Project overview

Code for evaluating a measles outbreak response vaccination outsize cold chain. The associated peer reviewed paper can be found here.

Requirements

Directories

1. app - contains the R scripts to run the shiny app (no longer being developed)
2. data - stores input data in csv format
3. figures - figures from analysis
4. model_output - stores the simulation output for further wrangling and visualizations
5. scripts - all analysis scripts

Simulation Design

Below, I outline how the flow of the simulation framework

Key scripts

NOTE: To run the analysis scripts, first run measles_orv_strategies.rproj to open an R project session.

1. strategy_list_complete.R - the complete list of all possible vaccination strategies.
2. scenarios.R - a complete set up of scenarios to run.
3. analyses_parameters.R - all shared parameters across scenarios go in this script a. add supply chain params to the sc_model_params list and epidemiological params to the orc_model_params list.
4. measles_functions.R - the discrete-time daily time step SEIR transmission dynamics model and associated functions, i.e., vaccination, and infection.
5. simulation_params.R - a script for create the table of simulation parameters by combining the configuration of the strategies, scenarios, and metapopulation parameters.
6. supply_chain_functions.R - functions for calculating individual units in the vaccine supply chain components, e.g., number of ice packs needed based on ambient temperature, number of doses per equipment type and vaccine type, etc.
7. wrappers_supply_chain.R - wrapper functions that combine individual functions in supply_chain_functions.R to achieve a more complex output, e.g., time needed to freeze ice.
8. full_analysis.R - run this script to execute a full analysis of both the supply chain and epidemiological model to produce plots and save simulation output to file.
9. Epidemics7 poster analysis: Go into the directory, then into <epidemics7_analysis> and run the following scripts in order:
   • sc_analysis_epidemics7.R
   • epi_analysis_epidemics7.R
10. plotting_functions.R: custom themes and functions for formatting plots for publications and presentations
11. visualizations.R: script for accessing and visualizing model output

This repo SHOULD contain:

1. Scripts for running the analysis
2. Simulation figures and outputs mostly as .csv, .rds, and the generic image formats

This repo SHOULDN'T contain:

1. Large files, for e.g., videos, audios, large data files (> 100 mb)
2. Microsoft office files, unless completely necessary because these filetypes will not be tracked

How to run analyses.

You can either source the script run_full_main_analysis.R or run the individual scripts in the order that they appear in "scripts\deterministic_framework_analysis\main_analysis\run_full_main_analysis.R".