translink_prob_transmit_mtsl: Calculate probability of transmission assuming...

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

Calculate probability of transmission assuming multiple-transmission and single-linkage

Description

This function calculates the probability that two cases are linked by direct transmission given that they have been linked by phylogenetic criteria. The multiple-transmission and single-linkage method assumes the following:

1. Each case i is, on average, the infector of R cases in the population (N)

2. Each case i is allowed to be linked by the linkage criteria to only one other case j in the sampled population (M).

Usage

translink_prob_transmit_mtsl(specificity, sensitivity, rho, M, R)

Arguments

specificity	scalar or vector giving the specificity of the linkage criteria
sensitivity	scalar or vector giving the sensitivity 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

Value

scalar or vector giving the probability of transmission between two cases given linkage by phylogenetic criteria

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_stsl(), translink_prob_transmit(), translink_samplesize(), translink_tdr()

Examples

# Perfect sensitivity and specificity
translink_prob_transmit_mtsl(sensitivity=1, specificity=1, rho=0.5, M=100, R=1)

translink_prob_transmit_mtsl(sensitivity=0.99, specificity=0.9, rho=1, M=50, R=1)

translink_prob_transmit_mtsl(sensitivity=0.99, specificity=0.9, rho=0.5, M=100, R=1)

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