true_pairs {phylosamp}

Calculate expected number of true transmission pairs

Description

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.

Usage

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

Author(s)

John Giles, Shirlee Wohl, and Justin Lessler

See Also

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

Examples

true_pairs(eta=0.99, rho=0.75, M=100, R=1)