Reference

Probability of transmission Functions to calculate the transmission probability in a sample
translink_fdr()	Calculate false discovery rate of identifying transmission pairs in a sample
translink_tdr()	Calculate true discovery rate of identifying transmission pairs
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
Observed transmission pairs Functions to calculate the expected number of observed transmission pairs in a sample
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
True transmission pairs Functions to calculate the expected number true transmission pairs in a sample
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
Sample size calculations for transmission linkage Functions to calculate the sample size needed to identify transmission pairs given a specified false discovery rate
translink_samplesize()	Calculate sample size needed to identify true transmission links
Genetic distance as a linkage criteria Functions and data to calculate the sensitivity and specificity of genetic distance measures
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
optim_roc_threshold()	Find optimal ROC threshold
genDistSim	Simulations of the genetic distance distribution
gen_dists()	Calculate genetic distance distribution
Estimating variant frequency Functions to esimtate the pathogen variant frequency in a population
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
The coefficient of detection Functions to calculate coefficient of detection ratio between two pathogen variants
vartrack_cod_ratio()	Calculate the coefficient of detection ratio for two variants
Probability of variant detection Functions to estimate the probability of detecting a pathogen variant given a sample size
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
Sample size for variant detection Functions to calculate the sample size needed to detect a pathogen variant
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
Confidence in variant prevalence estimate Functions to estimate the confidence in a variant prevalence estimate given a sample size
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
Sample size for variant prevalence estimation Functions to calculate the sample size needed to estimate the prevalence of a variant in a population
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
Sample size for detecting differential transmission Functions to calculate the sample size needed to detect differential transmission between groups
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
Power for detecting differential transmission Functions to calculate the power given parameters used to detect differential transmission between groups
relR_power()	Calculate power for detecting differential transmission given a sample size
relR_power_simulated()	Simulate power for detecting differential transmission