Mnjowe/test running kenya analyses

src/scripts/contraception/kenya/analyses_contraception_kenya.py

@@ -0,0 +1,53 @@
+"""
+    a contraception analyses script for kenya
+"""
+import datetime
+from pathlib import Path
+
+from tlo import Date, Simulation, logging
+from tlo.analysis.utils import parse_log_file
+from tlo.methods import (
+    demography_nuhdss, contraception_nuhdss, demography
+)
+
+# The outputs' path. This is where will output be stored
+outputpath = Path("./outputs/")
+
+# date-stamp to label log files and any other outputs
+datestamp = datetime.date.today().strftime("__%Y_%m_%d")
+
+# Path to all resource files
+resourcefilepath = Path("./resources")
+
+# start and end dates of simulation.
+start_date = Date(2010, 1, 1)
+end_date = Date(2020, 1, 1)
+# population size
+popsize = 2000
+
+# a file that will store all logs. Here if you want you include logs to specific files you should declare their
+# logging level as logging.INFO. see below otherwise the logs for that particular module won't show in log file
+log_config = {
+    'filename': 'kenya_contraception_analyses',
+    'directory': outputpath/'kenya_contraception_analyses',
+    'custom_levels': {"*": logging.WARNING,
+                      "tlo.methods.demography_nuhdss": logging.INFO
+                      }
+}
+
+# Establish the simulation object. assign to simulation log configuration above if you want log file created
+sim = Simulation(start_date=start_date, seed=0, log_config=log_config)
+
+# Register the appropriate modules
+sim.register(
+    demography_nuhdss.Demography(resourcefilepath=resourcefilepath)
+)
+
+sim.make_initial_population(n=popsize)
+sim.simulate(end_date=end_date)
+
+# read results
+output = parse_log_file(sim.log_filepath)
+print(f"the outputs are {output['tlo.methods.demography_nuhdss']}")
+
+# following the parsed outputs above you can proceed to extracting data and do your analyses

src/scripts/contraception/kenya/scenarios/run_analysis_contraception_no_diseases.py

@@ -0,0 +1,82 @@
+"""
+This file defines a batch run to get sims results to be used by the analysis_contraception_plot_table.
+Run on the remote batch system using:
+```tlo batch-submit src/scripts/contraception/kenya/scenarios/run_analysis_contraception_no_diseases.py```
+or locally using:
+```tlo scenario-run src/scripts/contraception/kenya/scenarios/run_analysis_contraception_no_diseases.py```
+
+
+SCENARIO SETTINGS
+-----------------
+used modules:
+* Demography
+* HealthSystem
+    - cons_availability="all", i.e. all consumables are assumed to be always available,
+* Contraception, for which SimplifiedPregnancyAndLabour is used
+    - use_interventions=False/True according to what we need (False => without interventions,
+    True => interventions since 2023; it needs to be set in the ResourceFile_ContraceptionParams.csv)
+* DummyHivModule (a supporting module required by Contraception module)
+
+logging above warning level:
+* contraception:
+    - INFO if only analysis_all_calibration or figs but not the table from analysis_contraception_plot_table required,
+    - DEBUG if tabel from analysis_contraception_plot_table required.
+* demography: INFO.
+NB. For analysis_all_calibration this is enough only if analysis_hsi_descriptions are not required, and the analysis
+needs to be changed accordingly to run properly. We use an adjusted analysis_all_calibration script, stored in the
+EvaJ/contraception_2023-02_inclPR807/AnalysisAllCalib_Contraception branch.
+
+
+CONTRACEPTION PAPER (Tim C et al. 2023):
+---------------------------------------
+- 1 draw & 1 run/per draw with 250K initial_population_size
+- use_interventions=False/True for simulation without/with interventions,
+- for analysis_all_calibration adjusted in the branch
+EvaJ/contraception_2023-02_inclPR807/AnalysisAllCalib_Contraception with the analysis_hsi_descriptions excluded (Fig 2):
+    2010-2099 simulated with contraception logging at the level INFO (a job to simulate that many years with DEBUG
+    logging fails)
+- for analysis_contraception_plot_table (Fig 3, Fig 4, Tab 4, and Fig A6.1):
+    2010-2050 simulated with contraception logging at the level DEBUG
+"""
+
+from tlo import Date, logging
+from tlo.methods import demography, contraception_nuhdss, demography_nuhdss
+from tlo.scenario import BaseScenario
+
+
+class RunAnalysisCo(BaseScenario):
+    def __init__(self):
+        super().__init__(
+            seed=0,
+            start_date=Date(2010, 1, 1),
+            end_date=Date(2020, 12, 31),
+            initial_population_size=1000,  # selected size for the Tim C at al. 2023 paper: 250K
+            number_of_draws=1,  # <- one scenario
+            runs_per_draw=1,  # <- repeated this many times
+        )
+
+    def log_configuration(self):
+        return {
+            'filename': 'run_analysis_contraception_no_diseases',  # <- (specified only for local running)
+            'directory': './outputs',  # <- (specified only for local running)
+            'custom_levels': {
+                '*': logging.WARNING,
+                "tlo.methods.demography_nuhdss": logging.INFO
+            }
+        }
+
+    def modules(self):
+        return [
+            # Core Modules
+            demography_nuhdss.Demography(resourcefilepath=self.resources)
+        ]
+
+    def draw_parameters(self, draw_number, rng):
+        # Using default parameters in all cases
+        return
+
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+
+    scenario_run([__file__])

