prob_trans_stsl: Probability of transmission assuming single-transmission and...

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

Probability of transmission assuming single-transmission and single-linkage

Description

This function calculates the probability that two cases are linked by direct transmission given that they have been linked by phylogenetic criteria. The single-transmission and single-linkage method assumes the following:

1. Each case i is linked by transmission to only one other case j in the population (N).

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

For perfect sensitivity, set eta = 1.

Usage

prob_trans_stsl(eta, chi, rho, M)

Arguments

eta	scalar or vector giving the sensitivity of the linkage criteria
chi	scalar or vector giving the specificity 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

Value

scalar or vector giving the probability of transmission between two cases given linkage by phylogenetic criteria

Author(s)

John Giles, Shirlee Wohl, and Justin Lessler

See Also

Other prob_trans: prob_trans_mtml(), prob_trans_mtsl()

Examples

# perfect sensitivity and specificity
prob_trans_stsl(eta=1, chi=1, rho=0.2, M=100)

# perfect sensitivity only
prob_trans_stsl(eta=1, chi=0.95, rho=0.2, M=100)

prob_trans_stsl(eta=0.99, chi=0.95, rho=0.9, M=50)

prob_trans_stsl(eta=0.99, chi=0.95, rho=0.05, M=100)

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