Merge pull request #167 from ilabcode/dev

regorganization of actionmodels dependencies
ComputationalPsychiatry · Oct 8, 2024 · ee23276 · ee23276 · PTWaade · Oct 8, 2024
2 parents ef01e41 + cdfa85b
commit ee23276
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Showing 12 changed files with 29 additions and 60 deletions.
diff --git a/src/ActionModels_variations/core/plot_predictive_simulation.jl b/src/ActionModels_variations/core/plot_predictive_simulation.jl
diff --git a/...s_variations/core/create_premade_agent.jl → ...Models_variations/create_premade_agent.jl b/...s_variations/core/create_premade_agent.jl → ...Models_variations/create_premade_agent.jl
diff --git a/...ionModels_variations/utils/get_history.jl → src/ActionModels_variations/get_history.jl b/...ionModels_variations/utils/get_history.jl → src/ActionModels_variations/get_history.jl
diff --git a/...Models_variations/utils/get_parameters.jl → ...ActionModels_variations/get_parameters.jl b/...Models_variations/utils/get_parameters.jl → ...ActionModels_variations/get_parameters.jl
diff --git a/...tionModels_variations/utils/get_states.jl → src/ActionModels_variations/get_states.jl b/...tionModels_variations/utils/get_states.jl → src/ActionModels_variations/get_states.jl
diff --git a/...ionModels_variations/utils/give_inputs.jl → src/ActionModels_variations/give_inputs.jl b/...ionModels_variations/utils/give_inputs.jl → src/ActionModels_variations/give_inputs.jl
diff --git a/...Models_variations/core/plot_trajectory.jl → ...ctionModels_variations/plot_trajectory.jl b/...Models_variations/core/plot_trajectory.jl → ...ctionModels_variations/plot_trajectory.jl
diff --git a/src/ActionModels_variations/utils/reset.jl → src/ActionModels_variations/reset.jl b/src/ActionModels_variations/utils/reset.jl → src/ActionModels_variations/reset.jl
diff --git a/...Models_variations/utils/set_parameters.jl → ...ActionModels_variations/set_parameters.jl b/...Models_variations/utils/set_parameters.jl → ...ActionModels_variations/set_parameters.jl
diff --git a/...dels_variations/utils/set_save_history.jl → ...tionModels_variations/set_save_history.jl b/...dels_variations/utils/set_save_history.jl → ...tionModels_variations/set_save_history.jl
diff --git a/src/HierarchicalGaussianFiltering.jl b/src/HierarchicalGaussianFiltering.jl
@@ -7,7 +7,7 @@ using ActionModels, Distributions, RecipesBase
 export init_node, init_hgf, premade_hgf, check_hgf, update_hgf!
 export get_prediction, get_surprise
 export premade_agent,
-    init_agent, plot_predictive_simulation, plot_trajectory, plot_trajectory!
+    init_agent, plot_trajectory, plot_trajectory!
 export get_history,
     get_parameters, get_states, set_parameters!, reset!, give_inputs!, set_save_history!
 export ParameterGroup
@@ -36,16 +36,15 @@ end
 include("create_hgf/hgf_structs.jl")
 
 #Overloading ActionModels functions
-include("ActionModels_variations/core/create_premade_agent.jl")
-include("ActionModels_variations/core/plot_predictive_simulation.jl")
-include("ActionModels_variations/core/plot_trajectory.jl")
-include("ActionModels_variations/utils/get_history.jl")
-include("ActionModels_variations/utils/get_parameters.jl")
-include("ActionModels_variations/utils/get_states.jl")
-include("ActionModels_variations/utils/give_inputs.jl")
-include("ActionModels_variations/utils/reset.jl")
-include("ActionModels_variations/utils/set_parameters.jl")
-include("ActionModels_variations/utils/set_save_history.jl")
+include("ActionModels_variations/create_premade_agent.jl")
+include("ActionModels_variations/plot_trajectory.jl")
+include("ActionModels_variations/get_history.jl")
+include("ActionModels_variations/get_parameters.jl")
+include("ActionModels_variations/get_states.jl")
+include("ActionModels_variations/give_inputs.jl")
+include("ActionModels_variations/reset.jl")
+include("ActionModels_variations/set_parameters.jl")
+include("ActionModels_variations/set_save_history.jl")
 
 #Functions for updating the HGF
 include("update_hgf/update_hgf.jl")

diff --git a/test/testsuite/test_fit_model.jl b/test/testsuite/test_fit_model.jl
@@ -1,18 +1,17 @@
 using ActionModels
 using HierarchicalGaussianFiltering
 using Test
-using Plots
 using StatsPlots
 using Distributions
-using Turing
+using ActionModels: Turing
 
 @testset "Model fitting" begin
 
     @testset "Continuous 2level" begin
 
         #Set inputs and responses
-        test_input = [1.0, 2, 3, 4, 5]
-        test_responses = [1.1, 2.2, 3.3, 4.4, 5.5]
+        test_input = [1.0, 1.0, 1.0, 1.0, 1.0]
+        test_responses = [1.0, 1.0, 1.0, 1.0, 1.0]
 
         #Create HGF
         test_hgf = premade_hgf("continuous_2level", verbose = false)
@@ -22,20 +21,18 @@ using Turing
 
         # Set fixed parsmeters and priors for fitting
         test_fixed_parameters = Dict(
-            ("x", "initial_mean") => 100,
+            ("x", "initial_mean") => 1,
             ("xvol", "initial_mean") => 1.0,
-            ("xvol", "initial_precision") => 600,
+            ("xvol", "initial_precision") => 1,
             ("x", "xvol", "coupling_strength") => 1.0,
             "action_noise" => 0.01,
-            ("xvol", "volatility") => -4,
+            ("xvol", "volatility") => -10,
             ("u", "input_noise") => 4,
             ("xvol", "drift") => 1,
         )
 
         test_param_priors = Dict(
-            ("x", "volatility") => Normal(log(100.0), 4),
-            ("x", "initial_mean") => Normal(1, sqrt(100.0)),
-            ("x", "drift") => Normal(0, 1),
+            ("x", "volatility") => Normal(-10, 0.1),
         )
 
         #Create model
@@ -44,6 +41,18 @@ using Turing
         #Fit single chain with defaults
         fitted_model = fit_model(model; n_iterations = 10, n_chains = 1)
 
+        chains = fitted_model.chains
+        renamed_model = rename_chains(chains, model)
+        #Extract agent parameters
+        agent_parameters = extract_quantities(model, chains)
+
+        estimates_df = get_estimates(agent_parameters)
+        estimates_dict = get_estimates(agent_parameters, Dict)
+
+        #Extract state trajectories
+        state_trajectories = get_trajectories(model, chains, [("x", "value_prediction_error"), "action"])
+        trajectory_estimates_df = get_estimates(state_trajectories)
+
         @test fitted_model isa ActionModels.FitModelResults
 
         #Plot the parameter distribution