) county_lat_lon['fips'] = (county_lat_lon['STATEFP'] + county_lat_lon['COUNTYFP'])#.astype(np.int64) # add predictions NUM_DAYS_LIST = [1, 2, 3, 4, 5] df_county = add_preds(df_county, NUM_DAYS_LIST=NUM_DAYS_LIST, cached_dir=data_dir) # join lat / lon to df_county # This does not seem necessary as lat and lon is already in the df_county #df_county = df_county.join(county_lat_lon.set_index('fips'), on='countyFIPS', how='left').rename( # columns={'LATITUDE': 'lat', 'LONGITUDE': 'lon'} #) # create county-level predictions plot viz_map.plot_counties_slider(df_county, auto_open=False, n_past_days=1, target_days=np.array(NUM_DAYS_LIST), filename=oj(parentdir, 'results', 'deaths.html')) # load in hospital data and merge df_hospital = load_data.load_hospital_level(data_dir=oj(parentdir, 'data_hospital_level')) df = merge_data.merge_county_and_hosp(df_county, df_hospital) df = severity_index.add_severity_index(df, NUM_DAYS_LIST) # load counties geojson counties_json = json.load(open(oj(parentdir, 'data', 'geojson-counties-fips.json'), "r")) # create hospital-level severity index plot viz_map.plot_hospital_severity_slider( df, target_days=np.array(NUM_DAYS_LIST), df_county=df_county, counties_json=counties_json, dark=True, auto_open=False, filename=oj(parentdir, 'results', 'severity_map.html') )
cached_dir=data_dir) deaths_fig = viz_map.plot_cumulative_deaths_map_with_slider( df_county, auto_open=False, target_days=np.array([0] + NUM_DAYS_LIST), filename=oj(parentdir, 'results', 'deaths.html')) print('successfully updated map of deaths') deaths_fig.write_image(oj(parentdir, 'results', 'deaths.png'), width=900, height=600, scale=2) print('successfully updated png of map of deaths') # load in hospital data and merge df_hospital = load_data.load_hospital_level( data_dir=oj(os.path.dirname(parentdir), 'covid-19-private-data')) df = merge_data.merge_county_and_hosp(df_county, df_hospital) df = severity_index.add_severity_index(df, NUM_DAYS_LIST) # load counties geojson # counties_json = json.load(open(oj(parentdir, 'data', 'geojson-counties-fips.json'), "r")) # create hospital-level severity index plot severity_fig = viz_map.plot_hospital_severity_slider( df, target_days=np.array(NUM_DAYS_LIST), plot_choropleth=False, dark=True, auto_open=False, filename=oj(parentdir, 'results', 'severity_map.html'))
import numpy as np import pandas as pd from os.path import join as oj import pygsheets import pandas as pd import sys sys.path.append('../modeling') sys.path.append('..') import load_data from fit_and_predict import add_preds from functions import merge_data if __name__ == '__main__': NUM_DAYS_LIST = [1] df_county = load_data.load_county_level(data_dir='../data') df_hospital = load_data.load_hospital_level( data_dir='../data_hospital_level') df_county = add_preds( df_county, NUM_DAYS_LIST=NUM_DAYS_LIST) # adds keys like "Predicted Deaths 1-day" print('succesfully ran pipeline!')