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%md

# COVID-19 Display Testing Time Series
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%auto
%default_mode python3
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import pandas as pd
import numpy as np
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state = 'il'
# use testing series collected by The Covid Tracking Project
# https://covidtracking.com/api/
# state abbreviation must be lower case
if state == 'US':
    url = f"https://covidtracking.com/api/us/daily.csv"
else:
    url = f"https://covidtracking.com/api/v1/states/{state}/daily.csv"

url
︡82723ce2-7775-48ce-befb-2d21e90f2f46︡{"stdout":"'https://covidtracking.com/api/v1/states/il/daily.csv'"}︡{"done":true}
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# fetch state data from Covid Tracking Project
# keep only a few columns
df = pd.read_csv(url, parse_dates=['date', 'dateChecked'])[['date','positive','death','total']]

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# use date as x-axis for displays so make it the index
df.set_index('date', inplace=True)
df.set_index(df.index.strftime('%m/%d'), inplace=True)
df.sort_index(inplace=True)
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df.head(2)
︡ce3df052-3578-48bd-8002-c337ff8348d2︡{"html":"<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>positive</th>\n      <th>death</th>\n      <th>total</th>\n    </tr>\n    <tr>\n      <th>date</th>\n      <th></th>\n      <th></th>\n      <th></th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>03/04</th>\n      <td>4</td>\n      <td>NaN</td>\n      <td>155</td>\n    </tr>\n    <tr>\n      <th>03/05</th>\n      <td>5</td>\n      <td>NaN</td>\n      <td>197</td>\n    </tr>\n  </tbody>\n</table>\n</div>"}︡{"done":true}
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df.tail()
︡a35f1e1e-f25f-4561-a523-e1bbf73991f8︡{"html":"<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>positive</th>\n      <th>death</th>\n      <th>total</th>\n    </tr>\n    <tr>\n      <th>date</th>\n      <th></th>\n      <th></th>\n      <th></th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>06/18</th>\n      <td>135639</td>\n      <td>6718.0</td>\n      <td>1284693</td>\n    </tr>\n    <tr>\n      <th>06/19</th>\n      <td>136470</td>\n      <td>6718.0</td>\n      <td>1312003</td>\n    </tr>\n    <tr>\n      <th>06/20</th>\n      <td>137104</td>\n      <td>6829.0</td>\n      <td>1337968</td>\n    </tr>\n    <tr>\n      <th>06/21</th>\n      <td>137762</td>\n      <td>6851.0</td>\n      <td>1361784</td>\n    </tr>\n    <tr>\n      <th>06/22</th>\n      <td>138224</td>\n      <td>6875.0</td>\n      <td>1380003</td>\n    </tr>\n  </tbody>\n</table>\n</div>"}︡{"done":true}
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title = f"COVID-19 cumulative numbers\npositive tests and total tests in {state}"
df[-30:].plot(y=['positive','total'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);

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df['positive/total'] = df.loc[:,'positive']/df.loc[:,'total']
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title = f"COVID-19 positive tests / total tests in {state}"
df[-30:].plot(y=['positive/total'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);
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# just the confirmed (positives)
title = f"COVID-19 cumulative confirmed cases in {state}"
df[-30:].plot(y=['positive'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);


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df['new_cases_per_day'] = df['positive'].diff()
title = f"COVID-19 new cases reported each day in {state}"
df[-30:].plot(y=['new_cases_per_day'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);

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title = f"COVID-19 7-day moving avg new cases in {state}"
df['7d_avg_new_cases'] = df['new_cases_per_day'].rolling(7).mean()
df[-30:].plot(y=['7d_avg_new_cases'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);


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# deaths
title = f"COVID-19 deaths in {state}"
df[-30:].plot(y=['death'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);

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df['deaths_each_day'] = df['death'].diff()
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title = f"COVID-19 deaths each day in {state}"
df[-30:].plot(y=['deaths_each_day'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);
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title = f"COVID-19 7-day moving avg deaths in {state}"
df['7d_avg_deaths'] = df['deaths_each_day'].rolling(7).mean()
df[-30:].plot(y=['7d_avg_deaths'], kind="bar", figsize=[8, 5], rot=45, fontsize=7, title=title);

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