translink_tdr: Calculate true discovery rate of identifying transmission...

In HopkinsIDD/phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

Calculate true discovery rate of identifying transmission pairs

Description

This function calculates the true discovery rate (proportion of true transmission pairs) in a sample given the sensitivity and specificity of the linkage criteria, and sample size M. Assumptions about transmission and linkage (single or multiple) can be specified.

Usage

translink_tdr(sensitivity, specificity, rho, M, R = NULL, assumption = "mtml")

Arguments

sensitivity	scalar or vector giving the sensitivity of the linkage criteria
specificity	scalar or vector giving the specificity of the linkage criteria
rho	scalar or vector giving the proportion of the final outbreak size that is sampled
M	scalar or vector giving the number of cases sampled
R	scalar or vector giving the effective reproductive number of the pathogen (default=NULL)
assumption	a character vector indicating which assumptions about transmission and linkage criteria. Default = 'mtml'. Accepted arguments are: 'stsl' for the single-transmission single-linkage assumption. 'mtsl' for the multiple-transmission single-linkage assumption. 'mtml' for the multiple-transmission multiple-linkage assumption.

Value

scalar or vector giving the true discovery rate

Author(s)

John Giles, Shirlee Wohl, and Justin Lessler

See Also

Other transmission linkage functions: translink_expected_links_obs_mtml(), translink_expected_links_obs_mtsl(), translink_expected_links_obs_stsl(), translink_expected_links_obs(), translink_expected_links_true_mtml(), translink_expected_links_true_mtsl(), translink_expected_links_true_stsl(), translink_expected_links_true(), translink_fdr(), translink_prob_transmit_mtml(), translink_prob_transmit_mtsl(), translink_prob_transmit_stsl(), translink_prob_transmit(), translink_samplesize()

Examples

# The simplest case: single-transmission, single-linkage, and perfect sensitivity
translink_tdr(sensitivity=1, specificity=0.9, rho=0.5, M=100, assumption='stsl')

# Multiple-transmission and imperfect sensitivity
translink_tdr(sensitivity=0.99, specificity=0.9, rho=1, M=50, R=1, assumption='mtsl')

# Small outbreak, larger sampling proportion
translink_tdr(sensitivity=0.99, specificity=0.95, rho=1, M=50, R=1, assumption='mtml')

# Large outbreak, small sampling proportion
translink_tdr(sensitivity=0.99, specificity=0.95, rho=0.5, M=1000, R=1, assumption='mtml')

HopkinsIDD/phylosamp documentation built on May 28, 2023, 3:21 a.m.