Random Draws For SEIR Parameters Per Slot

examples/tutorials/config_sample_2pop_modifiers_test_random.yml

@@ -0,0 +1,132 @@
+name: sample_2pop
+setup_name: minimal
+start_date: 2020-02-01
+end_date: 2020-08-31
+nslots: 1
+
+subpop_setup:
+  geodata: model_input/geodata_sample_2pop.csv
+  mobility: model_input/mobility_sample_2pop.csv
+
+initial_conditions:
+  method: SetInitialConditions
+  initial_conditions_file: model_input/ic_2pop.csv
+  allow_missing_subpops: TRUE
+  allow_missing_compartments: TRUE
+
+compartments:
+  infection_stage: ["S", "E", "I", "R"]
+
+seir:
+  integration:
+    method: rk4
+    dt: 1
+  parameters:
+    sigma:
+      value: 1 / 4
+    gamma:
+      value: 1 / 5
+    Ro:
+      value: 
+        distribution: truncnorm
+        mean: 2.5
+        sd: 0.1
+        a: 1.1
+        b: 3
+  transitions:
+    - source: ["S"]
+      destination: ["E"]
+      rate: ["Ro * gamma"]
+      proportional_to: [["S"],["I"]]
+      proportion_exponent: ["1","1"]
+    - source: ["E"]
+      destination: ["I"]
+      rate: ["sigma"]
+      proportional_to: ["E"]
+      proportion_exponent: ["1"]
+    - source: ["I"]
+      destination: ["R"]
+      rate: ["gamma"]
+      proportional_to: ["I"]
+      proportion_exponent: ["1"]
+
+seir_modifiers:
+  scenarios:
+    - Ro_all
+  modifiers:
+    Ro_lockdown:
+      method: SinglePeriodModifier
+      parameter: Ro
+      period_start_date: 2020-03-15
+      period_end_date: 2020-05-01
+      subpop: "all"
+      value: 0.4
+    Ro_relax:
+      method: SinglePeriodModifier
+      parameter: Ro
+      period_start_date: 2020-05-01
+      period_end_date: 2020-08-31
+      subpop: "all"
+      value: 
+        distribution: truncnorm
+        mean: 0.8
+        sd: 0.1
+        a: 0.5
+        b: 1
+    Ro_all:
+      method: StackedModifier
+      modifiers: ["Ro_lockdown","Ro_relax"]
+
+
+outcomes:
+  method: delayframe
+  outcomes:
+    incidCase: #incidence of detected cases
+      source:
+        incidence:
+          infection_stage: "I"
+      probability:
+        value: 0.5
+      delay:
+        value: 5
+    incidHosp: #incidence of hospitalizations
+      source:
+        incidence:
+          infection_stage: "I"
+      probability:
+        value: 0.05
+      delay:
+        value: 7
+      duration:
+        value: 10
+        name: currHosp # will track number of current hospitalizations (ie prevalence)
+    incidDeath: #incidence of deaths
+      source: incidHosp
+      probability:
+        value: 0.2
+      delay:
+        value: 
+          distribution: truncnorm
+          mean: 14
+          sd: 2
+          a: 7
+          b: 21
+
+outcome_modifiers:
+  scenarios:
+    - test_limits
+  modifiers:
+    # assume that due to limitations in testing, initially the case detection probability was lower
+    test_limits:
+      method: SinglePeriodModifier
+      parameter: incidCase::probability
+      subpop: "all"
+      period_start_date: 2020-02-01
+      period_end_date: 2020-06-01
+      value: 
+        distribution: truncnorm
+        mean: 0.5
+        sd: 0.1
+        a: 0.1
+        b: 0.9
+

