate of a sample
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
Calculate the expected number of links in a sample
exp_links()
Calculate expected number of links in a sample
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
Calculate the expected number true transmission pairs in 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
Sample size needed to obtain specified false discovery rate
samplesize()
Calculate sample size
Calculate the sensitivity and specificity for genetic distance measures
gen_dist_sim
Simulations of the genetic distance distribution
gen_dists()
Calculate genetic distance distribution
sens_spec_calc()
Calculate sensitivity and specificity
sens_spec_roc()
Make ROC from sensitivity and specificity
get_optim_roc()
Find optimal ROC threshold