Probability of transmission

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

Expected pairs

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

True transmission pairs

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

Power calculations

Sample size needed to obtain specified false discovery rate

samplesize()

Calculate sample size

Performance of a linkage criteria

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