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 modelling of African swine fever in wild boar and domestic pigs: epidemic forecasting and comparison of disease management strategies.
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 herdsSubfolders are:
Phase1
: files for Phase 1 model; refer todocumentation_phase1_ph.pdf
for detailsPhase2
: files for Phase 2 model; refer todocumentation_phase2_ph.pdf
for detailsPhase3
: files for Phase 3 model; refer todocumentation_phase3_ph.pdf
for details
-
wild_boar_component
: contains files for modelling ASF infection dynamics in wild boarSubfolders are:
- Phase 1: files for Phase 1 model; refer to
documentation_phase1_wb.pdf
for details - Phase 2: files for Phase 2 model; refer to
documentation_phase2_wb.pdf
for details - Phase 3: files for Phase 3 model; refer to
documentation_phase3_wb.pdf
for details
- Phase 1: files for Phase 1 model; refer to
-
time_series_plots_all
: contains files for producing incidence plots of model predictions under the disease management measures and sensitivity analysis scenarios consideredSubfolders are:
scripts
: contains the filesorganize_data_for_plots.R
, for organizing data for plots; andtime_series_plots_script.R
, for producing plots given plotting data
data
: containsplotting_data_scenarios.rda
, which holds all data for incidence plots
The 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
.
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,
- navigate to the desired phase folder
- run
master_script_....R
in thescripts
folder.
To reproduce results for pig herds at any phase,
- navigate to the desired phase folder
- run
ASF_model.R
in theModel_Predict
folder.
Queries and suggestions are always welcome. Please email Emmanuelle at emmanuelledankwa@gmail.com with such.
MIT License