samplesize: Calculate sample size

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

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: '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 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)

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