def get_data(download=False):
"""Download data from web or from file
Keyword Arguments:
download {bool} -- get data from source (default: {False})
Returns:
DataFrame -- florida covid19 cases and deaths data
"""
if download:
# instantiate covid19 pdf scraper
pdf = PdfScraper()
pdf.get_pages()
# covid19 cases
cases = pdf.get_data(marker=r'Case[^s]')
deaths = pdf.get_data(marker=r'Death[^s]')
_db = DataBase()
_db.add_table(FL_CASES_TABLE, cases, index=False)
_db.add_table(FL_DEATHS_TABLE, deaths, index=False)
_db.close()
else:
# read from database
_db = DataBase()
cases = _db.get_table(FL_CASES_TABLE, parse_dates=['date'])
deaths = _db.get_table(FL_DEATHS_TABLE, parse_dates=['date'])
_db.close()
return cases, deaths
def add_metadata():
"""Updates options, dates and levels database tables
Updates:
database table -- OPTIONS
database table -- DATES
database table -- LEVELS
"""
_db = DataBase()
_db.update(DROP_US_MAP_PIVOT_VIEW)
_db.update(US_MAP_PIVOT_VIEW)
data = _db.get_table(NYTIMES_COUNTIES_TABLE, parse_dates=['dates'])
_db.close()
data['date'] = pd.to_datetime(data['date'])
# last 15 days
dates = []
latest_date = data['date'].max()
for day in range(15):
date = latest_date - pd.to_timedelta(day, 'days')
dates.append(date)
# meta data
_db = DataBase()
_db.add_table(LEVELS_TABLE, pd.DataFrame({'level': LEVELS}), index=False)
_db.add_table(DATES_TABLE, pd.DataFrame({'date': dates}), index=False)
_db.update(DROP_OPTIONS_TABLE)
_db.update(CREATE_OPTIONS_TABLE)
_db.update(INSERT_USA_OPTION)
_db.close()
def clean_states_data():
"""Clean US States data from NY Times
Returns:
DataFrame -- clean us states data
Updates:
database table -- NYTIMES_STATES_TABLEs
database view -- STATES_VIEW
"""
# covid19 data and metadata
_db = DataBase()
data = _db.get_table(US_STATES_TABLE, parse_dates=['date'])
states = _db.get_geotable(STATE_MAP_TABLE)
_db.close()
start = len(data)
# add state ids
states['name'] = states['name'].str.lower()
lookup = states.set_index('name')['state_id'].to_dict()
data['state_id'] = data['state'].str.lower().map(lookup)
# get rid of data that is not in county meta data
data = data[data['state_id'].isin(list(
states['state_id']))].copy(deep=True)
# days from lastest reported date
delta_day = pd.to_timedelta(1, unit='days')
data['day'] = (data['date'].max() - data['date']) / delta_day
data['day'] = data['day'].astype('Int32')
end = len(data)
# ny times table
data = data[['state_id', 'date', 'day', 'cases', 'deaths']].copy(deep=True)
data.reset_index(drop=True, inplace=True)
# ignored lines
print(
f'ignored lines: {start-end}/{start} = {(100*(start-end)/start):.01f}%'
)
# table to database
_db = DataBase()
_db.add_table(NYTIMES_STATES_TABLE, data.set_index('state_id'))
_db.update(DROP_STATES_VIEW)
_db.update(STATES_VIEW)
_db.close()
return data
def download_fldem():
"""Get, clean and store covid19 data from FL DEM
"""
get_data(True)
_db = DataBase()
# cases
data = clean_data(FL_CASES_TABLE)
_db.add_table(FLDEM_CASES_TABLE, data.set_index('case_id'))
# deaths
data = clean_data(FL_DEATHS_TABLE)
_db.add_table(FLDEM_DEATHS_TABLE, data.set_index('case_id'))
# view
_db.update(DROP_FLDEM_VIEW)
_db.update(FLDEM_VIEW)
_db.close()
def download_nytimes():
"""Read NY Times data from github
"""
# read covid19 county by county data from url
data = pd.read_csv(URL_COUNTIES, dtype={'fips': 'str'})
_db = DataBase()
_db.add_table(US_COUNTIES_TABLE, data, index=False)
_db.close()
# read covid19 state by state data from url
data = pd.read_csv(URL_STATES, dtype={'fips': 'str'})
