14-day cumulative number of COVID-19 cases per 100 000

At the end of the page, we provide a detailed description of how the numbers are calculated.

Compute data

In [1]:
import pandas as pd
pd.set_option("display.max_rows", None)
from oscovida import get_incidence_rates_countries

Table for all countries

In [2]:
cases_incidence, deaths_incidence = get_incidence_rates_countries()

Downloaded data: last data point 1/25/23 from https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv
Downloaded data: last data point 1/25/23 from https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv

/tank/oscovida/work/oscovida.github.io/oscovida.github.io/.venv/lib/python3.9/site-packages/oscovida/oscovida.py:597: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
  cases = cases.groupby(cases.index).sum().astype(int)
/tank/oscovida/work/oscovida.github.io/oscovida.github.io/.venv/lib/python3.9/site-packages/oscovida/oscovida.py:598: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
  deaths = deaths.groupby(deaths.index).sum().astype(int)
/tank/oscovida/work/oscovida.github.io/oscovida.github.io/.venv/lib/python3.9/site-packages/oscovida/oscovida.py:520: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
  population
In [3]:
cases_incidence
Out[3]:
14-day-sum population 14-day-incidence-rate
Country
Afghanistan 424 38928341 1.1
Albania 129 2877800 4.5
Algeria 92 43851043 0.2
Andorra 39 77265 50.5
Angola 89 32866268 0.3
Antarctica 0 0 NaN
Antigua and Barbuda 0 97928 0.0
Argentina 28030 45195777 62.0
Armenia 32 2963234 1.1
Australia 61807 25459700 242.8
Austria 28574 9006400 317.3
Azerbaijan 725 10139175 7.2
Bahamas 0 393248 0.0
Bahrain 803 1701583 47.2
Bangladesh 151 164689383 0.1
Barbados 252 287371 87.7
Belarus 0 9449321 0.0
Belgium 6693 11492641 58.2
Belize 213 397621 53.6
Benin 7 12123198 0.1
Bhutan 47 771612 6.1
Bolivia 11054 11673029 94.7
Bosnia and Herzegovina 168 3280815 5.1
Botswana 657 2351625 27.9
Brazil 189812 212559409 89.3
Brunei 2574 437483 588.4
Bulgaria 1323 6948445 19.0
Burkina Faso 0 20903278 0.0
Burma 84 54409794 0.2
Burundi 49 11890781 0.4
Cabo Verde 10 555988 1.8
Cambodia 37 16718971 0.2
Cameroon 0 26545864 0.0
Canada 24280 38246108 63.5
Central African Republic 10 4829764 0.2
Chad 1 16425859 0.0
Chile 34092 19116209 178.3
China 64562 1411778724 4.6
Colombia 5297 50882884 10.4
Comoros 6 869595 0.7
Congo (Brazzaville) 0 5518092 0.0
Congo (Kinshasa) 300 89561404 0.3
Costa Rica 10569 5094114 207.5
Cote d'Ivoire 6 26378275 0.0
Croatia 1301 4105268 31.7
Cuba 168 11326616 1.5
Cyprus 6020 1207361 498.6
Czechia 3697 10708982 34.5
Denmark 2845 5837213 48.7
Diamond Princess 0 0 NaN
Djibouti 0 988002 0.0
Dominica 0 71991 0.0
Dominican Republic 412 10847904 3.8
Ecuador 10776 17643060 61.1
Egypt 0 102334403 0.0
El Salvador 0 6486201 0.0
Equatorial Guinea 0 1402985 0.0
Eritrea 0 3546427 0.0
Estonia 688 1326539 51.9
Eswatini 61 1160164 5.3
Ethiopia 469 114963583 0.4
Fiji 37 896444 4.1
Finland 3432 5540718 61.9
France 69578 65249843 106.6
Gabon 0 2225728 0.0
Gambia 0 2416664 0.0
Georgia 4821 3989175 120.9
Germany 133430 83155031 160.5
Ghana 42 31072945 0.1
Greece 0 10423056 0.0
Grenada 0 112519 0.0
Guatemala 10116 17915567 56.5
Guinea 30 13132792 0.2
Guinea-Bissau 0 1967998 0.0
Guyana 340 786559 43.2
