petermacp/BlantyreTBEpi

Research compendium for Spatial analysis of TB notifications in Blantyre, Malawi BlantyreTBEpi ------------- This package contains data and code to replicate the analysis of the manuscript: *"Disparities in access to diagnosis and care in Blantyre, Malawi identified through enhanced citywide tuberculosis surveillance and spatial analysis"* Authors: Peter MacPherson PhD 1,2 , McEwen Khundi MSc 1 , Marriott Nliwasa MBBS 3 , Augustine T Choko MSc 1,4 , Vincent K Phiri BSc 1 , Emily L Webb PhD 4 , James Mpunga 5 , Peter J Dodd PhD 6 , Ted Cohen DPH 7 , Rebecca Harris 1,4 , Elizabeth L Corbett F. Med Sci 1,4 Affiliations: 1. TB/HIV Group, Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi 2. Department of Clinical Sciences, Liverpool School of Tropical Medicine, UK 3. Helse-Nord TB Programme, College of Medicine, University of Malawi, Malawi 4. MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, UK 5. National TB Programme, Lilongwe, Malawi 6. School of Health and Related Research, University of Sheffield, UK 7. Yale School of Public Health, Yale University, USA Installation ------------ You can install the package from GitHub with: ``` r # install.packages("devtools") devtools::install_github("petermacp/BlantyreTBEpi") library(BlantyreTBEpi) ``` Replicable code --------------- The script `BlantyreTBEpi_analysis.rmd` should be opened, and can be knitted using the `rmarkdown` package, or the `knit` button in RStudio to produce an .html output copy of analysis included within the manuscript. Data ---- Incuded within the package `data/` folder are minimially-reproducable datasets that are used in the analysis code. To load a dataset, run the following command: ``` r # install.packages("devtools") devtools::install_github("petermacp/BlantyreTBEpi") library(BlantyreTBEpi) data("dat", package="BlantyreTBEpi") ``` The following datasets and variables are included within the `data/` folder of the package: ### `all_cases_sf.rda` Individual-level dataset including records of …