_db = DataBase()
_db.add_table(US_STATES_TABLE, data, index=False)
_db.close()
clean_counties_data()
clean_states_data()
add_metadata()
def predict():
"""main module function to predict covid19 cases and deaths
Inputs from databae:
US_STATES_TABLE {database table} -- nytimes covid19 data
Outputs to database:
ARIMA_CASES_TABLE {database table} -- cases[predict, upper, lower]
ARIMA_DEATHS_TABLE {database table } -- deaths[predict, upper, lower]
"""
_db = DataBase()
data = _db.get_table(STATES_VIEW_TABLE, parse_dates=['date'])
_db.close()
# predict cases
result = run_arima(data, 'cases')
# only data after 3/15/2020
slicer = result['date'] > pd.to_datetime('3/15/2020')
result = result.loc[slicer, :].copy(deep=True)
result.sort_values(['date', 'state'], inplace=True)
result = result.round(0)
_db = DataBase()
_db.add_table(ARIMA_CASES_TABLE, data=result, index=False)
_db.close()
# predict deaths
result = run_arima(data, 'deaths')
# only data after 3/15/2020
slicer = result['date'] > pd.to_datetime('3/15/2020')
result = result.loc[slicer, :].copy(deep=True)
result.sort_values(['date', 'state'], inplace=True)
result = result.round(0)
_db = DataBase()
_db.add_table(ARIMA_DEATHS_TABLE, data=result, index=False)
_db.close()
def clean_counties_data():
"""Clean US Counties data from NY Times
Returns:
DataFrame -- clean us counties data
Updates:
database table -- NYTIMES_COUNTIES_TABLEs
database view -- COUNTIES_VIEW
"""
_db = DataBase()
data = _db.get_table(US_COUNTIES_TABLE, parse_dates=['date'])
counties = _db.get_geotable(US_MAP_TABLE)
states = _db.get_geotable(STATE_MAP_TABLE)
_db.close()
start = len(data)
# use new york county fips for new york city
data.loc[data['county'] == 'New York City', 'fips'] = '36061'
# add state ids
lookup = states.set_index('name')['state_id'].to_dict()
data['state_id'] = data['state'].map(lookup)
# add county ids - first attempt
data['id'] = data['county'].str.lower() + data['state_id']
counties['id'] = counties['name'].str.lower() + counties['state_id']
lookup = counties[['id',
'county_id']].set_index('id')['county_id'].to_dict()
data['county_id'] = data['id'].map(lookup)
# add county ids - last attempt
condition = (~data['fips'].isna()) & (data['county_id'].isna())
data.loc[condition, 'county_id'] = data.loc[condition, 'fips']
# get rid of data that is not in county meta data
data = data[data['county_id'].isin(list(
counties['county_id']))].copy(deep=True)
# state ids base on county_ids
lookup = counties.set_index('county_id')['state_id'].to_dict()
data['state_id'] = data['county_id'].map(lookup)
# days from lastest day
delta_day = pd.to_timedelta(1, unit='days')
data['day'] = (data['date'].max() - data['date']) / delta_day
data['day'] = data['day'].astype('Int32')
end = len(data)
# ny times counties table
cols = ['county_id', 'state_id', 'date', 'day', 'cases', 'deaths']
data = data[cols].copy(deep=True)
data.reset_index(drop=True, inplace=True)
data['case_level'] = pd.cut(data['cases'],
LEVELS,
labels=range(1, len(LEVELS)))
data['case_level'] = pd.to_numeric(data['case_level'], 'coerce').fillna(0)
data['case_level'] = data['case_level'].astype('Int32')
# ignored lines
print(
f'ignored lines: {start-end}/{start} = {(100*(start-end)/start):.01f}%'
)
# tables to database
_db = DataBase()
_db.add_table(NYTIMES_COUNTIES_TABLE, data.set_index(['county_id', 'day']))
_db.update(DROP_COUNTIES_VIEW)
_db.update(COUNTIES_VIEW)
_db.close()
return data
