Prefix method

pipeline/src/constructors/make_Rt.jl

@@ -150,8 +150,6 @@ reproduction number is 1.0, that is the following holds:
 
 This implies that the long-term muliplicative growth of the infected community is 1.0.
 
-
-
 # Arguments
 - `pipeline::RoughEndemicPipeline`: The `RoughEndemicPipeline` object for which Rt is being constructed.
 - `N_steps::Int = 10`: The number of steps to generate random values for Rt.

pipeline/src/infer/generate_inference_results.jl

@@ -15,16 +15,12 @@ Generate inference results based on the given configuration of inference model o
 """
 function generate_inference_results(
         truthdata, inference_config, pipeline::AbstractEpiAwarePipeline;
-        tspan, inference_method,
-        prefix_name = "observables", datadir_name = "epiaware_observables")
+        tspan, inference_method, datadir_name = "epiaware_observables")
     config = InferenceConfig(
         inference_config; case_data = truthdata["y_t"], tspan, epimethod = inference_method)
 
     # produce or load inference results
-    prfx = prefix_name * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
-           string(inference_config["gi_mean"])
+    prfx = _inference_prefix(truthdata, inference_config, pipeline)
 
     inference_results, inferencefile = produce_or_load(
         infer, config, datadir(datadir_name); prefix = prfx)
@@ -51,15 +47,12 @@ which is deleted after the function call.
 """
 function generate_inference_results(
         truthdata, inference_config, pipeline::EpiAwareExamplePipeline;
-        tspan, inference_method, prefix_name = "testmode_observables")
+        tspan, inference_method)
     config = InferenceConfig(inference_config; case_data = truthdata["y_t"],
         tspan = tspan, epimethod = inference_method)
 
     # produce or load inference results
-    prfx = prefix_name * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
-           string(inference_config["gi_mean"])
+    prfx = _inference_prefix(truthdata, inference_config, pipeline)
 
     datadir_name = mktempdir()
 
@@ -73,14 +66,12 @@ Method for prior predictive modelling.
 """
 function generate_inference_results(
         inference_config, pipeline::RtwithoutRenewalPriorPipeline;
-        tspan, prefix_name = "prior_observables")
+        tspan)
     config = InferenceConfig(
         inference_config; case_data = missing, tspan, epimethod = DirectSample())
 
     # produce or load inference results
-    prfx = prefix_name * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(inference_config["gi_mean"])
+    prfx = _inference_prefix(truthdata, inference_config, pipeline)
 
     datadir_name = mktempdir()
 

pipeline/src/infer/infer.jl

@@ -1,4 +1,5 @@
 include("InferenceConfig.jl")
+include("inference_prefix.jl")
 include("generate_inference_results.jl")
 include("map_inference_results.jl")
 include("define_epiprob.jl")

pipeline/src/infer/inference_prefix.jl

@@ -0,0 +1,54 @@
+"""
+This is an internal method that generates the prefix for the inference results file name.
+"""
+function _inference_prefix(truthdata, inference_config, pipeline::AbstractEpiAwarePipeline)
+    return "observables" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
+           string(inference_config["gi_mean"])
+end
+
+function _inference_prefix(truthdata, inference_config, pipeline::EpiAwareExamplePipeline)
+    return "testmode_observables" * "_igp_" * string(inference_config["igp"]) *
+           "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
+           string(inference_config["gi_mean"])
+end
+
+function _inference_prefix(
+        truthdata, inference_config, pipeline::RtwithoutRenewalPriorPipeline)
+    return "prior_observables" * "_igp_" * string(inference_config["igp"]) *
+           "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(inference_config["gi_mean"])
+end
+
+function _inference_prefix(truthdata, inference_config, pipeline::SmoothOutbreakPipeline)
+    return "smooth_outbreak" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
+           string(inference_config["gi_mean"])
+end
+
+function _inference_prefix(truthdata, inference_config, pipeline::MeasuresOutbreakPipeline)
+    return "measures_outbreak" * "_igp_" * string(inference_config["igp"]) *
+           "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
+           string(inference_config["gi_mean"])
+end
+
+function _inference_prefix(truthdata, inference_config, pipeline::SmoothEndemicPipeline)
+    return "smooth_endemic" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
+           string(inference_config["gi_mean"])
+end
+
+function _inference_prefix(truthdata, inference_config, pipeline::RoughEndemicPipeline)
+    return "rough_endemic" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
+           string(inference_config["gi_mean"])
+end

pipeline/src/simulate/generate_truthdata.jl

@@ -21,13 +21,15 @@ the `simulate` function to generate the truth data. This is the default method.
 """
 function generate_truthdata(
         truth_data_config, pipeline::AbstractEpiAwarePipeline; plot = true,
-        datadir_str = "truth_data", prefix = "truth_data")
+        datadir_str = "truth_data")
     default_params = make_default_params(pipeline)
     config = TruthSimulationConfig(
         truth_process = default_params["Rt"], gi_mean = truth_data_config["gi_mean"],
         gi_std = truth_data_config["gi_std"], logit_daily_ascertainment = default_params["logit_daily_ascertainment"],
         cluster_factor = default_params["cluster_factor"], I0 = default_params["I0"])
 
+    prefix = _simulate_prefix(pipeline)
+
     truthdata, truthfile = produce_or_load(
         simulate, config, datadir(datadir_str); prefix = prefix)
     if plot

pipeline/src/simulate/simulate.jl

@@ -1,2 +1,3 @@
 include("TruthSimulationConfig.jl")
+include("simulate_prefix.jl")
 include("generate_truthdata.jl")

pipeline/src/simulate/simulate_prefix.jl

@@ -0,0 +1,12 @@
+"""
+Internal method for setting the prefix for the truth data file name.
+"""
+_simulate_prefix(pipeline::AbstractEpiAwarePipeline) = "truth_data"
+
+_simulate_prefix(pipeline::SmoothOutbreakPipeline) = "truth_data_smooth_outbreak"
+
+_simulate_prefix(pipeline::MeasuresOutbreakPipeline) = "truth_data_measures_outbreak"
+
+_simulate_prefix(pipeline::SmoothEndemicPipeline) = "truth_data_smooth_endemic"
+
+_simulate_prefix(pipeline::RoughEndemicPipeline) = "truth_data_rough_endemic"