diff --git a/README.md b/README.md index 79448ca..47f5dfb 100644 --- a/README.md +++ b/README.md @@ -30,13 +30,13 @@ All data required to run the code are contained in the [data](data) folder and a ## Running the code -The odin model code is contained in [covid_multi_strain.R](inst/odin/covid_multi_strain.R). If required, the model can be modified by editing this code, and then recompiled by calling +The odin model code is contained in [inst/odin/covid_multi_strain.R](inst/odin/covid_multi_strain.R). If required, the model can be modified by editing this code, and then recompiled by calling ```R odin_dust("inst/odin/covid_multi_strain.R") ``` as in [fit_covid_multi_strain.R](R/fit_covid_multi_strain.R). -The workflow is as follows. The model can be fit to the data for French Polynesia using the adaptive MCMC algorithm in [pmcmc.R](R/pmcmc.R) by running: +The workflow for fitting the model and running counterfactual simulations is as follows. The model can be fit to the data for French Polynesia using the adaptive MCMC algorithm in [pmcmc.R](R/pmcmc.R) by running: ```R source("R/fit_FP.R") ```