Simple up to date data retrieval tools.
| Source | Description |
|---|---|
| Oxford COVID-19 Government Response Tracker | Stringency ratings for different government responses. |
| Google COVID-19 Community Mobility Reports | Mobility trends for different areas and types of places. |
| 2019-nCoV Data Repository by Johns Hopkins CSSE | Tracking cases by country. |
python 3.5+
internet access
Combine all data in one dictionary with two dataframes:
from data import DatasetManager
import yaml
with open('file_cfg.yml') as f:
cfg = yaml.safe_load(f)
# to get up to date data from online sources each time
# uncomment the next part:
# cfg['reload'] = True
with open(cfg['auxiliary']['geojson']) as f:
geodata = json.load(f)
data = DatasetManager(cfg).get_data()
assert list(data.keys()) == ['world', 'russia']Or get reports separately:
from data import CSSEParser, OxfordParser, GoogleParser
parsers = [
CSSEParser(cfg),
OxfordParser(cfg),
GoogleParser(cfg)
]
data = [parser.load_data() for parser in parsers]Train a SEIR model approximation per country:
from models import CompartmentalOptimizer
optimizer = CompartmentalOptimizer(optim_days=14)
cases = [1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 5, 7, 7, 8, 9, 10, 13]
deaths = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2]
population = 397628
result = optimizer.fit(cases, deaths, population)or follow examples from the
examples
folder
The main file configuration parameters can be found in the file_cfg.yml. Each of the main data parsers should have a root folder. Set to "./report_files" by default.
root: ./report_files
Default naming convention is "iso_alpha3" (3-letter country code). The "countries.csv" file holds some additional information.
convention: iso_alpha3
countries: ./countries.csv
Three data sources each have their specific configuration options.
csse: {}
google: {}
oxford: {}
Specify the "reload" option as true to retrieve up to date information each time. Do not unnecessarily overload the public servers though.
reload: false
python -m pytest .
New data sources
Prediction models
Online dashboard