This repo contains python code for 3 different COVID-19 infection forecasting models, each at a state-level, for states within the U.S. There are 3 models: SIR, Curve fitting (IHME) and a "Phase Space" model. Training data is available on S3, and updates daily. Attributions cite external public data sources that we use to create the training dataset, and external references for model methodology.
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More info on our work at: covid.arena-ai.com
- SIR
from arenacovid.models import sir
# Set total population
N = 1e6
DAYS_TO_PREDICT = 180
# Initial Conditions
S = np.zeros(DAYS_TO_PREDICT)
I = np.zeros(DAYS_TO_PREDICT)
I[0] = 1
S[0] = N - I[0]
S_t, I_t = sir.simulate(S, I, N, lam=0.3, gamma=0.1)- Phase Space
from arenacovid.models import phase_space
# cumulative cases time series for a single State
y = data.set_index('date')['cumulative_cases']
m = phase_space.PhaseFitter(tau=2, b_default=-.05).fit(y)
....- Curve fitting
from arenacovid.models import curve_fitting
# Fit multiple states + countries at the same time
m = curve_fitting.HierarchicalCurveFitter(mu_lower_bound=mu_lower_bound, mu_upper_bound=mu_upper_bound)
m.fit(data["new_deaths_per_million"].values, data["group_id"].values, data["t"].values)Daily Death Time Series:
s3://arena-covid-public/covid_data/death_time_series_uss3://arena-covid-public/covid_data/death_time_series_combined
Normalized death data for each state in the US, as well as normalized death data for US + International Countries. Cumulative death rate are quoted "per million" of population.
Daily Death + Case Series:
s3://arena-covid-public/covid_data/nyt_cases
A processed, state-aggregated view of the New York Times reported case and deaths data.
import pyarrow.parquet as pq
import s3fs
fs = s3fs.S3FileSystem(anon=True)
s3_uri = 's3://arena-covid-public/covid_data/death_time_series_combined'
df = pq.ParquetDataset(s3_uri, filesystem=fs).read().to_pandas()- NY Times data: https://github.com/nytimes/covid-19-data
- UW Model: http://www.healthdata.org/covid
- Ferguson & Imperial College SIR model: https://spiral.imperial.ac.uk:8443/bitstream/10044/1/77482/5/Imperial%20College%20COVID19%20NPI%20modelling%2016-03-2020.pdf
- COVID-tracking project: https://covidtracking.com/
- State and County level ICU bed and 60+ population data: https://khn.org/news/as-coronavirus-spreads-widely-millions-of-older-americans-live-in-counties-with-no-icu-beds/#lookup
- Government actions data: https://www.kff.org/health-costs/issue-brief/state-data-and-policy-actions-to-address-coronavirus/
- Government actions data: https://en.wikipedia.org/wiki/U.S._state_and_local_government_response_to_the_2020_coronavirus_pandemic
- Government actions data (crowdsourced by Rex Douglass): https://github.com/rexdouglass/TIGR
- State and city populations: https://data.nber.org/data/census-intercensal-county-population.html