Probability of transmission assuming multiple-transmission and single-linkage

This function calculates the probability that two cases are linked by direct transmission given that they have been linked by phylogenetic criteria. 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 (\(M\)).

prob_trans_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 probability of transmission between two cases given linkage by phylogenetic criteria

See also

Other prob_trans: prob_trans_mtml(), prob_trans_stsl()

Author

John Giles, Shirlee Wohl, and Justin Lessler

Examples

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

prob_trans_mtsl(eta=0.99, chi=0.9, rho=1, M=50, R=1)
#> [1] 0.8626143

prob_trans_mtsl(eta=0.99, chi=0.9, rho=0.5, M=100, R=1)
#> [1] 0.6284302