Calculate expected number of true transmission pairs

Source: R/true_pairs.R

[Deprecated] This function calculates the expected number true transmission pairs in a sample of size M. Assumptions about transmission and linkage (single or multiple) can be specified.

true_pairs(eta, rho, M, R = NULL, assumption = "mtml")

Arguments

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 (default=NULL)

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 (prob_trans_stsl()).

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

  3. 'mtml' for the multiple-transmission multiple-linkage assumption (prob_trans_mtml()).

Value

scalar or vector giving the expected number of true transmission pairs in the sample

See also

Other true_pairs: true_pairs_mtml(), true_pairs_mtsl(), true_pairs_stsl()

Author

John Giles, Shirlee Wohl, and Justin Lessler

Examples

true_pairs(eta=0.99, rho=0.75, M=100, R=1)
#> Warning: `true_pairs()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `translink_expected_links_true()` instead.
#> Warning: The `eta` argument of `true_pairs()` is deprecated as of phylosamp 1.0.0.
#> ℹ Please use the `sensitivity` argument of `translink_expected_links_true()`
#>   instead.
#> Calculating expected number of links assuming multiple-transmission and multiple-linkage
#> [1] 74.25