sjfox / malaria-risk

Malaria transmission risk estimation

Description of code

• To run the code first you have to run convert-mosq-raster-to-county.R which takes all of the mosquito occurrence probabilities and averages them at the county level. It then saves the county mosquito probabilities into a nice usable format.
• Run get-county-gdp.R to gather all of the county per capita GDP estimates from ACD
• Run calc-malaria-county-rnots.R to calculate the R0s based on all of the data and parameter estimates gathered.
• Run posterior-malaria-rnots.R to calculate the posterior distributions for R0 based on the prior distribution and the importations estimated.
• Run main-transmission-risk-fig.R to make some maps and make sure everything worked correctly.
• calc-county-temperatures.R is not needed if using Mathew's provided temperature data

Data needed for running

• You need the anopholes_maps/ folder in raw-data, which has the compressed zip of mosquito occurrence provided by the malaria atlas project. You can unzip them yourself or the code can do it for you.
• Right now you don't need the uscounties_malaria_case.csv file in raw-data, but eventually that will probably be used.