francescochecchi/sdn_mortality_2024

Input dataset and R scripts to replicate a capture-recapture analysis of population mortality in Sudan, 2023-2024. ## Population mortality in Sudan, 2023-2024: A multiple-systems estimation analysis ### Description of input dataset and R analysis scripts October 2024 Funding support: United States Centers for Disease Control and Prevention; United Kingdom Foreign, Commonwealth and Development Office ## General description This repository contains data and R scripts needed to replicate the above analysis. The two datasets required are found in the `\in` folder, and are read automatically when the code is run. Every row in dataset `sdn_cam_data_final_public.xlsx` contains an individual record of a deceased person, as contained in one of three independent lists generated by the study. The Excel file also contains a variable dictionary. All the code is found in the `\code` folder. To replicate the analysis, follow these steps: * Download and unzip the repository to any folder in your computer (other than the Downloads folder, which usually gets wiped automatically). The folder is identified automatically when the code is run. * Download R and RStudio (see download links on [posit.co]). While R is sufficient to run the analysis, it is recommended to instead run the scripts from the RStudio interface. * Open and run the entire `00_master_code.R` script (just press Alt+Ctrl+R). This will create an `\out` folder with further sub-folders, to which output tables and graphs will be saved automatically. As this scripts calls all the others, it alone is sufficient to replicate the analysis. On a cheap laptop, it should take about 5-10 hours to run the analysis (95% of this time is spent on the simulation in code 05, but the time can be cut down to minutes if the user specifies a lower number of runs (search for the 'n_runs' parameter in script 05 and modify it from 1000 to, say, 10). ## Description of each R script * `00_master_code.R` installs or loads R packages needed for this analysis, sets general parameters and sources the other scripts in logical o …