diff --git a/vignettes/likelihood-free-mcmc.Rmd b/vignettes/likelihood-free-mcmc.Rmd index b835bf9a..1a231062 100644 --- a/vignettes/likelihood-free-mcmc.Rmd +++ b/vignettes/likelihood-free-mcmc.Rmd @@ -63,15 +63,15 @@ obs_data <- unname(as.integer(get_today_total(model_sir))) ```{r lfmcmc-setup} # Define Simulation Function simfun <- function(params, m) { - set_param(model_sir, "Recovery Rate", params[0]) - set_param(model_sir, "Transmission Rate", params[1]) + set_param(model_sir, "Recovery Rate", params[1]) + set_param(model_sir, "Transmission Rate", params[2]) reset(model_sir) run( model_sir, ndays = 50, seed = model_seed ) - res <- get_today_total(model_sir) + res <- unname(as.integer(get_today_total(model_sir))) return(res) } @@ -87,9 +87,6 @@ sumfun <- function(res, dat, m) { return() } - -# Set initial parameters -par0 <- as.double(c(0.5, 0.5)) ``` ## Init LFMCMC @@ -104,12 +101,16 @@ lfmcmc_model <- LFMCMC(model_sir) |> ## Run LFMCMC ```{r lfmcmc-run} -# run_lfmcmc( -# lfmcmc = lfmcmc_model, -# params_init_ = par0, -# n_samples_ = 2000, -# epsilon_ = 1.0 -# ) +# Set initial parameters +par0 <- as.double(c(0.5, 0.5)) + +# Run LFMCMC +run_lfmcmc( + lfmcmc = lfmcmc_model, + params_init_ = par0, + n_samples_ = 2000, + epsilon_ = 1.0 +) # set_stats_names(lfmcmc_model, get_states(model_sir)) # set_par_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))