Dengue in La Reunion

Data and source code to reproduce the analyses from this article.

Dependencies

1. A C++ compiler, like gcc
2. GNU make
3. The boost C++ libraries
4. R (optional, for visualization)

How to run the code

• cd into the code folder.
• Compile with: make
• Run with the desired options (described in main.cpp), for example:

./dengue.exe data20190823.txt lamb 15 11 0.15 0.1 10000 46

• The program will generate 4 output files:
  1. output.csv: MCMC output (log-likelihood, parameters, and acceptance rates)
  2. output_sims.csv: Simulations (average temperature scenario)
  3. output_sims_cold.csv: Simulations (cold temperature scenario)
  4. output_sims_warm.csv: Simulations (warm temperature scenario)

Note

• The data folder contains the epidemiological and climate data used for the analyses
• The output folder contains an example of visualization of simulated trajectories