The R code presented here provides all the scripts required to run the superensemble of probabilistic dengue models
presented in the paper "Probabilistic seasonal dengue forecasting in Vietnam: A modelling study using superensembles"
published in PLoS Medicine by FJ Colón-González et al. (2021). The code comprises seven ordered sub-routines. Each sub-routine has
a number that indicates its location in a sequence of steps starting at 00 and ending at 06. The sub-routine called
06_Run_routines.R contains all the commands required to load and perform all operations in sequence. We suggest
users only run that script. A description of each sub-routine is provided below.
- 00_Functions.R: Loads all developer-defined functions required for the correct functionality of the system.
- 01_Load_packages.R: Installs (if not already installed) and loads all the packages required for the correct functionality of the system.
- 02_Monthly_data.R: Reads annual observations of land-cover and population data, and generates monthly time series for their incorporation into the modelling framework.
- 03_Pre-processing.R: Performs data wrangling and generates a clean data set of observed and foreacsted dengue and ancillary data.
- 04_Fit_models.R: Fits all probabilistic models required to generate the superensemble, and creates a superensemble of probabilistic dengue models using an Integrated nested Laplace approximations (INLA) approach and the Continuous Rank Probability Score.
- 05_Model_outputs.R: Generates csv output files and stores them in the sub-folder output.
- 06_Run_routines.R: Runs all previous sub-routines. In this file, users will need to specify the folder and sub-folders where data and scripts are stored.
For any issues with the code please contact Felipe J Colón-González