2024-11-06 update : changing tau to sigma_ww.

src/mcmcdiags_vis.jl

@@ -15,7 +15,7 @@ function mcmcdiags_vis(;
         ["E_init", "I_init", "H_init"],
         ["gamma", "nu", "epsilon"],
         ["rt_init", "w_init"],
-        ["rho_gene", "tau"],
+        ["rho_gene", "sigma_ww"],
         ["sigma_hosp"]
     ],
     actual_non_time_varying_vals::uciwweihr_sim_params = nothing,

src/uciwweihr_model.jl

@@ -44,7 +44,7 @@ The defaults for this fuction will follow those of the default simulation in gen
         # Parameters for wastewater
         rho_gene_non_centered ~ Normal() # gene detection rate
 
-        tau_non_centered ~ Normal() # for showing identifyability issue
+        sigma_ww_non_centered ~ Normal() # for showing identifyability issue
 
         # Parameters for hospital
 
@@ -74,7 +74,7 @@ The defaults for this fuction will follow those of the default simulation in gen
         # Parameters for wastewater
         rho_gene = exp(rho_gene_non_centered * params.rho_gene_sd + params.log_rho_gene_mean)
 
-        tau = exp(tau_non_centered * params.tau_sd + params.log_tau_mean) # for showing identifyability issue
+        sigma_ww = exp(sigma_ww_non_centered * params.sigma_ww_sd + params.log_sigma_ww_mean) # for showing identifyability issue
 
         # Parameters for hospital
 
@@ -134,7 +134,7 @@ The defaults for this fuction will follow those of the default simulation in gen
         # Likelihood calculations------------
         for i in 1:l_obs_ww
             #data_wastewater[i] ~ Normal(log_W_means[i], params.sigma_wastewater)
-            data_wastewater[i] ~ Normal(log_W_means[i], tau)
+            data_wastewater[i] ~ Normal(log_W_means[i], sigma_ww)
         end
         for i in 1:l_obs_hosp
             #data_hosp[i] ~ NegativeBinomial2(H_means[i], params.sigma_hosp)

src/uciwweihr_model_params.jl

@@ -18,7 +18,7 @@ Struct for holding parameters used in the UCIWWEIHR ODE compartmental model.  Us
 - `log_epsilon_mean::Float64=log(1/5)`: Mean for the rate of hospitalization recovery on the log scale.
 - `rho_gene_sd::Float64=0.02`: Standard deviation for the rho prior.
 - `log_rho_gene_mean::Float64=log(0.011)`: Mean for the row prior on log scale.
-- `sigma_wastewater::Float64=log(0.1)`: Standard deviation for the negative binomial distribution for wastewater data.  Not infered.
+- `sigma_ww::Float64=log(0.1)`: Standard deviation for the normal distribution for wastewater data.  Not infered.
 - `sigma_hosp::Float64=500.0`: Standard deviation for the negative binomial distribution for hospital data.  Not infered.
 - `Rt_init_sd::Float64=0.3`: Standard deviation for the initial value of the time-varying reproduction number.
 - `Rt_init_mean::Float64=0.2`: Mean for the initial value of the time-varying reproduction number.
@@ -44,11 +44,11 @@ struct uciwweihr_model_params
     log_epsilon_mean::Float64
     rho_gene_sd::Float64
     log_rho_gene_mean::Float64
-    #sigma_wastewater::Float64
+    #sigma_ww::Float64
     #sigma_hosp::Float64
 
-    tau_sd::Float64
-    log_tau_mean::Float64
+    sigma_ww_sd::Float64
+    log_sigma_ww_mean::Float64
     sigma_hosp_sd::Float64
     sigma_hosp_mean::Float64
 
@@ -84,7 +84,7 @@ function create_uciwweihr_model_params(;
     #sigma_wastewater::Float64=0.1,
     #sigma_hosp::Float64=500.0,
 
-    tau_sd::Float64=0.02, log_tau_mean::Float64=log(0.1),
+    sigma_ww_sd::Float64=0.02, log_sigma_ww_mean::Float64=log(0.1),
     sigma_hosp_sd::Float64=50.0, sigma_hosp_mean::Float64=500.0,
 
     Rt_init_sd::Float64=0.3, Rt_init_mean::Float64=0.2,
@@ -104,7 +104,7 @@ function create_uciwweihr_model_params(;
         rho_gene_sd, log_rho_gene_mean,
         #sigma_wastewater, sigma_hosp,
 
-        tau_sd, log_tau_mean,
+        sigma_ww_sd, log_sigma_ww_mean,
         sigma_hosp_sd, sigma_hosp_mean,
 
         Rt_init_sd, Rt_init_mean,

src/uciwweihr_visualizer.jl

@@ -62,7 +62,7 @@ function uciwweihr_visualizer(
         ["gamma", "nu", "epsilon"],
         ["rt_init", "w_init"],
         ["sigma_w", "sigma_Rt"],
-        ["tau", "sigma_hosp"], # For identifyability issue checking
+        ["sigma_ww", "sigma_hosp"], # For identifyability issue checking
         ["rho_gene"]
     ],
     time_varying_params = ["rt_vals", "w_t"],
@@ -198,7 +198,7 @@ function uciwweihr_visualizer(
         ["gamma", "nu", "epsilon"],
         ["rt_init", "w_init"],
         ["sigma_w", "sigma_Rt"],
-        ["tau", "sigma_hosp"], # For identifyability issue checking
+        ["sigma_ww", "sigma_hosp"], # For identifyability issue checking
         ["rho_gene"]
     ],
     time_varying_params = ["rt_vals", "w_t"],