gafuglstad/prevalence-mapping

Case studies of small area estimation of vaccination coverage in Nigeria and neonatal mortality rate in Malawi. Code for "The Two Cultures for Prevalence Mapping: Small Area Estimation and Spatial Statistics" arXiv preprint Prerequisites Code is written in R and uses packages on CRAN Additionally, the testing version of INLA needs to be installed: r-inla.org Description The paper concerns spatial estimation of prevalences in administrative areas. This repository contains the code for two case studies: spatial estimation of vaccination coverage in Nigeria in 2018, and spatio-temporal estimation of neonatal mortality rate (NMR) in Malawi in 2000–2019. The former is part of the current version of the paper, and the latter was part of an earlier part of the paper. Case studies Spatial estimation of vaccination coverage Start by running "Nigeria-Vac/Code/CaseStudy_Nigeria.R". Goal We consider vaccination coverage for the first dose of measles-containing-vaccine (MCV1) among children aged 12–23 months in Nigeria. The goal of the analysis is estimation of MCV1 coverage for admin1, which consists of 36 states and the federal capital area, and admin2, which consists of 774 local government areas (LGAs), and to this end we analyze the 2018 Nigeria Demographic and Health Survey. Code files Nigeria-Vac/Code/CaseStudy_Nigeria.R: Main script. Runs all models and validation and creates figures and data for tables. Nigeria-Vac/Code/functions.R: Support code. Provides functions for fitting models and for aggregation. Data files Nigeria-Vac/Data/gadm36_NGA_shp: Shape file for admin0, admin1 and admin2. Nigeria-Vac/Data/Nigeria_2017_proj: Urban proportions in updated sampling frame from 2017. Nigeria-Vac/Data/Nigeria_AGG_DHS: Data extracted from Nigeria 2018 DHS survey. Nigeria-Vac/Data/Nigeria_pop: Population rasters. Nigeria-Vac/Data/preparedCovRasters: Prepared covariate rasters. Data sources WorldPop Poverty map for 2010 ($2 a day limit): worldpop.org Population (all age, all sex) 2017: https: …