Minimizing severity of dengue serotype 1 infection by transmissible interfering particles

This repository makes available the source code for the work: "Minimizing severity of dengue serotype 1 infection by transmissible interfering particles", available online as an open access preprint on bioRxive: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4108267.

Prerequisites

To run the codes you will require R(>=3.30) and latest version of RStudio.

Directory structure

├── project
│   ├── data
│   ├── images
│   ├── results
│   ├── src
│   │   ├── plot_raw_data_and_sensivity.R
│   │   ├── run_models_sim.R
│   │   ├── analyze_fits.R
│   │   ├── TIPs_therapy.R
|   |   ├── model_a_sim.stan
|   |   ├── model_b_sim.stan

• The data folder contains all preprocessed datasets reqruired to run the codes in the src folder.
• The images folder contains plots generated from the codes in src folder.
• The results folder contains all results saved (as .RData format) after runing the codes in the src folder.
• The src folder contains all source codes required to produce the results and images.

How to run scripts

1. Run the script plot_raw_data_and_sensivity.R to generate plots for Fig 1 and Fig 2 shown in the images folder
2. Run the script run_models_sim.R to fit the Bayesian hierarchical model model_a_sim.stan or model_b_sim.stan. These models are written using the Stan programing language.
3. Run the scrip analyze_fits.R to analyze results of the fits and to generate plots for Figures 3-4 S1, S2 and S5 shown in the images folder.
4. Run the scrip TIPs_therapy.R to simulate results for experiments 1, 2 and the individual effects. This script is also used to generate plots for Figures 5-7, S3, S4 and S6-S16 shown in the images folder.

Note: some simulation results are too large to to be uploaded in the repository, but all can be generated from the scripts.