relR_samplesize {phylosamp}

Calculate sample size needed to detect differential transmission

Description

Function for calculating sample size given a set of assumptions. This is the high level wrapper function that users should call directly.

Usage

relR_samplesize(
  R_a,
  R_b,
  p_a,
  N,
  alpha = 0.05,
  alternative = c("two_sided", "less", "greater"),
  power = 0.8,
  sensitivity = 1,
  specificity = 1,
  overdispersion = NULL,
  correct_for_imbalance = FALSE
)

Arguments

R_a

Numeric (Positive). The assumed R among the group in the denominator of the ratio. Input value must be greater than 0.

R_b

Numeric (Positive). The assumed R among the group in the numerator of the ratio. Input value must be greater than 0.

p_a

Numeric. The proportion of the population in group a. Must be between 0 and 1.

N

Numeric (Positive). The size of the infected pool. Only one of rho or N should be specified.

alpha

Numeric. The desired alpha level. Default: 0.05

alternative

Character. Specifies the alternative hypothesis. Must be: two_sided (Default), less, or greater

power

Numeric. The desired power. Must be a value between 0 and 1. Default: 0.8.

sensitivity

Numeric. The sensitivity of the linkage criteria. Must be between 0 and 1. Default: 1.

specificity

Numeric. The specificity of the linkage criteria. Must be between 0 and 1. Default: 1.

overdispersion

Numeric (Positive). An overdispersion parameter, set if the assumed distribution of the number of edges is negative binomial. If NULL the assumed distribution is Poisson (equivalent to an overdispersion parameter of infinity) Default: NULL Note that this is equivalent to setting the overdispersion parameter to Inf.

correct_for_imbalance

Logical. Should we use simulation to correct for being over/under powered due to large differences in group sizes? Default: FALSE.

Value

Sample size needed achieve desired type I and II error rates under assumptions. Will return NA and throw a warning if impossible.

Examples

## Calculate sample size needed to detect a difference between groups where 
## group A has a reproductive value of 2, group B has a reproductive 
## value of 2.5, the groups are balanced, and the total outbreak size is 
## 1,000

relR_samplesize(R_a = 2, 
                R_b = 2.5, 
                p_a = 0.5,
                N = 1000)

## Update the above calculation to account for imperfect sensitivity = 0.7
relR_samplesize(R_a = 2, 
                R_b = 2.5, 
                p_a = 0.5,
                N = 1000,
                sensitivity = 0.7)

## Update the above calculation to allow for overdispersion
relR_samplesize(R_a = 2, 
                R_b = 2.5, 
                p_a = 0.5,
                N = 1000,
                sensitivity = 0.7,
                overdispersion = 2000)