translink_samplesize: Calculate sample size needed to identify true transmission links

Description

This function calculates the sample size needed to identify transmission links at a predefined false discovery rate, given a final outbreak size \(N\).

Usage

translink_samplesize(
  sensitivity,
  specificity,
  N,
  R = NULL,
  tdr,
  min_pairs = 1,
  assumption = "mtml"
)

Value

scalar or vector giving the sample size needed to meet the given conditions

Arguments

sensitivity

scalar or vector giving the sensitivity of the linkage criteria

specificity

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

tdr

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.
'mtsl' for the multiple-transmission single-linkage assumption.
'mtml' for the multiple-transmission multiple-linkage assumption.

Author

John Giles, Shirlee Wohl, and Justin Lessler

Other transmission linkage functions: translink_expected_links_obs_mtml(), translink_expected_links_obs_mtsl(), translink_expected_links_obs_stsl(), translink_expected_links_obs(), translink_expected_links_true_mtml(), translink_expected_links_true_mtsl(), translink_expected_links_true_stsl(), translink_expected_links_true(), translink_fdr(), translink_prob_transmit_mtml(), translink_prob_transmit_mtsl(), translink_prob_transmit_stsl(), translink_prob_transmit(), translink_tdr()

Examples

Run this code

translink_samplesize(sensitivity=0.99, specificity=0.995, N=100, R=1, tdr=0.75)