PeterJemley / EvidSynthTB

Bayesian Multi-Parameter Evidence Synthesis (MPES) to estimate TB epidemiological parameters.

EvidSynthTB

The goal of EvidSynthTB is to use Bayesian Multi-Parameter Evidence Synthesis (MPES) to estimate TB epidemiological parameters LTBI prevalence and active TB progression rate.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("n8thangreen/EvidSynthTB")

Data

Input data sets used in this analysis are:

• Enhanced TB Surveillance (ETS)
• PREDICT-TB

Model

We want to obtain posterior distributions for LTBI prevalence, pl, and active TB activation rate, lambda. The other model parameters are:

• Xm1: Cohort size (observed)
• Xp1: Number positive test results (observed)
• Xl1: Number latent TB (unobserved)
• XTB1: Number active TB (observed)
• Xm2: Cohort size (observed)
• XTB2: Number active TB (observed)
• p_pos: Test positivity (functional)
• pTB: Probability active TB (functional)
• sens, spec: Test sensitivity and specificity (prior)

A Directed Acyclic Graph of the model is given below.

Example

This is a basic example which shows you how to solve a common problem:

library(EvidSynthTB)
## basic example code