from apps.covid_19 import calibration as base
from apps.covid_19.calibration import (
add_standard_dispersion_parameter,
add_standard_philippines_params,
add_standard_philippines_targets,
provide_default_calibration_params,
)
from autumn.region import Region
from autumn.utils.params import load_targets
targets = load_targets("covid_19", Region.PHILIPPINES)
TARGET_OUTPUTS = add_standard_philippines_targets(targets)
PAR_PRIORS = provide_default_calibration_params()
PAR_PRIORS = add_standard_philippines_params(PAR_PRIORS, Region.PHILIPPINES)
PAR_PRIORS = add_standard_dispersion_parameter(PAR_PRIORS, TARGET_OUTPUTS,
"icu_occupancy")
PAR_PRIORS = add_standard_dispersion_parameter(PAR_PRIORS, TARGET_OUTPUTS,
"accum_deaths")
PAR_PRIORS = add_standard_dispersion_parameter(PAR_PRIORS, TARGET_OUTPUTS,
"notifications")
def run_calibration_chain(max_seconds: int, run_id: int, num_chains: int):
base.run_calibration_chain(
max_seconds,
run_id,
num_chains,
Region.PHILIPPINES,
PAR_PRIORS,
TARGET_OUTPUTS,
mode="autumn_mcmc",
def get_priors(target_outputs: list):
# Get common parameters for all Covid applications
priors = provide_default_calibration_params()
# Add multiplier for each Victorian cluster
for region in Region.VICTORIA_METRO:
region_name = region.replace("-", "_")
priors += [
{
"param_name":
f"victorian_clusters.contact_rate_multiplier_{region_name}",
"distribution": "trunc_normal",
"distri_params":
[1.0, 0.5], # Shouldn't be too peaked with these values
"trunc_range": [0.5, np.inf],
},
]
priors += [
{
"param_name":
f"victorian_clusters.contact_rate_multiplier_barwon_south_west",
"distribution": "trunc_normal",
"distri_params":
[1.0, 0.5], # Shouldn't be too peaked with these values
"trunc_range": [0.5, np.inf],
"jumping_sd": 0.05,
},
{
"param_name":
f"victorian_clusters.contact_rate_multiplier_regional",
"distribution": "trunc_normal",
"distri_params":
[1.0, 0.5], # Shouldn't be too peaked with these values
"trunc_range": [0.5, np.inf],
"jumping_sd": 0.05,
},
{
"param_name": "contact_rate",
"distribution": "uniform",
"distri_params": [0.015, 0.06],
"jumping_sd": 0.002,
},
{
"param_name": "victorian_clusters.intercluster_mixing",
"distribution": "uniform",
"distri_params": [0.005, 0.05],
"jumping_sd": 0.001,
},
{
"param_name": "infectious_seed",
"distribution": "uniform",
"distri_params": [
22.5,
67.5,
], # Should be multiplied by 4/9 because seed is removed from regional clusters
"jumping_sd": 2.0,
},
{
"param_name": "seasonal_force",
"distribution": "uniform",
"distri_params": [0.0, 0.5],
"jumping_sd": 0.015,
},
{
"param_name":
"clinical_stratification.props.symptomatic.multiplier",
"distribution": "trunc_normal",
"distri_params": [1.0, 0.2],
"trunc_range": [0.5, np.inf],
},
{
"param_name":
"clinical_stratification.non_sympt_infect_multiplier",
"distribution": "uniform",
"distri_params": [0.15, 0.7],
"jumping_sd": 0.01,
},
{
"param_name": "clinical_stratification.props.hospital.multiplier",
"distribution": "uniform",
"distri_params": [0.5, 3.0],
"jumping_sd": 0.1,
},
{
"param_name": "infection_fatality.multiplier",
"distribution": "uniform",
"distri_params": [0.5, 4.0],
"jumping_sd": 0.05,
},
{
"param_name": "testing_to_detection.assumed_cdr_parameter",
"distribution": "uniform",
"distri_params": [0.2, 0.5],
"jumping_sd": 0.01,
},
{
"param_name": "sojourn.compartment_periods.icu_early",
"distribution": "trunc_normal",
"distri_params": [12.7, 4.0],
"trunc_range": [3.0, np.inf],
"jumping_sd": 2.0,
},
{
"param_name":
"victorian_clusters.metro.mobility.microdistancing.behaviour_adjuster.parameters.effect",
"distribution": "uniform",
"distri_params": [0.0, 0.5],
"jumping_sd": 0.005,
},
{
"param_name":
"victorian_clusters.metro.mobility.microdistancing.face_coverings_adjuster.parameters.effect",
"distribution": "uniform",
"distri_params": [0.0, 0.5],
"jumping_sd": 0.005,
},
{
"param_name": "target_output_ratio",
"distribution": "uniform",
"distri_params": [0.1, 0.4],
"jumping_sd": 0.005,
},
]
return priors