phylosamp (version 1.0.1)

translink_prob_transmit_mtml: Calculate probability of transmission assuming multiple-transmission and multiple-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 multiple-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 multiple cases \(j\) in the sampled population (\(M\)).

3. Linkage events are independent of one another (i.e, linkage of case \(i\) to case \(j\) has no bearing on linkage of case \(i\) to any other sample).

Usage

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

Value

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

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

Author

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_mtsl(), translink_prob_transmit_stsl(), translink_prob_transmit(), translink_samplesize(), translink_tdr()

Examples

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

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

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