francescochecchi/mogadishu_burial_analysis

R scripts and dataset for analysis of burial patterns in Mogadishu, Somalia (2017-2020), as part of an effort to quantify mortality attributable to the COVID-19 pandemic. # Burial patterns during the first COVID-19 epidemic wave in Mogadishu, Somalia: Analysis of satellite imagery Warsame et al. (2021) ijidonline.com)00758-X/fulltext # Notes on data and R analysis code 30 March 2021 Francesco Checchi Department of Infectious Disease Epidemiology Faculty of Epidemiology and Population Health, Keppel St London School of Hygiene and Tropical Medicine Francesco.checchi@lshtm.ac.uk ## Background on the study This repository contains data and R scripts required to replicate an analysis of very high-resolution satellite images covering Banadir Region (the administrative level 1 unit encompassing the capital, Mogadishu), Somalia during a period between 2016 and September 2020. The analysis was conducted by the Somali Disaster Resilience Institute (sdri.so), The Satellite Applications Catapult (sa.catapult.org.uk) and the London School of Hygiene and Tropical Medicine (www.lshtm.ac.uk). We sought to quantify the rate of burials over time in all cemeteries we were able to identify and source imagery for across Mogadishu. We compared pre-2020 to 2020 trends to estimate the rate of excess burials associated with the pandemic. We also scaled the curve of excess burials to varying assumed levels of crude death rate, and combined this with displacement-adjusted estimates of population size over time to quantify the number of excess deaths over Jan-Sep 2020 in Banadir Region. ## Datasets All datasets required to replicate the analysis are included in the file . The file includes a ‘dictionary’ tab, whose column ‘use’ determines which variables are read into R analysis (below). Only variables marked as ‘yes’ for this column are necessary to replicate the analysis. ## R code scripts The script `banadir_covid_control_code.R` loads necessary R packages, sets parameters (these can be modified by the user), loads datasets, calls dependent scripts (below) and outputs some tables and figures. Only this …