phylosamp (version 1.0.1)

translink_prob_transmit_stsl: Calculate probability of transmission assuming single-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 single-transmission and single-linkage method assumes the following:

1. Each case \(i\) is linked by transmission to only one other case \(j\) in the population (\(N\)).

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

Usage

translink_prob_transmit_stsl(sensitivity, specificity, rho, M)

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

Author

John Giles, Shirlee Wohl, and Justin Lessler

Details

For perfect sensitivity, set sensitivity = 1.

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(), translink_samplesize(), translink_tdr()

Examples

# perfect sensitivity and specificity
translink_prob_transmit_stsl(sensitivity=1, specificity=1, rho=0.2, M=100)

# perfect sensitivity only
translink_prob_transmit_stsl(sensitivity=1, specificity=0.95, rho=0.2, M=100)

translink_prob_transmit_stsl(sensitivity=0.99, specificity=0.95, rho=0.9, M=50)

translink_prob_transmit_stsl(sensitivity=0.99, specificity=0.95, rho=0.05, M=100)