modify mean of R(t) RW step size

CDCgov · Oct 30, 2024 · f192eee · f192eee
1 parent 06e79f8
commit f192eee
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git 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
@@ -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
@@ -85,6 +85,7 @@ data {
   real sd_log_sigma_ww_site_prior_mode;
   real<lower=0> sd_log_sigma_ww_site_prior_sd;
   real<lower=0> eta_sd_sd;
+  real<lower=0> eta_sd_mean;
   real p_hosp_prior_mean;
   real<lower=0> p_hosp_sd_logit;
   real<lower=0> 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);