def __init__(self, region: str):
self.region = region
self._run_model = build_model_runner(
model_name="dr_tb_malancha",
param_set_name=self.region,
build_model=self.build_model,
params=self.params,
)
def __init__(self, region: str):
self.region = region
self._run_model = build_model_runner(
model_name="sir_example",
param_set_name=self.region,
build_model=self.build_model,
params=self.params,
)
def __init__(self, country: str):
self.country = country
self._run_model = build_model_runner(
model_name=f"sir_drug_resistance_{country}",
build_model=self.build_model,
params=self.params,
post_processing_config=pp_config,
plots_config=plots_config,
)
def run_all_phases(decision_variables,
country=Region.UNITED_KINGDOM,
config=0,
calibrated_params={},
mode="by_age"):
running_model = RegionApp(country)
build_model = running_model.build_model
if mode == "by_location":
new_decision_variables = {
"other_locations": decision_variables[0],
"school": decision_variables[1],
"work": decision_variables[2]
}
decision_variables = new_decision_variables
params = copy.deepcopy(running_model.params)
# update params with optimisation default config
params["default"].update(opti_params["default"])
# update params with calibrated parameters
params["default"] = update_params(params['default'], calibrated_params)
# prepare importation rates for herd immunity testing
params["default"]["data"] = {
'times_imported_cases': [0],
'n_imported_cases': [0]
}
params["scenarios"][1] = build_params_for_phases_2_and_3(
decision_variables, config, mode)
run_models = build_model_runner(model_name="covid_19",
param_set_name=country,
build_model=build_model,
params=params)
run_models()
Build the Mongolia model runner
"""
import os
import yaml
from autumn.model_runner import build_model_runner
from autumn.tool_kit.utils import merge_dicts
from .model import build_model
FILE_DIR = os.path.dirname(os.path.abspath(__file__))
PARAMS_PATH = os.path.join(FILE_DIR, "params.yml")
MLE_PARAMS_PATH = os.path.join(FILE_DIR, "params-mle.yml")
POST_PROCESSING_PATH = os.path.join(FILE_DIR, "post-processing.yml")
PLOTS_PATH = os.path.join(FILE_DIR, "plots.yml")
with open(PARAMS_PATH, "r") as f:
params = yaml.safe_load(f)
with open(MLE_PARAMS_PATH, "r") as f:
mle_params = yaml.safe_load(f)
# Incorporate max likelihood params from MCMC runs
params["default"] = merge_dicts(mle_params, params["default"])
run_model = build_model_runner(
model_name="mongolia", param_set_name=None, build_model=build_model, params=params
)
"""
Build the Marshall Islands model runner
"""
import os
import yaml
from autumn.model_runner import build_model_runner
from . import calibration
from .model import build_model
FILE_DIR = os.path.dirname(os.path.abspath(__file__))
PARAMS_PATH = os.path.join(FILE_DIR, "params.yml")
POST_PROCESSING_PATH = os.path.join(FILE_DIR, "post-processing.yml")
PLOTS_PATH = os.path.join(FILE_DIR, "plots.yml")
with open(PARAMS_PATH, "r") as f:
params = yaml.safe_load(f)
run_model = build_model_runner(
model_name="marshall_islands",
param_set_name=None,
build_model=build_model,
params=params,
)
"""
import os
import yaml
from autumn.model_runner import build_model_runner
from .model import build_model
FILE_DIR = os.path.dirname(os.path.abspath(__file__))
PARAMS_PATH = os.path.join(FILE_DIR, "params.yml")
POST_PROCESSING_PATH = os.path.join(FILE_DIR, "post-processing.yml")
PLOTS_PATH = os.path.join(FILE_DIR, "plots.yml")
with open(PARAMS_PATH, "r") as f:
params = yaml.safe_load(f)
with open(POST_PROCESSING_PATH, "r") as f:
pp_config = yaml.safe_load(f)
with open(PLOTS_PATH, "r") as f:
plots_config = yaml.safe_load(f)
run_model = build_model_runner(
model_name="marshall_islands",
build_model=build_model,
params=params,
post_processing_config=pp_config,
plots_config=plots_config,
)
from .model import build_model
FILE_DIR = os.path.dirname(os.path.abspath(__file__))
PARAMS_PATH = os.path.join(FILE_DIR, "params.yml")
MLE_PARAMS_PATH = os.path.join(FILE_DIR, "params-mle.yml")
POST_PROCESSING_PATH = os.path.join(FILE_DIR, "post-processing.yml")
PLOTS_PATH = os.path.join(FILE_DIR, "plots.yml")
with open(PARAMS_PATH, "r") as f:
params = yaml.safe_load(f)
with open(MLE_PARAMS_PATH, "r") as f:
mle_params = yaml.safe_load(f)
# Incorporate max likelihood params from MCMC runs
params["default"] = merge_dicts(mle_params, params["default"])
with open(POST_PROCESSING_PATH, "r") as f:
pp_config = yaml.safe_load(f)
with open(PLOTS_PATH, "r") as f:
plots_config = yaml.safe_load(f)
run_model = build_model_runner(
model_name="mongolia",
build_model=build_model,
params=params,
post_processing_config=pp_config,
plots_config=plots_config,
)
