Sample Size Calculations for Molecular and Phylogenetic Studies

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Documentation for package ‘phylosamp’ version 1.0.1

• 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
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