Haiti 39 11402533 0.3
Holy See 0 809 0.0
Honduras 2289 9904608 23.1
Hungary 1493 9660350 15.5
Iceland 146 341250 42.8
India 1755 1380004385 0.1
Indonesia 3993 273523621 1.5
Iran 1453 83992953 1.7
Iraq 0 40222503 0.0
Ireland 2478 4937796 50.2
Israel 9399 8655541 108.6
Italy 135948 60461828 224.8
Jamaica 439 2961161 14.8
Japan 1404322 126476458 1110.3
Jordan 0 10203140 0.0
Kazakhstan 7877 18776707 42.0
Kenya 166 53771300 0.3
Kiribati 70 117606 59.5
Korea, North 0 25778815 0.0
Korea, South 377609 51269183 736.5
Kosovo 153 1810366 8.5
Kuwait 111 4270563 2.6
Kyrgyzstan 5 6524191 0.1
Laos 36 7275556 0.5
Latvia 393 1886202 20.8
Lebanon 3153 6825442 46.2
Lesotho 0 2142252 0.0
Liberia 10 5057677 0.2
Libya 5 6871287 0.1
Liechtenstein 14 38137 36.7
Lithuania 3324 2722291 122.1
Luxembourg 675 625976 107.8
MS Zaandam 0 0 NaN
Madagascar 57 27691019 0.2
Malawi 285 19129955 1.5
Malaysia 3762 32365998 11.6
Maldives 11 540542 2.0
Mali 4 20250834 0.0
Malta 223 441539 50.5
Marshall Islands 0 58413 0.0
Mauritania 229 4649660 4.9
Mauritius 703 1271767 55.3
Mexico 63790 127792286 49.9
Micronesia 429 113815 376.9
Moldova 857 4027690 21.3
Monaco 37 39244 94.3
Mongolia 62 3278292 1.9
Montenegro 778 628062 123.9
Morocco 218 36910558 0.6
Mozambique 775 31255435 2.5
Namibia 127 2540916 5.0
Nauru 0 10834 0.0
Nepal 48 29136808 0.2
Netherlands 4195 17134873 24.5
New Zealand 33216 4822233 688.8
Nicaragua 34 6624554 0.5
Niger 35 24206636 0.1
Nigeria 0 206139587 0.0
North Macedonia 333 2083380 16.0
Norway 900 5421242 16.6
Oman 0 5106622 0.0
Pakistan 171 220892331 0.1
Palau 10 18008 55.5
Panama 1814 4314768 42.0
Papua New Guinea 0 8947027 0.0
Paraguay 7255 7132530 101.7
Peru 5825 32971846 17.7
Philippines 3459 109581085 3.2
Poland 4472 37846605 11.8
Portugal 4948 10196707 48.5
Qatar 1107 2881060 38.4
Romania 6456 19237682 33.6
Russia 72414 145934460 49.6
Rwanda 27 12952209 0.2
Saint Kitts and Nevis 14 53192 26.3
Saint Lucia 44 183629 24.0
Saint Vincent and the Grenadines 18 110947 16.2
Samoa 14 196130 7.1
San Marino 113 33938 333.0
Sao Tome and Principe 0 219161 0.0
Saudi Arabia 432 34813867 1.2
Senegal 0 16743930 0.0
Serbia 9346 8737370 107.0
Seychelles 0 98340 0.0
Sierra Leone 0 7976985 0.0
Singapore 4492 5850343 76.8
Slovakia 1432 5434712 26.3
Slovenia 4411 2078932 212.2
Solomon Islands 0 652858 0.0
Somalia 8 15893219 0.1
South Africa 3913 59308690 6.6
South Sudan 0 11193729 0.0
Spain 29199 46754783 62.5
Sri Lanka 36 21413250 0.2
Sudan 27 43849269 0.1
Summer Olympics 2020 0 0 NaN
Suriname 0 586634 0.0
Sweden 7117 10099270 70.5
Switzerland 1263 8654618 14.6
Syria 27 17500657 0.2
Taiwan* 261811 23816775 1099.3
Tajikistan 0 9537642 0.0
Tanzania 133 59734213 0.2
Thailand 1596 69799978 2.3
Timor-Leste 8 1318442 0.6
Togo 3 8278737 0.0
Tonga 82 105697 77.6
Trinidad and Tobago 900 1399491 64.3
Tunisia 2549 11818618 21.6
Turkey 0 84339067 0.0
Tuvalu 0 11792 0.0
US 635574 329466283 192.9
Uganda 49 45741000 0.1
Ukraine 6317 43733759 14.4
United Arab Emirates 1218 9890400 12.3
United Kingdom 49851 67886004 73.4
Uruguay 5771 3473727 166.1
Uzbekistan 361 33469199 1.1
Vanuatu 0 292680 0.0
Venezuela 549 28435943 1.9
Vietnam 402 97338583 0.4
West Bank and Gaza 0 5101416 0.0
Winter Olympics 2022 0 0 NaN
Yemen 0 29825968 0.0
Zambia 3414 18383956 18.6
Zimbabwe 1625 14862927 10.9

