Template for Model Run

import datetime import logging import os from pathlib import Path

from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( chronicsyndrome, contraception, demography, dx_algorithm_child, enhanced_lifestyle, healthburden, healthseekingbehaviour, healthsystem, mockitis, symptommanager, )

Output path [NB. Working directory must be set to the root of TLO: TLOmodel]

outputpath = Path('./outputs')

The Resource files [NB. Working directory must be set to the root of TLO: TLOmodel]

resourcefilepath = Path('./resources')

Establish the simulation object

start_date = Date(year=2010, month=1, day=1) end_date = Date(year=2010, month=12, day=31) popsize = 2000 sim = Simulation(start_date=start_date)

date-stamp to label log files and any other outputs

datestamp = datetime.date.today().strftime("__%Y_%m_%d")

Establish the logger``

logfile = outputpath + 'LogFile' + datestamp + '.log'

if os.path.exists(logfile): os.remove(logfile) fh = logging.FileHandler(logfile) fr = logging.Formatter("%(levelname)s|%(name)s|%(message)s") fh.setFormatter(fr) logging.getLogger().addHandler(fh)

Make all services available:

service_availability = ['*']

Register the appropriate modules``

sim.register(demography.Demography(resourcefilepath=resourcefilepath)) sim.register(contraception.Contraception(resourcefilepath=resourcefilepath)) sim.register(enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath)) sim.register(healthsystem.HealthSystem(resourcefilepath=resourcefilepath, service_availability=service_availability, mode_appt_constraints=2, capabilities_coefficient=1.0, ignore_cons_constraints=False, disable=False))

(NB. will run much faster with disable=True in the declaration of the HealthSystem)

sim.register(symptommanager.SymptomManager(resourcefilepath=resourcefilepath)) sim.register(healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath)) sim.register(dx_algorithm_child.DxAlgorithmChild(resourcefilepath=resourcefilepath)) sim.register(healthburden.HealthBurden(resourcefilepath=resourcefilepath))

Register disease modules:

<< ---- >>

Run the simulation and flush the logger

sim.seed_rngs(0) sim.make_initial_population(n=popsize) sim.simulate(end_date=end_date) fh.flush()

Read the results

output = parse_log_file(logfile)