Man pages for HopkinsIDD/phylosamp
Sample Size Calculations for Molecular and Phylogenetic Studies
| exp_links | Calculate expected number of links in a sample |
| falsediscoveryrate | Calculate false discovery rate of a sample |
| gendist_distribution | Calculate genetic distance distribution |
| gendist_roc_format | Make ROC curve from sensitivity and specificity |
| gen_dists | Calculate genetic distance distribution |
| gendist_sensspec_cutoff | Calculate sensitivity and specificity of a genetic distance... |
| genDistSim | Simulations of the genetic distance distribution |
| get_optim_roc | Find optimal ROC threshold |
| obs_pairs_mtml | Expected number of observed pairs assuming... |
| obs_pairs_mtsl | Expected number of observed pairs assuming... |
| obs_pairs_stsl | Expected number of observed pairs assuming... |
| optim_roc_threshold | Find optimal ROC threshold |
| phylosamp-package | phylosamp: Sample Size Calculations for Molecular and... |
| prob_trans_mtml | Probability of transmission assuming multiple-transmission... |
| prob_trans_mtsl | Probability of transmission assuming multiple-transmission... |
| prob_trans_stsl | Probability of transmission assuming single-transmission and... |
| relR_power | Calculate power for detecting differential transmission given... |
| relR_power_simulated | Simulate power for detecting differential transmission |
| relR_samplesize | Calculate sample size needed to detect differential... |
| relR_samplesize_basic | Calculate simple derived sample size for detecting... |
| relR_samplesize_ci | Calculate sample size for detecting differential transmission... |
| relR_samplesize_linkerr | Calculate sample size for detecting differential transmission... |
| relR_samplesize_opterr | Function to calculate the error in estimated sample size for... |
| relR_samplesize_simsolve | Calculate optimized sample size for detecting differential... |
| relR_samplesize_solve | Calculate optimal sample size for detecting differential... |
| 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... |
| translink_expected_links_obs_mtsl | Calculate expected number of observed pairs assuming... |
| translink_expected_links_obs_stsl | Calculate expected number of observed pairs assuming... |
| translink_expected_links_true | Calculate expected number of true transmission pairs |
| translink_expected_links_true_mtml | Calculate expected number of true transmission pairs assuming... |
| translink_expected_links_true_mtsl | Calculate expected number of true transmission pairs assuming... |
| translink_expected_links_true_stsl | Calculate expected number of true transmission pairs assuming... |
| translink_fdr | Calculate false discovery rate of identifying transmission... |
| translink_prob_transmit | Calculate probability of transmission |
| translink_prob_transmit_mtml | Calculate probability of transmission assuming... |
| translink_prob_transmit_mtsl | Calculate probability of transmission assuming... |
| translink_prob_transmit_stsl | Calculate probability of transmission assuming... |
| translink_samplesize | Calculate sample size needed to identify true transmission... |
| translink_tdr | Calculate true discovery rate of identifying transmission... |
| 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... |
| true_pairs_mtsl | Expected number of true transmission pairs assuming... |
| true_pairs_stsl | Expected number of true transmission pairs assuming... |
| varfreq_cdf_logistic | Calculate cumulative observed variant prevalence at time t... |
| varfreq_expected_mbias | Calculate multiplicative bias (observed / actual) in variant... |
| varfreq_freq_logistic | Calculate observed variant prevalence at time t given... |
| 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... |
| vartrack_prob_detect_cont | Calculate probability of detecting a variant given a... |
| vartrack_prob_detect_xsect | Calculate probability of detecting a variant assuming... |
| vartrack_prob_prev | Calculate confidence in a variant estimate given a sample... |
| vartrack_prob_prev_xsect | Calculate confidence in a variant estimate assuming... |
| vartrack_samplesize_detect | Calculate sample size needed for variant detection given a... |
| vartrack_samplesize_detect_cont | Calculate sample size needed for variant detection assuming... |
| vartrack_samplesize_detect_xsect | Calculate sample size needed for variant detection assuming... |
| vartrack_samplesize_prev | Calculate sample size needed for estimating variant... |
| vartrack_samplesize_prev_xsect | Calculate sample size needed for variant prevalence... |
