Infectious disease

Exploring Estimates of the Tuberculosis Case Fatality Ratio - with getTBinR

This is a quick post exploring estimates of the case fatality ratio for Tuberculosis (TB) from data published by the World Health Organisation (WHO). It makes use of getTBinR (which is now on CRAN), pacman for package management, hrbrthemes for plot themes, and pathwork for combining multiple plots into a storyboard. For an introduction to using getTBinR to explore the WHO TB data see this post. It is estimated that in 2016 there was more than 10 million cases of active TB, with 1.

Exploring Global Trends in Tuberculosis Incidence Rates - with GetTBinR

In November I attended Epidemics, which is a conference focused on modelling infectious diseases. There was a lot of great work and perhaps most excitingly a lot of work being offered as R packages. I’ve recently begun wrapping all my analytical work in R packages, as it makes producing reproducible research a breeze! Unfortunately all of this work is still making it’s way towards publication and for a variety of reasons can’t be shared until it has passed this hurdle.

Tuberculosis Incidence and Interventions in England and Wales, 1913-2016

This interactive dashboard uses data on Tuberculosis incidence from 1913-1916 released by Public Health England and combines it with data on the interventions against Tuberculosis that have been discovered/implemented over the last century. The data was cleaned and imported into R using the tbinenglanddataclean R package, which also contains information on how to apply for additional data, scripts to clean data extracts and graphing functions to visualise them. The dashboard is a work in progress and additional interventions, new figures and increased interactivity will be added over time.