diff --git a/R/get_stan_data.R b/R/get_stan_data.R index 797209e3..25f8293e 100644 --- a/R/get_stan_data.R +++ b/R/get_stan_data.R @@ -619,6 +619,7 @@ get_stan_data <- function(input_count_data, sd_log_sigma_ww_site_prior_sd = params$sd_log_sigma_ww_site_prior_sd, eta_sd_sd = params$eta_sd_sd, + eta_sd_mean = params$eta_sd_mean, sigma_i_first_obs_prior_mode = params$sigma_i_first_obs_prior_mode, sigma_i_first_obs_prior_sd = params$sigma_i_first_obs_prior_sd, p_hosp_prior_mean = params$p_hosp_mean, diff --git a/inst/extdata/example_params.toml b/inst/extdata/example_params.toml index 9c0b98b6..0d929c64 100644 --- a/inst/extdata/example_params.toml +++ b/inst/extdata/example_params.toml @@ -41,9 +41,11 @@ offset_ref_initial_exp_growth_rate_prior_sd = 0.025 autoreg_p_hosp_a = 1 # shape1 parameter of autoreg term on IHR(t) trend autoreg_p_hosp_b = 100 # shape2 parameter of autoreg term on IHR(t) trend -eta_sd_sd = 0.01 -infection_feedback_prior_logmean = 0 # log(mode) + q^2 mode = 1, q = 0.3 -infection_feedback_prior_logsd = 3 +eta_sd_mean = 0.0278 # from posteriorof long time series fit +eta_sd_sd = 0.0097 +infection_feedback_prior_logmean = 4.498 # log(~90) from posterior of fit to long +# time series +infection_feedback_prior_logsd = 0.636 # log(~1.9) [hospital_admission_observation_process] # Hospitalization parameters (informative priors) diff --git a/inst/stan/wwinference.stan b/inst/stan/wwinference.stan index ba6f0cad..c078b1a5 100644 --- a/inst/stan/wwinference.stan +++ b/inst/stan/wwinference.stan @@ -85,6 +85,7 @@ data { real sd_log_sigma_ww_site_prior_mode; real sd_log_sigma_ww_site_prior_sd; real eta_sd_sd; + real eta_sd_mean; real p_hosp_prior_mean; real p_hosp_sd_logit; real p_hosp_w_sd_sd; @@ -325,7 +326,7 @@ model { offset_ref_logit_i_first_obs_prior_sd); offset_ref_initial_exp_growth_rate ~ normal(offset_ref_initial_exp_growth_rate_prior_mean, offset_ref_initial_exp_growth_rate_prior_sd); - eta_sd ~ normal(0, eta_sd_sd); + eta_sd ~ normal(eta_sd_mean, eta_sd_sd); autoreg_rt_subpop ~ beta(autoreg_rt_subpop_a, autoreg_rt_subpop_b); autoreg_rt ~ beta(autoreg_rt_a, autoreg_rt_b);