2024-10-17 update : fixed issue 58.

cbernalz · Oct 17, 2024 · 4bdfbb0 · 4bdfbb0
1 parent d61cd9b
commit 4bdfbb0
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Showing 5 changed files with 36 additions and 35 deletions.
diff --git a/src/generate_simulation_data_uciwweihr.jl b/src/generate_simulation_data_uciwweihr.jl
@@ -24,26 +24,27 @@ Struct for holding parameters used in the UCIWWEIHR ODE compartmental model simu
 - `w_init::Float64`: Initial value of the time-varying hospitalization rate, NOT USER SPECIFIED `create_uciwweihr_params` TAKES CARE OF THIS.
 """
 struct uciwweihr_sim_params
-    time_points::Int64
-    seed::Int64
-    E_init::Int64
-    I_init::Int64
-    H_init::Int64
-    gamma::Float64
-    nu::Float64
-    epsilon::Float64
-    rho_gene::Float64
-    tau::Float64
-    df::Float64
-    sigma_hosp::Float64
-    Rt::Union{Float64, Vector{Float64}}
-    sigma_Rt::Float64
-    w::Union{Float64, Vector{Float64}}
-    sigma_w::Float64
-    rt_init::Float64
-    w_init::Float64
+    time_points::Union{Int64, Nothing}
+    seed::Union{Int64, Nothing}
+    E_init::Union{Int64, Nothing}
+    I_init::Union{Int64, Nothing}
+    H_init::Union{Int64, Nothing}
+    gamma::Union{Float64, Nothing}
+    nu::Union{Float64, Nothing}
+    epsilon::Union{Float64, Nothing}
+    rho_gene::Union{Float64, Nothing}
+    tau::Union{Float64, Nothing}
+    df::Union{Float64, Nothing}
+    sigma_hosp::Union{Float64, Nothing}
+    Rt::Union{Float64, Vector{Float64}, Nothing}
+    sigma_Rt::Union{Float64, Nothing}
+    w::Union{Float64, Vector{Float64}, Nothing}
+    sigma_w::Union{Float64, Nothing}
+    rt_init::Union{Float64, Nothing}
+    w_init::Union{Float64, Nothing}
 end
 
+
 """
 create_uciwweihr_sim_params(; kwargs...)
 

diff --git a/src/mcmcdiags_vis.jl b/src/mcmcdiags_vis.jl
@@ -57,7 +57,7 @@ function mcmcdiags_vis(;
                     )            
                     push!(cat_plots, plt) 
 
-                    if !isnothing(actual_non_time_varying_vals)
+                    if !isnothing(actual_non_time_varying_vals.time_points)
                         actual_param_value = round(getfield(actual_non_time_varying_vals, Symbol(param)), digits=3)
                         scatter!(plt, [1], Float64[actual_param_value],
                                 label = "Actual Value : $actual_param_value", 

