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 |
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 |
gen_dists |
Calculate 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 |
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 |
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 |
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 |