R/translink_prob_transmit_stsl.R
translink_prob_transmit_stsl.RdThis 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:
Each case \(i\) is linked by transmission to only one other case \(j\) in the population (\(N\)).
Each case \(i\) is linked by the linkage criteria to only one other case \(j\) in the sampled population (\(M\)).
translink_prob_transmit_stsl(sensitivity, specificity, rho, M)scalar or vector giving the sensitivity of the linkage criteria
scalar or vector giving the specificity of the linkage criteria
scalar or vector giving the proportion of the final outbreak size that is sampled
scalar or vector giving the number of cases sampled
scalar or vector giving the probability of transmission between two cases given linkage by phylogenetic criteria
For perfect sensitivity, set sensitivity = 1.
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()
# perfect sensitivity and specificity
translink_prob_transmit_stsl(sensitivity=1, specificity=1, rho=0.2, M=100)
#> [1] 1
# perfect sensitivity only
translink_prob_transmit_stsl(sensitivity=1, specificity=0.95, rho=0.2, M=100)
#> [1] 0.2010021
translink_prob_transmit_stsl(sensitivity=0.99, specificity=0.95, rho=0.9, M=50)
#> [1] 0.898971
translink_prob_transmit_stsl(sensitivity=0.99, specificity=0.95, rho=0.05, M=100)
#> [1] 0.04979498