diff --git a/src/non_time_varying_param_vis.jl b/src/non_time_varying_param_vis.jl
@@ -15,7 +15,6 @@ Used in the `uciwweihr_visualizer` to create visuals for non-time varying parame
 - `forecast_weeks`: An integer to indicate the number of weeks to forecast, used only if user desired priors next to posteriors.
 - `gq_samples`: Generated quantities samples from the posterior/prior distribution, index 2 in uciwweihr_gq_pp output.
 - `desired_params`: A list of lists of parameters to visualize. Each list will be visualized in a separate plot. Default is any parameter not in this list : ["alpha_t", "w_t", "rt_vals", "log_genes_mean", "H"]
-- `bayes_dist_type`: A string to indicate if user is using Posterior or Prior distribution. Default is "Posterior".
 - `actual_non_time_varying_vals::uciwweihr_sim_params`: A uciwweihr_sim_params object of actual non-time varying parameter values if user has access to them. Default is nothing.
 - `save_plots::Bool=false`: A boolean to indicate if user wants to save the plots as pngs into a plots folder.
 - `plot_name_to_save`: A string to indicate the name of the plot to save. Default is "mcmc_nontime_varying_parameter_plots".
@@ -30,7 +29,6 @@ function non_time_varying_param_vis(
     forecast_weeks;
     gq_samples=nothing,
     desired_params=nothing,
-    bayes_dist_type="Posterior",
     actual_non_time_varying_vals::uciwweihr_sim_params = nothing,
     save_plots::Bool=false,
     plot_name_to_save = "mcmc_nontime_varying_parameter_plots"
@@ -71,15 +69,15 @@ function non_time_varying_param_vis(
                            alpha = 0.1)
                 histogram!(plt, curr_param_chain_df[:, curr_param], 
                                 label = "Chain $chain (Posterior)", 
-                                title = "$bayes_dist_type $curr_param",
+                                title = "$curr_param",
                                 bins = 50,
                                 normalize = :probability,
                                 xlabel = "Value for $curr_param",
                                 ylabel = "Probability",
                                 alpha = 0.7,
                                 color = :blue,
                                 legend = :topright)
-                if !isnothing(actual_non_time_varying_vals)
+                if !isnothing(actual_non_time_varying_vals.time_points)
                     actual_param_value = round(getfield(actual_non_time_varying_vals, Symbol(curr_param)), digits=3)
                     vline!(plt, 
                             [actual_param_value],
@@ -129,7 +127,6 @@ function non_time_varying_param_vis(
     forecast_weeks;
     gq_samples=nothing,
     desired_params=nothing,
-    bayes_dist_type="Posterior",
     actual_non_time_varying_vals::uciwweihr_sim_params = nothing,
     save_plots::Bool=false,
     plot_name_to_save = "mcmc_nontime_varying_parameter_plots"
@@ -174,15 +171,15 @@ function non_time_varying_param_vis(
                            alpha = 0.1)
                 histogram!(plt, curr_param_chain_df[:, curr_param], 
                                 label = "Chain $chain (Posterior)", 
-                                title = "$bayes_dist_type $curr_param",
+                                title = "$curr_param",
                                 bins = 50,
                                 normalize = :probability,
                                 xlabel = "Value for $curr_param",
                                 ylabel = "Probability",
                                 alpha = 0.7,
                                 color = :blue,
                                 legend = :topright)
-                if !isnothing(actual_non_time_varying_vals)
+                if !isnothing(actual_non_time_varying_vals.time_points)
                     actual_param_value = round(getfield(actual_non_time_varying_vals, Symbol(curr_param)), digits=3)
                     vline!(plt, 
                             [actual_param_value],
@@ -223,7 +220,6 @@ end
 function non_time_varying_param_vis(;
     gq_samples=nothing,
     desired_params=nothing,
-    bayes_dist_type="Posterior",
     actual_non_time_varying_vals::uciwweihr_sim_params = nothing,
     save_plots::Bool=false,
     plot_name_to_save = "mcmc_nontime_varying_parameter_plots"
@@ -237,7 +233,7 @@ function non_time_varying_param_vis(;
                 curr_param_chain_df = filter(row -> row.chain == chain, gq_samples)
                 plt = histogram(curr_param_chain_df[:, curr_param], 
                                 label = "Chain $chain", 
-                                title = "$bayes_dist_type $curr_param",
+                                title = "$curr_param",
                                 bins = 50,
                                 normalize = :probability,
                                 xlabel = "Probability",
@@ -247,7 +243,7 @@ function non_time_varying_param_vis(;
                                 titlefont = font(10), 
                                 legendfont = font(8),
                                 legend = :topright)
-                if !isnothing(actual_non_time_varying_vals)
+                if !isnothing(actual_non_time_varying_vals.time_points)
                     actual_param_value = round(getfield(actual_non_time_varying_vals, Symbol(curr_param)), digits=3)
                     vline!(plt, 
                             [actual_param_value],

