Python build_model_runnerの例

コード例 #1

ファイル: app.py プロジェクト: emmamcbryde/AuTuMN-1

 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,
     )

コード例 #2

 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,
     )

コード例 #3

ファイル: countries.py プロジェクト: emmamcbryde/AuTuMN-1

 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,
     )

コード例 #4

ファイル: mixing_opti.py プロジェクト: emmamcbryde/AuTuMN-1

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()

コード例 #5

ファイル: __init__.py プロジェクト: emmamcbryde/AuTuMN-1

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
)

コード例 #6

"""
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,
)

コード例 #7

ファイル: __init__.py プロジェクト: MattSegal/AuTuMN

"""
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,
)

コード例 #8

ファイル: __init__.py プロジェクト: MattSegal/AuTuMN

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,
)