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

Source: R/obs_pairs_mtsl.R

[Deprecated] This function calculates the expected number of pairs observed in a sample of size M. The multiple-transmission and single-linkage method assumes the following:

  1. Each case \(i\) is, on average, the infector of R cases in the population (\(N\))

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

obs_pairs_mtsl(chi, eta, rho, M, R)

Arguments

chi

scalar or vector giving the specificity of the linkage criteria

eta

scalar or vector giving the sensitivity 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

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_stsl()

Author

John Giles, Shirlee Wohl and Justin Lessler

Examples

# Perfect sensitivity and specificity
obs_pairs_mtsl(eta=1, chi=1, rho=0.5, M=100, R=1)
#> Warning: `obs_pairs_mtsl()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `translink_expected_links_obs_mtsl()` instead.
#> Warning: The `eta` argument of `obs_pairs_mtsl()` is deprecated as of phylosamp 1.0.0.
#> ℹ Please use the `sensitivity` argument of
#>   `translink_expected_links_obs_mtsl()` instead.
#> Warning: The `chi` argument of `obs_pairs_mtsl()` is deprecated as of phylosamp 1.0.0.
#> ℹ Please use the `specificity` argument of
#>   `translink_expected_links_obs_mtsl()` instead.
#> [1] 50

obs_pairs_mtsl(eta=0.99, chi=0.9, rho=1, M=50, R=1)
#> [1] 57.3837

obs_pairs_mtsl(eta=0.99, chi=0.9, rho=0.5, M=100, R=1)
#> [1] 78.7677