diff --git a/src/uciwweihr_model.jl b/src/uciwweihr_model.jl
@@ -147,8 +147,10 @@ The defaults for this fuction will follow those of the default simulation in gen
             gamma = gamma,
             nu = nu,
             w_t = w_t,
+            sigma_w = sigma_w,
             epsilon = epsilon,
             rt_vals = rt_vals,
+            sigma_Rt = sigma_Rt,
             rho_gene = rho_gene,
             tau = tau,
             df = df,
@@ -274,8 +276,10 @@ The defaults for this fuction will follow those of the default simulation in gen
             gamma = gamma,
             nu = nu,
             w_t = w_t,
+            sigma_w = sigma_w,
             epsilon = epsilon,
             rt_vals = rt_vals,
+            sigma_Rt = sigma_Rt,
             sigma_hosp = sigma_hosp,
             H = sol_hosp,
             rt_init = rt_init,

diff --git a/src/uciwweihr_visualizer.jl b/src/uciwweihr_visualizer.jl
@@ -48,11 +48,12 @@ function uciwweihr_visualizer(
     obs_data_wastewater = nothing,
     actual_rt_vals = nothing,
     actual_w_t = nothing,
-    actual_non_time_varying_vals::uciwweihr_sim_params = nothing,
+    actual_non_time_varying_vals::uciwweihr_sim_params = uciwweihr_sim_params(ntuple(x->nothing, fieldcount(uciwweihr_sim_params))...),
     desired_params = [
         ["E_init", "I_init", "H_init"],
         ["gamma", "nu", "epsilon"],
         ["rt_init", "w_init"],
+        ["sigma_w", "sigma_Rt"],
         ["rho_gene", "tau", "df"],
         ["sigma_hosp"]
     ],
@@ -117,7 +118,6 @@ function uciwweihr_visualizer(
             forecast_weeks;
             gq_samples = gq_samples,
             desired_params = desired_params,
-            bayes_dist_type = bayes_dist_type,
             actual_non_time_varying_vals = actual_non_time_varying_vals,
             save_plots = save_plots,
             plot_name_to_save = plot_name_to_save_non_time_varying
@@ -164,11 +164,12 @@ function uciwweihr_visualizer(
     obs_data_wastewater = nothing,
     actual_rt_vals = nothing,
     actual_w_t = nothing,
-    actual_non_time_varying_vals::uciwweihr_sim_params = nothing,
+    actual_non_time_varying_vals::uciwweihr_sim_params = uciwweihr_sim_params(ntuple(x->nothing, fieldcount(uciwweihr_sim_params))...),
     desired_params = [
         ["E_init", "I_init", "H_init"],
         ["gamma", "nu", "epsilon"],
         ["rt_init", "w_init"],
+        ["sigma_w", "sigma_Rt"],
         ["rho_gene", "tau", "df"],
         ["sigma_hosp"]
     ],
@@ -237,7 +238,6 @@ function uciwweihr_visualizer(
             forecast_weeks;
             gq_samples = gq_samples,
             desired_params = desired_params,
-            bayes_dist_type = bayes_dist_type,
             actual_non_time_varying_vals = actual_non_time_varying_vals,
             save_plots = save_plots,
             plot_name_to_save = plot_name_to_save_non_time_varying
@@ -276,11 +276,12 @@ function uciwweihr_visualizer(
     obs_data_wastewater = nothing,
     actual_rt_vals = nothing,
     actual_w_t = nothing,
-    actual_non_time_varying_vals::uciwweihr_sim_params = nothing,
+    actual_non_time_varying_vals::uciwweihr_sim_params = uciwweihr_sim_params(ntuple(x->nothing, fieldcount(uciwweihr_sim_params))...),
     desired_params = [
         ["E_init", "I_init", "H_init"],
         ["gamma", "nu", "epsilon"],
         ["rt_init", "w_init"],
+        ["sigma_w", "sigma_Rt"],
         ["rho_gene", "tau", "df"],
         ["sigma_hosp"]
     ],
@@ -331,7 +332,6 @@ function uciwweihr_visualizer(
         non_time_varying_param_vis(
             gq_samples = gq_samples,
             desired_params = desired_params,
-            bayes_dist_type = bayes_dist_type,
             actual_non_time_varying_vals = actual_non_time_varying_vals,
             save_plots = save_plots,
             plot_name_to_save = plot_name_to_save_non_time_varying