From 04dc3f13bec27f892011f57bd55be13e8bc236dc Mon Sep 17 00:00:00 2001
From: Kaitlyn Johnson <94390107+kaitejohnson@users.noreply.github.com>
Date: Thu, 14 Nov 2024 13:28:39 -0500
Subject: [PATCH] remove sigma rt (#244)

---
 R/get_stan_data.R                | 1 -
 R/initialization.R               | 1 -
 inst/extdata/example_params.toml | 1 -
 inst/stan/wwinference.stan       | 4 ----
 4 files changed, 7 deletions(-)

diff --git a/R/get_stan_data.R b/R/get_stan_data.R
index 824c7afb..a39b478e 100644
--- a/R/get_stan_data.R
+++ b/R/get_stan_data.R
@@ -662,7 +662,6 @@ get_stan_data <- function(input_count_data,
     ww_site_mod_sd_sd = params$ww_site_mod_sd_sd,
     inf_feedback_prior_logmean = params$infection_feedback_prior_logmean,
     inf_feedback_prior_logsd = params$infection_feedback_prior_logsd,
-    sigma_rt_prior = params$sigma_rt_prior,
     log_phi_g_prior_mean = params$log_phi_g_prior_mean,
     log_phi_g_prior_sd = params$log_phi_g_prior_sd,
     log_phi_mu_prior = params$log_phi_mu_prior,
diff --git a/R/initialization.R b/R/initialization.R
index bccee0bf..6d28e35f 100644
--- a/R/initialization.R
+++ b/R/initialization.R
@@ -63,7 +63,6 @@ get_inits_for_one_chain <- function(stan_data, stdev = 0.01) {
     ),
     autoreg_rt_subpop = abs(stats::rnorm(1, 0.5, 0.05)),
     autoreg_p_hosp = abs(stats::rnorm(1, 1 / 100, 0.001)),
-    sigma_rt = abs(stats::rnorm(1, 0, stdev)),
     i_first_obs_over_n =
       stats::plogis(stats::rnorm(1, logit_i_frac_est), 0.05),
     mean_initial_exp_growth_rate = stats::rnorm(1, 0, stdev),
diff --git a/inst/extdata/example_params.toml b/inst/extdata/example_params.toml
index 4f054711..18929782 100644
--- a/inst/extdata/example_params.toml
+++ b/inst/extdata/example_params.toml
@@ -13,7 +13,6 @@ log_scaling_factor_sd_prior = 0.5
 
 r_prior_mean = 1
 r_prior_sd = 1
-sigma_rt_prior = 0.1
 dur_inf = 7
 
 sigma_i_first_obs_prior_mode = 0
diff --git a/inst/stan/wwinference.stan b/inst/stan/wwinference.stan
index aeda96f6..a9b813e1 100644
--- a/inst/stan/wwinference.stan
+++ b/inst/stan/wwinference.stan
@@ -94,7 +94,6 @@ data {
   real<lower=0> p_hosp_sd_logit;
   real<lower=0> p_hosp_w_sd_sd;
   real<lower=0> ww_site_mod_sd_sd;
-  real<lower=0> sigma_rt_prior;
   real log_phi_g_prior_mean;
   real<lower=0> log_phi_g_prior_sd;
   real inf_feedback_prior_logmean;
@@ -150,8 +149,6 @@ parameters {
   // AR process on first differences in log R(t)
   real log_r_t_first_obs; // central log R(t) at the time of
   // the first observation
-  real<lower=0> sigma_rt; // magnitude of subpopulation level
-  // R(t) heterogeneity
   real<lower=0, upper=1> autoreg_rt_subpop;
   real<lower=0, upper=1> autoreg_p_hosp;
   matrix[n_subpops-1, n_subpops > 1 ? n_weeks : 0] error_rt_subpop;
@@ -410,7 +407,6 @@ model {
   autoreg_p_hosp ~ beta(autoreg_p_hosp_a, autoreg_p_hosp_b);
   log_r_t_first_obs ~ normal(r_logmean, r_logsd);
   to_vector(error_rt_subpop) ~ std_normal();
-  sigma_rt ~ normal(0, sigma_rt_prior);
   i_first_obs_over_n ~ beta(i_first_obs_over_n_prior_a,
                              i_first_obs_over_n_prior_b);
   sigma_i_first_obs ~ normal(sigma_i_first_obs_prior_mode,