true_pairs: Calculate expected number of true transmission pairs

In HopkinsIDD/phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

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: 'stsl' for the single-transmission single-linkage assumption (prob_trans_stsl()). 'mtsl' for the multiple-transmission single-linkage assumption (prob_trans_mtsl()). '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)

HopkinsIDD/phylosamp documentation built on May 28, 2023, 3:21 a.m.