Expected number of observed pairs assuming single-transmission and single-linkage

Source: R/obs_pairs_stsl.R

[Deprecated] 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 (\(M\)).

obs_pairs_stsl(eta, chi, rho, M)

Arguments

eta

scalar or vector giving the sensitivity of the linkage criteria

chi

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

Value

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

See also

Other obs_pairs: exp_links(), obs_pairs_mtml(), obs_pairs_mtsl()

Author

John Giles, Shirlee Wohl, and Justin Lessler

Examples

# perfect sensitivity and specificity
obs_pairs_stsl(eta=1, chi=1, rho=0.5, M=100)
#> Warning: `obs_pairs_stsl()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `translink_expected_links_obs_stsl()` instead.
#> Warning: The `eta` argument of `obs_pairs_stsl()` is deprecated as of phylosamp 1.0.0.
#> ℹ Please use the `sensitivity` argument of
#>   `translink_expected_links_obs_stsl()` instead.
#> Warning: The `chi` argument of `obs_pairs_stsl()` is deprecated as of phylosamp 1.0.0.
#> ℹ Please use the `specificity` argument of
#>   `translink_expected_links_obs_stsl()` instead.
#> [1] 25

obs_pairs_stsl(eta=0.99, chi=0.9, rho=1, M=50)
#> [1] 24.99841

obs_pairs_stsl(eta=0.99, chi=0.9, rho=0.5, M=100)
#> [1] 49.99925