Application of mcstate pmcmc to ANC data from various settings
-sim_main.R: Generates simulated data, fits pMCMC, and summarises results.
-data_gen.R: Generates simulated data
-equilibrium_check.R: Out puts first step derivs based on current equilibrium solution and runs the model with a constant EIR.
-Folder sim_datasets: 3 example simulated datasets
-nnp_submit.R: Submits the pmcmc to the cluster
-nnp_summarize.R: Creates plots to summarize results
-nnp_readdata.R: Processes raw data for use with the pmcmc
-wkenya_submit.R: Submits pmcmc to cluster
-ANC_cMIS_summary.R: Produce plots
-run_pmcmc.R: Fits the mcstate pMCMC (differs from the file in the shared folder as this fits to multiple ages)
-odinmodelmatchedstoch.R: Odin model with stochastic update of EIR
-odin_model_stripped_matched.R: Odin model without the stochastic update, used to generate simulated data.
-run_pmcmc.R: Fits the mcstate pMCMC
-plot_particle_filter.R: Plots the pmcmc trajectory against the observed prevalence.
-addCIs.R: Add binomial confidence intervals to observed prevalence data