mustafasikder/wash_cholera

Contains scripts used in the analysis for the Water, Sanitation and Cholera in sub-Saharan Africa manuscript ## WASH Cholera This repo contains scripts to complete the analyses of the Water, Sanitation and Cholera in sub-Saharan Africa manuscript **Description** Univariate country-level and district-level analyses: `country_district_univariate.R` Multivariate regression models: `incidence_rf_gbm.R` Multivariate classification models: `hotspot_rf_gbm.R` Multivariate classification models with hotspot data: `hotspot_rf_gbm_high_incidence.R` **Country Level Data Summary** Aggregated population weighted water and sanitation access/reliance percentage and incidence of cholera per 1,000 by country using the estimates from ref30278-3) and ref33050-7) for 2010-2016. | Country |Piped Water |Other Improved Water |Piped Sanitation | Other Improved Sanitation|Unimproved water|Surface Water|Unimproved Sanitation|Open Defecation|Incidence/1,000| |----|-----|-----|----|-----|----|-----|-----|----|------| Angola|32|26.6|32.6|9.5|11.5|29.9|28.4|29.5|0.09904 Burundi|36.4|46.4|5|47.6|11.4|5.8|43.1|4.3|0.2468 Benin|39.1|33.2|3.6|23.9|21.6|6.1|7.7|64.8|0.04665 Burkina Faso|18|58.4|1.3|29.6|21.7|1.9|3.3|65.8|0.00358 Central African Rep.|12.1|46.4|0.4|32.3|37.6|4|39.1|28.2|0.02886 Côte d'Ivoire|42.6|35.2|15.8|29.2|14.3|7.8|17.2|37.7|0.01891 Cameroon|35.7|34.6|9.7|44.6|20.7|9|37.2|8.5|0.50913 DR Congo|21.2|22.3|3.9|35.9|45.3|11.2|43.9|16.3|0.36399 Republic of Congo|27.1|34.2|4.8|26.2|21.3|17.4|50.3|18.8|0.20317 Ethiopia|37.5|23.2|1.9|17.2|23.4|16|40.6|40.3|0.06755 Gabon|61.9|20.7|20.9|16|1.8|15.6|49.3|13.8|0.00033 Ghana|28.3|54.9|13.3|48.3|4.7|12.1|7.6|30.9|0.40156 Guinea|23.9|49.8|9.5|32.3|13|13.3|38.6|19.6|0.20086 Gambia|63|23.4|7.3|56.2|13.4|0.2|12.3|24.1|0.00612 Guinea-Bissau|23.8|34.7|7|46|41.1|0.4|20.8|26.1|0.39827 Equatorial Guinea|39|30.8|8.3|33.8|16.3|13.8|50.9|7|0.001 Kenya|31.5|28.5|6.2|41.5|13.4|26.6|33.4|18.9|0.17645 Liberia|2.9|69.8|9.8|22.8|7.5|19.8|12.5|54.9|0.11201 Madagascar|23.9|19.1|3.2|8.6|32.7|24.3|36.8|51.4|0.00895 Mali|32.6|34.4|4.1|37.8|29.1|3.9|44.1|14|0.032 …