phylosamp1.0.1 package

Calculate sample size needed for variant detection assuming periodic s...

Calculate sample size needed for variant detection assuming cross-sect...

Calculate sample size needed for estimating variant prevalence given a...

Expected number of observed pairs assuming multiple-transmission and m...

Calculate expected number of links in a sample

Calculate false discovery rate of a sample

Calculate genetic distance distribution

Calculate genetic distance distribution

Make ROC curve from sensitivity and specificity

Calculate sensitivity and specificity of a genetic distance cutoff

Find optimal ROC threshold

Expected number of observed pairs assuming multiple-transmission and s...

Expected number of observed pairs assuming single-transmission and sin...

Find optimal ROC threshold

phylosamp: Sample Size Calculations for Molecular and Phylogenetic Stu...

Probability of transmission assuming multiple-transmission and multipl...

Probability of transmission assuming multiple-transmission and single-...

Probability of transmission assuming single-transmission and single-li...

Calculate power for detecting differential transmission given a sample...

Simulate power for detecting differential transmission

Calculate sample size needed to detect differential transmission

Calculate simple derived sample size for detecting differential transm...

Calculate sample size for detecting differential transmission with unc...

Calculate sample size for detecting differential transmission correcti...

Function to calculate the error in estimated sample size for use in op...

Calculate optimized sample size for detecting differential transmissio...

Calculate optimal sample size for detecting differential transmission ...

Calculate sample size

Calculate sensitivity and specificity

Make ROC from sensitivity and specificity

Calculate expected number of transmission links in a sample

Calculate expected number of observed pairs assuming multiple-transmis...

Calculate expected number of observed pairs assuming multiple-transmis...

Calculate expected number of observed pairs assuming single-transmissi...

Calculate expected number of true transmission pairs

Calculate expected number of true transmission pairs assuming multiple...

Calculate expected number of true transmission pairs assuming multiple...

Calculate expected number of true transmission pairs assuming single-t...

Calculate false discovery rate of identifying transmission pairs in a ...

Calculate probability of transmission

Calculate probability of transmission assuming multiple-transmission a...

Calculate probability of transmission assuming multiple-transmission a...

Calculate probability of transmission assuming single-transmission and...

Calculate sample size needed to identify true transmission links

Calculate true discovery rate of identifying transmission pairs

Calculate expected number of true transmission pairs

Expected number of true transmission pairs assuming multiple-transmiss...

Expected number of true transmission pairs assuming multiple-transmiss...

Expected number of true transmission pairs assuming single-transmissio...

Calculate true discovery rate of a sample

Calculate cumulative observed variant prevalence at time t given logis...

Calculate multiplicative bias (observed / actual) in variant prevalenc...

Calculate observed variant prevalence at time t given logistic growth

Calculate observed variant prevalence

Calculate the coefficient of detection ratio for two variants

Calculate the probability of detecting a variant given a sample size

Calculate probability of detecting a variant given a per-timestep samp...

Calculate probability of detecting a variant assuming cross-sectional ...

Calculate confidence in a variant estimate given a sample size

Calculate confidence in a variant estimate assuming cross-sectional sa...

Calculate sample size needed for variant detection given a desired pro...

Calculate sample size needed for variant prevalence estimation under c...