examples/tutorials/config_sample_2pop_modifiers_test_random_subpop_groups.yml

@@ -0,0 +1,134 @@
+name: sample_2pop
+setup_name: minimal
+start_date: 2020-02-01
+end_date: 2020-08-31
+nslots: 1
+
+subpop_setup:
+  geodata: model_input/geodata_sample_2pop.csv
+  mobility: model_input/mobility_sample_2pop.csv
+
+initial_conditions:
+  method: SetInitialConditions
+  initial_conditions_file: model_input/ic_2pop.csv
+  allow_missing_subpops: TRUE
+  allow_missing_compartments: TRUE
+
+compartments:
+  infection_stage: ["S", "E", "I", "R"]
+
+seir:
+  integration:
+    method: rk4
+    dt: 1
+  parameters:
+    sigma:
+      value: 1 / 4
+    gamma:
+      value: 1 / 5
+    Ro:
+      value: 
+        distribution: truncnorm
+        mean: 2.5
+        sd: 0.1
+        a: 1.1
+        b: 3
+  transitions:
+    - source: ["S"]
+      destination: ["E"]
+      rate: ["Ro * gamma"]
+      proportional_to: [["S"],["I"]]
+      proportion_exponent: ["1","1"]
+    - source: ["E"]
+      destination: ["I"]
+      rate: ["sigma"]
+      proportional_to: ["E"]
+      proportion_exponent: ["1"]
+    - source: ["I"]
+      destination: ["R"]
+      rate: ["gamma"]
+      proportional_to: ["I"]
+      proportion_exponent: ["1"]
+
+seir_modifiers:
+  scenarios:
+    - Ro_all
+  modifiers:
+    Ro_lockdown:
+      method: SinglePeriodModifier
+      parameter: Ro
+      period_start_date: 2020-03-15
+      period_end_date: 2020-05-01
+      subpop: "all"
+      value: 0.4
+    Ro_relax:
+      method: SinglePeriodModifier
+      parameter: Ro
+      period_start_date: 2020-05-01
+      period_end_date: 2020-08-31
+      subpop: "all"
+      subpop_groups: "all"
+      value: 
+        distribution: truncnorm
+        mean: 0.8
+        sd: 0.1
+        a: 0.5
+        b: 1
+    Ro_all:
+      method: StackedModifier
+      modifiers: ["Ro_lockdown","Ro_relax"]
+
+
+outcomes:
+  method: delayframe
+  outcomes:
+    incidCase: #incidence of detected cases
+      source:
+        incidence:
+          infection_stage: "I"
+      probability:
+        value: 0.5
+      delay:
+        value: 5
+    incidHosp: #incidence of hospitalizations
+      source:
+        incidence:
+          infection_stage: "I"
+      probability:
+        value: 0.05
+      delay:
+        value: 7
+      duration:
+        value: 10
+        name: currHosp # will track number of current hospitalizations (ie prevalence)
+    incidDeath: #incidence of deaths
+      source: incidHosp
+      probability:
+        value: 0.2
+      delay:
+        value: 
+          distribution: truncnorm
+          mean: 14
+          sd: 2
+          a: 7
+          b: 21
+
+outcome_modifiers:
+  scenarios:
+    - test_limits
+  modifiers:
+    # assume that due to limitations in testing, initially the case detection probability was lower
+    test_limits:
+      method: SinglePeriodModifier
+      parameter: incidCase::probability
+      subpop: "all"
+      subpop_groups: "all"
+      period_start_date: 2020-02-01
+      period_end_date: 2020-06-01
+      value: 
+        distribution: truncnorm
+        mean: 0.5
+        sd: 0.1
+        a: 0.1
+        b: 0.9
+

flepimop/gempyor_pkg/src/gempyor/outcomes.py

@@ -91,6 +91,8 @@ def onerun_delayframe_outcomes(
     load_ID: bool = False,
     sim_id2load: int = None,
 ):
+    np.random.seed(seed=sim_id2write)
+
     with Timer("buildOutcome.structure"):
         parameters = read_parameters_from_config(modinf)
 

flepimop/gempyor_pkg/src/gempyor/parameters.py

@@ -169,6 +169,18 @@ def __init__(
         logging.debug(f"Index in arrays are: {self.pnames2pindex}")
         logging.debug(f"NPI overlap operation is {self.stacked_modifier_method} ")
 
+    def reinitialize_distributions(self) -> None:
+        """
+        Reinitialize all random distributions.
+
+        This method reinitializes all random distributions for the parameters contained
+        within this class. The random seed for each distribution is captured on
+        initialization so this method will change those seeds.
+        """
+        for pn in self.pnames:
+            if "dist" in self.pdata[pn]:
+                self.pdata[pn]["dist"] = self.pconfig[pn]["value"].as_random_distribution()
+
     def get_pnames2pindex(self) -> dict:
         """
         Read the `pnames2pindex` attribute.

flepimop/gempyor_pkg/src/gempyor/seir.py

@@ -1,5 +1,6 @@
 import itertools
 import logging
+import random
 import time
 
 import numpy as np
@@ -257,7 +258,9 @@ def onerun_SEIR(
     sim_id2load: int = None,
     config=None,
 ):
-    np.random.seed()
+    np.random.seed(seed=sim_id2write)
+    modinf.parameters.reinitialize_distributions()
+
     npi = None
     if modinf.npi_config_seir:
         npi = build_npi_SEIR(