mcewenkhundi/TBhotspotclustersplos

Research compendium for Neighbourhood prevalence-to-notification ratios for adult bacteriologically-confirmed tuberculosis reveals hotspots of underdiagnosis in Blantyre, Malawi # TBhotspotclustersplos The goal of TBhotspotclustersplos repository is to replicate the analysis of the manuscript: *“Neighbourhood prevalence-to-notification ratios for adult bacteriologically-confirmed tuberculosis reveals hotspots of underdiagnosis in Blantyre, Malawi”* Authors: McEwen Khundi 1,2 , James R Carpenter 1 , Elizabeth L Corbett 1,2 , Helena R A Feasey 1,2 , Rebecca Nzawa Soko 1,2 , Marriott Nliwasa 1,3 , Hussein Twabi 3 , Lingstone Chiume 1 , Rachael M Burke 1,2 , Katherine C Horton 2 , Peter J Dodd 4 , Ted Cohen 5 , Peter MacPherson 1,2 , 6 1. Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi, 2. London School of Hygiene and Tropical Medicine, UK, 3. Helse Nord TB Initiative, College of Medicine, University of Malawi, 4. School of Health and Related Research, University of Sheffield, Sheffield, UK, 5. Yale School of Public Health, New Haven, USA, 6. Department of Clinical Sciences, Liverpool School of Tropical Medicine, UK ## Replicable code (Rscript folder description) Description of the analysis scripts and source script of each output in the analysis 1. Part1\_exploratory\_analysis\_baseline\_graphs\_tables\_2021-09-29.Rmd - Script for producing table1, fig1 and fig2 2. Part2\_all\_models\_notif\_car.R - Script for producing notification icar models 3. Part2\_all\_models\_notif\_rintc.R - Script for producing notification random intercept models 4. Part2\_all\_models\_prev\_car.R - Script for producing prevalence icar models 5. Part2\_all\_models\_prev\_rintc.R - Script for producing prevalence random intercept models 6. Part3\_notification\_models\_loo\_comparison\_2021-09-29.R - Script for model comparison of all notification models 7. Part3\_prevalence\_models\_loo\_comparison\_2021-09-29.R - Script for model comparison of all prevalence models 8. Part4\_derive\_posteriors\_rintc\_2021-09-29.Rmd - Script for deriving posterior samples from the selected final m …