Errors in scneario analysis with theoretical dataset

[lisphilar]

Summary

When use theoretical data, we know the parameter values without estimation. It is the best way to apply parameter values with Scenario.add(), but this failed with errors.

Codes and outputs:

import covsirphy as cs
# Instance to save population values
population_data = cs.PopulationData(filename=None)
# Set tau value and start date of records
example_data = cs.ExampleData(tau=1440, start_date="01Jan2020")
# Preset of SIR-F parameters
preset_dict = cs.SIRF.EXAMPLE["param_dict"]
# Create dataset from 01Jan2020 to 31Jan2020
area = {"country": "Theoretical"}
example_data.add(cs.SIRF, step_n=30, **area)
# Register population value
population_data.update(cs.SIRF.EXAMPLE["population"], **area)
# Create Scenario class
snl = cs.Scenario(example_data, population_data, tau=1440, **area)
# Set 0th phase from 02Jan2020 to 31Jan2020 with preset parameter values
snl.clear(include_past=True)
snl.add(end_date="31Jan2020", model=cs.SIRF, **preset_dict)
# Add main scenario
snl.add(end_date="31Dec2020", name="Main")
# Add lockdown scenario
rho_lock = snl.get("rho", phase="0th") / 2
snl.add(end_date="31Dec2020", name="Lockdown", rho=rho_lock)
# Add medicine scenario
kappa_med = snl.get("kappa", phase="0th") / 2
sigma_med = snl.get("sigma", phase="0th") * 2
snl.add(end_date="31Dec2020", name="Medicine", kappa=kappa_med, sigma=sigma_med)
# Add vaccine scenario
snl.add(end_date="31Dec2020", name="Vaccine", model=cs.SIRFV, omega=0.001)
# Summarize
snl.summary()
# Compare scenarios
snl.describe(y0_dict={"Vaccinated": 0})

This causes KeyError in creation of PopulationData instance, IndexError in Scenario.add() and KeyError in Scenario.describe() when model was change in the future phases.

Environment

• CovsirPhy version: 2.6.0-alpha.fix.120
• Python version; 3.8
• Installation: pipenv
• OS: WSL

[lisphilar]

Parameter name "alpha1" must be change to "alpha1 [-]" as the same as that of SIR-F model.

[lisphilar]

Fixed in version 2.6.0-beta.fix.120.155