John-Polo/abc_R

abc_R

This repository contains code for running case studies 1-3 in the manuscript entitled "Approximate Bayesian Computation for infectious disease modelling" by Minter and Retkute.

Usage

Case study 1: Deterministic compartmental model

Case study can be run in the following manner:

Rscript ABC_rejection_1.R

Rscript ABC_rejection_2.R

Rscript ABC_rejection_3.R

Case study 2: Stochastic compartmental model

Case study can be run in the following manner:

Rscript case_2_ABC.R

Rscript case_2_ABC_SMC.R

Rscript case_2_ABC_SMC_MNN.R

Case study 3: Stochastic individual-based model

Case study can be run in the following manner:

Rscript case_3_ABC_SMC_MNN.R

Requirements

R code was run on R version 3.5.3. Case study 1 requires the package deSolve, case study 2 requires packages tmvtnorm, factoextra, ggpubr, and ggplot2, case study 3 requires package tmvtnorm.