Table sorted by 14-day-incidence

In [4]:
cases_incidence.sort_values(by=['14-day-incidence-rate'], ascending=False)
Out[4]:
14-day-sum population 14-day-incidence-rate
Country
Japan 1404322 126476458 1110.3
Taiwan* 261811 23816775 1099.3
Korea, South 377609 51269183 736.5
New Zealand 33216 4822233 688.8
Brunei 2574 437483 588.4
Cyprus 6020 1207361 498.6
Micronesia 429 113815 376.9
San Marino 113 33938 333.0
Austria 28574 9006400 317.3
Australia 61807 25459700 242.8
Italy 135948 60461828 224.8
Slovenia 4411 2078932 212.2
Costa Rica 10569 5094114 207.5
US 635574 329466283 192.9
Chile 34092 19116209 178.3
Uruguay 5771 3473727 166.1
Germany 133430 83155031 160.5
Montenegro 778 628062 123.9
Lithuania 3324 2722291 122.1
Georgia 4821 3989175 120.9
Israel 9399 8655541 108.6
Luxembourg 675 625976 107.8
Serbia 9346 8737370 107.0
France 69578 65249843 106.6
Paraguay 7255 7132530 101.7
Bolivia 11054 11673029 94.7
Monaco 37 39244 94.3
Brazil 189812 212559409 89.3
Barbados 252 287371 87.7
Tonga 82 105697 77.6
Singapore 4492 5850343 76.8
United Kingdom 49851 67886004 73.4
Sweden 7117 10099270 70.5
Trinidad and Tobago 900 1399491 64.3
Canada 24280 38246108 63.5
Spain 29199 46754783 62.5
Argentina 28030 45195777 62.0
Finland 3432 5540718 61.9
Ecuador 10776 17643060 61.1
Kiribati 70 117606 59.5
Belgium 6693 11492641 58.2
Guatemala 10116 17915567 56.5
Palau 10 18008 55.5
Mauritius 703 1271767 55.3
Belize 213 397621 53.6
Estonia 688 1326539 51.9
Andorra 39 77265 50.5
Malta 223 441539 50.5
Ireland 2478 4937796 50.2
Mexico 63790 127792286 49.9
Russia 72414 145934460 49.6
Denmark 2845 5837213 48.7
Portugal 4948 10196707 48.5
Bahrain 803 1701583 47.2
Lebanon 3153 6825442 46.2
Guyana 340 786559 43.2
Iceland 146 341250 42.8
Panama 1814 4314768 42.0
Kazakhstan 7877 18776707 42.0
Qatar 1107 2881060 38.4
Liechtenstein 14 38137 36.7
Czechia 3697 10708982 34.5
Romania 6456 19237682 33.6
Croatia 1301 4105268 31.7
Botswana 657 2351625 27.9
Saint Kitts and Nevis 14 53192 26.3
Slovakia 1432 5434712 26.3
Netherlands 4195 17134873 24.5
Saint Lucia 44 183629 24.0
Honduras 2289 9904608 23.1
Tunisia 2549 11818618 21.6
Moldova 857 4027690 21.3
Latvia 393 1886202 20.8
Bulgaria 1323 6948445 19.0
Zambia 3414 18383956 18.6
Peru 5825 32971846 17.7
Norway 900 5421242 16.6
Saint Vincent and the Grenadines 18 110947 16.2
North Macedonia 333 2083380 16.0
Hungary 1493 9660350 15.5
Jamaica 439 2961161 14.8
Switzerland 1263 8654618 14.6
Ukraine 6317 43733759 14.4
United Arab Emirates 1218 9890400 12.3
Poland 4472 37846605 11.8
Malaysia 3762 32365998 11.6
Zimbabwe 1625 14862927 10.9
Colombia 5297 50882884 10.4
Kosovo 153 1810366 8.5
Azerbaijan 725 10139175 7.2
Samoa 14 196130 7.1
South Africa 3913 59308690 6.6
Bhutan 47 771612 6.1
Eswatini 61 1160164 5.3
Bosnia and Herzegovina 168 3280815 5.1
