est.inc: Estimate incidence from cross-sectional data

In dmorrison01/CSICalc: Cross-Sectional Incidence Estimate and CI Calculator

Estimate incidence from cross-sectional data

Description

Estimate incidence from cross-sectional data

Usage

est.inc(
  X,
  N0,
  mu_estimate,
  mu_CI_low,
  mu_CI_high,
  mu_CI_level = 0.95,
  mu_prior = fit_gamma_distribution(mean = mu_estimate, lower = mu_CI_low, upper =
    mu_CI_high, confidence_level = mu_CI_level),
  mu_shape = mu_prior[1],
  mu_scale = mu_prior[2],
  incidence_CI_level = 0.95,
  alpha = 1 - incidence_CI_level,
  tol = 1e-08,
  max_incidence_CI_range = c(0, 100)
)

Arguments

X	The number of MAA-positive participants in the cross-sectional sample
N0	The number of seronegative participatns in the cross-sectional sample
mu_estimate	The estimated mean window period, mu
mu_CI_low	The lower confidence limit for the mean window period, mu (can skip this parameter if providing mu_shape and mu_scale)
mu_CI_high	The upper confidence limit for the mean window period, mu (can skip this parameter if providing mu_shape and mu_scale)
mu_CI_level	The confidence level for the mean window period, mu (can skip this parameter if providing 'mu_prior', or 'mu_shape' and 'mu_scale')
mu_prior	The Gamma parameters for the assumed prior distribution on mu (can skip this argument if providing mu_shape and mu_scale directly)
mu_shape	The shape (gamma) parameter for the prior distribution of the mean window period, mu.
mu_scale	The scale (beta) parameter for the prior distribution of the mean window period, mu.
incidence_CI_level	The desired confidence interval coverage probability
alpha	One minus the desired coverage probability
tol	The desired tolerance for matching the specified confidence level
max_incidence_CI_range	The range of incidence rate values to search over (if not wide enough, an error will be produced).

Value

a numeric vector containing the estimated incidence rate, lower confidence limit, and upper confidence limit, in units of new infections per 100 person-years.

dmorrison01/CSICalc documentation built on Aug. 2, 2022, 4:31 a.m.