phylosamp (version 1.0.1)

translink_expected_links_obs_stsl: Calculate expected number of observed pairs assuming single-transmission and single-linkage

Description

This function calculates the expected number of link pairs observed in a sample of size M. 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_expected_links_obs_stsl(sensitivity, specificity, rho, M)

Value

scalar or vector giving the expected number of linked pairs observed in the sample

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

See Also

Other transmission linkage functions: translink_expected_links_obs_mtml(), translink_expected_links_obs_mtsl(), 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(), translink_tdr()

Examples

# perfect sensitivity and specificity
translink_expected_links_obs_stsl(sensitivity=1, specificity=1, rho=0.5, M=100)

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

translink_expected_links_obs_stsl(sensitivity=0.99, specificity=0.9, rho=0.5, M=100)