The Probability of Transmission Given Phylogenetic Linkage

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Documentation for package ‘phylosamp’ version 0.1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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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