COVID-19 analysis code 04 - plot europe

covid19_analysis_06_plot_europe.py

# Utility function to retrieve data from a single country
def get_country_df(world_df, country_name):
    
    # Some countries have several Provinces/States, must aggregate
    country_df = world_df[world_df['Country/Region'] == country_name] \
        .groupby(["Country/Region", "Date"]) \
        .sum() \
        .sort_values(by='Date')
    
    # Restore columns
    country_df['Country/Region'] = [i[0] for i in country_df.index]
    country_df['Date'] = [i[1] for i in country_df.index]
    
    return country_df

# Plot 
ax = plt.gca()

sns.set_style("whitegrid", {'grid.linestyle': ':'})
ax.yaxis.set_major_locator(ticker.MultipleLocator(Y_GRID_TICK/5))
ax.xaxis.set_major_locator(ticker.MultipleLocator(3))
ax.xaxis.set_major_formatter(mdates.DateFormatter('%d-%m-%Y'))

countries_to_plot = [
    "Spain",
    "France",
    "Germany",
]

for cc in countries_to_plot:
    c_df = get_country_df(world_df, cc)
    c_df = c_df[c_df['Date'] > datetime(2020, 2,14).date()]
    
    c_df.plot(x='Date', y=["Confirmed"], figsize=(20,10), ax=ax, marker='o', alpha=0.2)
    pass

italy_delayed = get_country_df(world_df, "Italy")
italy_delayed = italy_delayed.iloc[:-9,:]

spain_df = get_country_df(world_df, "Spain")
italy_delayed['Date'] = list(spain_df[spain_df['Date'] >= datetime(2020, 2, 9).date()]['Date'])

# Update date dynamically
end_date_skandinavia = (datetime.today() - timedelta(days=6)).date().strftime("%m-%d-%Y")
# end_date_skandinavia = (datetime.today() - timedelta(days=20)).date().strftime("%m-%d-%Y")

norway_anticipated = get_country_df(world_df, "Norway")
norway_anticipated['Date'] = pd.date_range(end=end_date_skandinavia, periods=len(norway_anticipated))

sweden_anticipated = get_country_df(world_df, "Sweden")
sweden_anticipated['Date'] = pd.date_range(end=end_date_skandinavia, periods=len(sweden_anticipated))

# Plot adjusted countries
italy_delayed = italy_delayed[italy_delayed['Date'] > datetime(2020, 2,14).date()]
italy_delayed.plot(x='Date', y=["Confirmed"], figsize=(20,10), ax=ax, marker='x', ls="--")

norway_anticipated = norway_anticipated[norway_anticipated['Date'] > "2020-02-14"]
sweden_anticipated = sweden_anticipated[sweden_anticipated['Date'] > "2020-02-14"]

norway_anticipated.plot(x='Date', y=["Confirmed"], figsize=(20,10), ax=ax, marker='x')
sweden_anticipated.plot(x='Date', y=["Confirmed"], figsize=(20,10), ax=ax, marker='x')

ax.legend(countries_to_plot + ['Italy (delayed)', 'Norway (anticipated)', 'Sweden (anticipated)'])
ax.set_ylabel("# of confirmed cases")

plt.title("Date-aligned data");

# Uncomment if you want to save the image
# plt.savefig("europe_aligned_dates.png");