Calculate probability of transmission

This function calculates the probability that two cases are linked by direct transmission given that they have been linked by phylogenetic criteria. Assumptions about transmission and linkage (single or multiple) can be specified.

translink_prob_transmit(
  sensitivity,
  specificity,
  rho,
  M,
  R,
  assumption = "mtml"
)

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

assumption

a character vector indicating which assumptions about transmission and linkage criteria. Default = 'mtml'. Accepted arguments are:

1. 'stsl' for the single-transmission single-linkage assumption.

2. 'mtsl' for the multiple-transmission single-linkage assumption.

3. 'mtml' for the multiple-transmission multiple-linkage assumption.

Value

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

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_stsl(), translink_samplesize(), translink_tdr()

Author

John Giles, Shirlee Wohl, and Justin Lessler

Examples

translink_prob_transmit(sensitivity=0.99, specificity=0.9, rho=0.5, M=100, R=1)
#> Calculating probability of transmission assuming multiple-transmission and multiple-linkage
#> [1] 0.09175162