exp_links               Calculate expected number of links in a sample
falsediscoveryrate      Calculate false discovery rate of a sample
genDistSim              Simulations of the genetic distance
                        distribution
gen_dists               Calculate genetic distance distribution
gendist_distribution    Calculate genetic distance distribution
gendist_roc_format      Make ROC curve from sensitivity and specificity
gendist_sensspec_cutoff
                        Calculate sensitivity and specificity of a
                        genetic distance cutoff
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
optim_roc_threshold     Find optimal ROC threshold
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
relR_power              Calculate power for detecting differential
                        transmission given a sample size
relR_power_simulated    Simulate power for detecting differential
                        transmission
relR_samplesize         Calculate sample size needed to detect
                        differential transmission
relR_samplesize_basic   Calculate simple derived sample size for
                        detecting differential transmission
relR_samplesize_ci      Calculate sample size for detecting
                        differential transmission with uncertainty
                        bounds
relR_samplesize_linkerr
                        Calculate sample size for detecting
                        differential transmission correcting for
                        sensitivity and specificity
relR_samplesize_opterr
                        Function to calculate the error in estimated
                        sample size for use in optimize function
relR_samplesize_simsolve
                        Calculate optimized sample size for detecting
                        differential transmission
relR_samplesize_solve   Calculate optimal sample size for detecting
                        differential transmission with imperfect
                        specificity
samplesize              Calculate sample size
sens_spec_calc          Calculate sensitivity and specificity
sens_spec_roc           Make ROC from sensitivity and specificity
translink_expected_links_obs
                        Calculate expected number of transmission links
                        in a sample
translink_expected_links_obs_mtml
                        Calculate expected number of observed pairs
                        assuming multiple-transmission and
                        multiple-linkage
translink_expected_links_obs_mtsl
                        Calculate expected number of observed pairs
                        assuming multiple-transmission and
                        single-linkage
translink_expected_links_obs_stsl
                        Calculate expected number of observed pairs
                        assuming single-transmission and single-linkage
translink_expected_links_true
                        Calculate expected number of true transmission
                        pairs
translink_expected_links_true_mtml
                        Calculate expected number of true transmission
                        pairs assuming multiple-transmission and
                        multiple-linkage
translink_expected_links_true_mtsl
                        Calculate expected number of true transmission
                        pairs assuming multiple-transmission and
                        single-linkage
translink_expected_links_true_stsl
                        Calculate expected number of true transmission
                        pairs assuming single-transmission and
                        single-linkage
translink_fdr           Calculate false discovery rate of identifying
                        transmission pairs in a sample
translink_prob_transmit
                        Calculate probability of transmission
translink_prob_transmit_mtml
                        Calculate probability of transmission assuming
                        multiple-transmission and multiple-linkage
translink_prob_transmit_mtsl
                        Calculate probability of transmission assuming
                        multiple-transmission and single-linkage
translink_prob_transmit_stsl
                        Calculate probability of transmission assuming
                        single-transmission and single-linkage
translink_samplesize    Calculate sample size needed to identify true
                        transmission links
translink_tdr           Calculate true discovery rate of identifying
                        transmission pairs
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
truediscoveryrate       Calculate true discovery rate of a sample
varfreq_cdf_logistic    Calculate cumulative observed variant
                        prevalence at time t given logistic growth
varfreq_expected_mbias
                        Calculate multiplicative bias (observed /
                        actual) in variant prevalence
varfreq_freq_logistic   Calculate observed variant prevalence at time t
                        given logistic growth
varfreq_obs_freq        Calculate observed variant prevalence
vartrack_cod_ratio      Calculate the coefficient of detection ratio
                        for two variants
vartrack_prob_detect    Calculate the probability of detecting a
                        variant given a sample size
vartrack_prob_detect_cont
                        Calculate probability of detecting a variant
                        given a per-timestep sample size assuming
                        periodic sampling
vartrack_prob_detect_xsect
                        Calculate probability of detecting a variant
                        assuming cross-sectional sampling
vartrack_prob_prev      Calculate confidence in a variant estimate
                        given a sample size
vartrack_prob_prev_xsect
                        Calculate confidence in a variant estimate
                        assuming cross-sectional sampling
vartrack_samplesize_detect
                        Calculate sample size needed for variant
                        detection given a desired probability of
                        detection
vartrack_samplesize_detect_cont
                        Calculate sample size needed for variant
                        detection assuming periodic sampling
vartrack_samplesize_detect_xsect
                        Calculate sample size needed for variant
                        detection assuming cross-sectional sampling
vartrack_samplesize_prev
                        Calculate sample size needed for estimating
                        variant prevalence given a desired confidence
vartrack_samplesize_prev_xsect
                        Calculate sample size needed for variant
                        prevalence estimation under cross-sectional
                        sampling
