From 85ae0a2fd463c537f1b183cf79f3a63f10b96684 Mon Sep 17 00:00:00 2001 From: cbernalz Date: Wed, 6 Nov 2024 16:50:22 -0800 Subject: [PATCH] 2024-11-06 update : changing tau to sigma_ww. --- src/mcmcdiags_vis.jl | 2 +- src/uciwweihr_model.jl | 6 +++--- src/uciwweihr_model_params.jl | 12 ++++++------ src/uciwweihr_visualizer.jl | 4 ++-- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/mcmcdiags_vis.jl b/src/mcmcdiags_vis.jl index 89bc324..85a19d3 100644 --- a/src/mcmcdiags_vis.jl +++ b/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, diff --git a/src/uciwweihr_model.jl b/src/uciwweihr_model.jl index 6c5ae66..dea725e 100644 --- a/src/uciwweihr_model.jl +++ b/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) diff --git a/src/uciwweihr_model_params.jl b/src/uciwweihr_model_params.jl index 646d3f7..d030e7e 100644 --- a/src/uciwweihr_model_params.jl +++ b/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, diff --git a/src/uciwweihr_visualizer.jl b/src/uciwweihr_visualizer.jl index 8bcee25..8aafe7c 100644 --- a/src/uciwweihr_visualizer.jl +++ b/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"],