translink_samplesize: Calculate sample size needed to identify true transmission...

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

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"
)

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.

Value

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

Author(s)

John Giles, Shirlee Wohl, and Justin Lessler

See Also

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

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

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