Shiny App Documentation

Video Walkthrough

A 15 minute video documenting the various options of the UI and how to use them is available here.

Explanation of Output

There are two results that come out of the Shiny analysis. The first is the incidence estimates, and the second is the bootstrap results.

Incidence results

• 'incidence': The estimated incidence.
• 'transmission rate': The estimated transmission rate. This is the number infected per year per infected individual.
• 'pundiag': The estimated proportion of positive cases that are undiagnosed after removing treated cases and adjusting for miss-reporting.
• 'psay_undiag': The proportion of positive cases that report being undiagnosed.
• 'pmiss_class': The proportion whose diagnosis status is incorrectly reported by the individual and are observed as treated due to viral load or art biomarkers.
• 'phiv': The proportion with a positive diagnosis.
• 'ptester': The proportion who have ever been tested.
• 'mean_time_since_last_test': The mean tie since last test in years.
• 'tid': Mean time between infection and diagnosis in years.
• 'ptruth' The proportion of positive individuals that correctly report their status.
• 'ptreated': The proportion of positive individuals who are identified as treated by viral load or biomarker.

Bootstrap Results

• 'se' : The boostrap standard error.
• 'ci_lower' : The lower bound of the 95% confidence interval.
• 'ci_upper' : The upper bound of the 95% confidence interval.