recent: Incidence Estimation Using Recency Assays

Provides functions and methods to estimate incidence from a cross-sectional survey. A Recent Infection Testing Algorithm (RITA) is used to identify likely recent infections and the methods of Fellows (2022) are used to calculate incidence based on the frequency of these likely recent infections.

Installation

You can install from github using

devtools::install_github("fellstat/recent")

Documentation

A brief tour of the package

Technical paper

Hosted User Interface

Shiny web application

Example

library(recent)
data(assay_recent)
rita_incidence(
    recent=assay_data$recent,
    undiagnosed=assay_data$undiagnosed,
    elite_cntr=assay_data$elite_cntr,
    hiv=assay_data$hiv,
    weights=assay_data$weights,
    tslt=assay_data$tslt,
    ever_hiv_test=assay_data$ever_hiv_test
  )