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Issue 243: remove sigma_rt #244

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merged 2 commits into from
Nov 14, 2024
Merged

Issue 243: remove sigma_rt #244

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23262b6
remove sigma rt
kaitejohnson Nov 4, 2024
7c1097d
Merge branch 'spatial-main' into 243-remove-sigma-rt
kaitejohnson Nov 11, 2024
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1 change: 0 additions & 1 deletion R/get_stan_data.R
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Expand Up @@ -658,7 +658,6 @@ 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,
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1 change: 0 additions & 1 deletion R/initialization.R
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Expand Up @@ -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),
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1 change: 0 additions & 1 deletion inst/extdata/example_params.toml
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Expand Up @@ -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
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4 changes: 0 additions & 4 deletions inst/stan/wwinference.stan
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Expand Up @@ -93,7 +93,6 @@ 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;
Expand Down Expand Up @@ -149,8 +148,6 @@ 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;
Expand Down Expand Up @@ -408,7 +405,6 @@ 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,
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