samplesize {phylosamp}

Calculate sample size

Description

This function calculates the sample size needed to obtain at least a defined false discovery rate given a final outbreak size N.

Usage

samplesize(eta, chi, N, R = NULL, phi, min_pairs = 1, assumption = "mtml")

Arguments

eta

scalar or vector giving the sensitivity of the linkage criteria

chi

scalar or vector giving the specificity of the linkage criteria

N

scalar or vector giving the final outbreak size

R

scalar or vector giving the effective reproductive number of the pathogen

phi

scalar or vector giving the desired true discovery rate (1-false discovery rate)

min_pairs

minimum number of linked pairs observed in the sample, defaults to 1 pair (2 samples); this is to ensure reasonable results are obtained

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 sample size needed to meet the given conditions

Author(s)

John Giles, Shirlee Wohl, and Justin Lessler

Examples

samplesize(eta=0.99, chi=0.995, N=100, R=1, phi=0.75)