src/scripts/contraception/scenarios/run_analysis_contraception_no_diseases.py → src/scripts/contraception/malawi/scenarios/run_analysis_contraception_no_diseases.py

@@ -40,7 +40,7 @@
 """
 
 from tlo import Date, logging
-from tlo.methods import contraception, demography, healthsystem, hiv
+from tlo.methods import contraception, demography, healthsystem, hiv, demography_nuhdss
 from tlo.scenario import BaseScenario
 
 
@@ -50,7 +50,7 @@ def __init__(self):
             seed=0,
             start_date=Date(2010, 1, 1),
             end_date=Date(2099, 12, 31),
-            initial_population_size=250_000,  # selected size for the Tim C at al. 2023 paper: 250K
+            initial_population_size=1000,  # selected size for the Tim C at al. 2023 paper: 250K
             number_of_draws=1,  # <- one scenario
             runs_per_draw=1,  # <- repeated this many times
         )
@@ -69,19 +69,20 @@ def log_configuration(self):
     def modules(self):
         return [
             # Core Modules
-            demography.Demography(resourcefilepath=self.resources),
-            healthsystem.HealthSystem(resourcefilepath=self.resources,
-                                      cons_availability="all"),
+            #demography.Demography(resourcefilepath=self.resources),
+            Demography_Nuhdss.Demography(resourcefilepath=self.resources),
+            # healthsystem.HealthSystem(resourcefilepath=self.resources,
+            #                           cons_availability="all"),
 
             # - Contraception and replacement for Labour etc.
-            contraception.Contraception(resourcefilepath=self.resources,
-                                        use_healthsystem=True  # default: True <-- using HealthSystem
-                                        # if True initiation and switches to contraception require an HSI
-                                        ),
-            contraception.SimplifiedPregnancyAndLabour(),
-
-            # - Supporting Module required by Contraception
-            hiv.DummyHivModule(),
+            # contraception.Contraception(resourcefilepath=self.resources,
+            #                             use_healthsystem=False  # default: True <-- using HealthSystem
+            #                             # if True initiation and switches to contraception require an HSI
+            #                             ),
+            # contraception.SimplifiedPregnancyAndLabour(),
+
+            # # - Supporting Module required by Contraception
+            # hiv.DummyHivModule(),
         ]
 
     def draw_parameters(self, draw_number, rng):