Code for "Stochastic spatiotemporal of African swine fever in wild boar and domestic pigs: epidemic forecasting and comparison of disease management strategies".

About 

The scripts and data held in this repository reproduces the results of the African swine fever (ASF) model as presented in the manuscript:

Dankwa, E.A, Lambert, S., Hayes, S., Thompson, R.N., Donnelly, C.A. Stochastic spatiotemporal of African swine fever in wild boar and domestic pigs: epidemic forecasting and comparison of disease management strategies. 

Note: In the documentation below, folder names are in bold, while file names are in italics.

Contents

The repository contains three folders and three data documentation files.

The folders are:

• pig_herd_component: contains files for modelling ASF infection dynamics in pig herds     

     Subfolders are:    

1.   Phase1: files for Phase 1 model; refer to documentation_phase1_ph.pdf for details 
2.   Phase2: files for Phase 2 model; refer to documentation_phase2_ph.pdf for details     
3.   Phase3: files for Phase 3 model; refer to documentation_phase3_ph.pdf for details

• wild_boar_component: contains files for modelling ASF infection dynamics in wild boar   

     Subfolders are:  

1.   Phase 1: files for Phase 1 model; refer to documentation_phase1_wb.pdf for details 
2.   Phase 2: files for Phase 2 model; refer to documentation_phase2_wb.pdf for details 
3.   Phase 3: files for Phase 3 model; refer to documentation_phase3_wb.pdf for details    

• time_series_plots_all: contains files for producing incidence plots of model predictions under the disease management measures and sensitivity analysis scenarios considered 

     Subfolders are:

1.  scripts: contains the files

      - organize_data_for_plots.R, for organizing data for plots; and

      - time_series_plots_script.R, for producing plots given plotting data

       2.  data: contains plotting_data_scenarios.rda, which holds all data for incidence plots

The data documentation files are

•  Phase 1 model data documentation.pdf,
•  Phase 2 model data documentation.pdf, and
• Phase 3 model data documentation.pdf

for model input and output data at Phase 1, Phase 2 and Phase 3, respectively. These files are referenced in the phase-specific documentation in pig_herd_component and  wild_boar_component.  

Reproduce results 

The setup of the repository allows the pig herd and wild boar components of the model to be analyzed separately, and independently for each phase. 

To reproduce results for wild boar herds at any phase, 
 1.  navigate to the desired phase folder 
 2.  run master_script_....R in the scripts folder.
       
To reproduce results for pig herds at any phase,
 1. navigate to the desired phase folder
 2. run ASF_model.R in the Model_Predict folder.

Queries

Queries and suggestions are always welcome. Please email Emmanuelle at dankwa@stats.ox.ac.uk with such.