HopkinsIDD/cholera_outbreaks_ssa

Cholera outbreaks in sub-Saharan Africa during 2010-2019: A Descriptive Analysis # cholera_outbreaks_ssa This repository provides the data and source code for the following paper: Qulu Zheng, Francisco J Luquero, Iza Ciglenecki, Joseph F. Wamala, Abdinasir Abubakar, Placide Welo, Mukemil Hussen, Mesfin Wossen, Sebastian Yennan, Alama Keita, Justin Lessler, Andrew S. Azman, Elizabeth C. Lee. "Cholera outbreaks in sub-Saharan Africa during 2010-2019: A Descriptive Analysis." International Journal of Infectious Diseases. (DOI: 10.1016/j.ijid.2022.05.039) ## Data (reference_data/) 1. **Summarized characteristics of cholera outbreaks from 2010 through 2019: reference_data/outbreak_data.csv** * _location_: the name of the location where outbreak cases were reported and the name is made up of WHO region, country, and administrative units seperated by "::". * _outbreak_number_: the uid of outbreak occurred in a specific region. * _start_weekday_: the start weekday of the reported cases. * _duration_: the duration of the outbreak in weeks. * _threshold_: the outbreak threshold per week. * _total_suspected_cases_: the total number of suspected cholera cases in an outbreak. * _attack_rate_: the attach rate of an outbreak per 1,000 people. * _total_deaths_: the total number of cholera-associated deaths in an outbreak. NA means death data were not reported. * _cfr_: the case fatality rate of an outbreak. * _temporal_scale_: the temporal scale of the time series data (weekly data). * _country_: the country where the outbreak was reported. * _population_: the total population in the region where the outbreak was reported and in the year when the outbreak was detected. * _area_: the area of the region where the outbreak was reported. * _mean_R0_: the average of the instantaneous reproductive estimates over the first week of an outbreak. * _population_density_: the number of population per km2 in the region where the outbreak was reported. * _rural_urban_: urban regions are places where population density is equal to or higher than 1000 habitants per km2 and ru …