Namibia 127 2540916 5.0
Mauritania 229 4649660 4.9
China 64562 1411778724 4.6
Albania 129 2877800 4.5
Fiji 37 896444 4.1
Dominican Republic 412 10847904 3.8
Philippines 3459 109581085 3.2
Kuwait 111 4270563 2.6
Mozambique 775 31255435 2.5
Thailand 1596 69799978 2.3
Maldives 11 540542 2.0
Venezuela 549 28435943 1.9
Mongolia 62 3278292 1.9
Cabo Verde 10 555988 1.8
Iran 1453 83992953 1.7
Cuba 168 11326616 1.5
Malawi 285 19129955 1.5
Indonesia 3993 273523621 1.5
Saudi Arabia 432 34813867 1.2
Armenia 32 2963234 1.1
Afghanistan 424 38928341 1.1
Uzbekistan 361 33469199 1.1
Comoros 6 869595 0.7
Timor-Leste 8 1318442 0.6
Morocco 218 36910558 0.6
Laos 36 7275556 0.5
Nicaragua 34 6624554 0.5
Vietnam 402 97338583 0.4
Ethiopia 469 114963583 0.4
Burundi 49 11890781 0.4
Congo (Kinshasa) 300 89561404 0.3
Haiti 39 11402533 0.3
Kenya 166 53771300 0.3
Angola 89 32866268 0.3
Cambodia 37 16718971 0.2
Algeria 92 43851043 0.2
Central African Republic 10 4829764 0.2
Liberia 10 5057677 0.2
Rwanda 27 12952209 0.2
Tanzania 133 59734213 0.2
Syria 27 17500657 0.2
Sri Lanka 36 21413250 0.2
Guinea 30 13132792 0.2
Madagascar 57 27691019 0.2
Burma 84 54409794 0.2
Nepal 48 29136808 0.2
Libya 5 6871287 0.1
Uganda 49 45741000 0.1
Niger 35 24206636 0.1
India 1755 1380004385 0.1
Benin 7 12123198 0.1
Kyrgyzstan 5 6524191 0.1
Sudan 27 43849269 0.1
Bangladesh 151 164689383 0.1
Pakistan 171 220892331 0.1
Somalia 8 15893219 0.1
Ghana 42 31072945 0.1
Suriname 0 586634 0.0
Vanuatu 0 292680 0.0
Togo 3 8278737 0.0
Bahamas 0 393248 0.0
Burkina Faso 0 20903278 0.0
Yemen 0 29825968 0.0
Tajikistan 0 9537642 0.0
Tuvalu 0 11792 0.0
Turkey 0 84339067 0.0
Belarus 0 9449321 0.0
West Bank and Gaza 0 5101416 0.0
Antigua and Barbuda 0 97928 0.0
Jordan 0 10203140 0.0
South Sudan 0 11193729 0.0
Equatorial Guinea 0 1402985 0.0
Korea, North 0 25778815 0.0
Lesotho 0 2142252 0.0
Holy See 0 809 0.0
Guinea-Bissau 0 1967998 0.0
Mali 4 20250834 0.0
Grenada 0 112519 0.0
Marshall Islands 0 58413 0.0
Greece 0 10423056 0.0
Gambia 0 2416664 0.0
Gabon 0 2225728 0.0
Nauru 0 10834 0.0
Eritrea 0 3546427 0.0
Nigeria 0 206139587 0.0
El Salvador 0 6486201 0.0
Solomon Islands 0 652858 0.0
Oman 0 5106622 0.0
Egypt 0 102334403 0.0
Papua New Guinea 0 8947027 0.0
Dominica 0 71991 0.0
Djibouti 0 988002 0.0
Iraq 0 40222503 0.0
Congo (Brazzaville) 0 5518092 0.0
Chad 1 16425859 0.0
Sao Tome and Principe 0 219161 0.0
Senegal 0 16743930 0.0
Cameroon 0 26545864 0.0
Seychelles 0 98340 0.0
Sierra Leone 0 7976985 0.0
Cote d'Ivoire 6 26378275 0.0
Antarctica 0 0 NaN
Diamond Princess 0 0 NaN
MS Zaandam 0 0 NaN
Summer Olympics 2020 0 0 NaN
Winter Olympics 2022 0 0 NaN

Tutorial: Detailed calculation for one country

In [5]:
from oscovida import fetch_cases, get_population
import datetime
In [6]:
period = 14 # Days we compute the incidence rate over
In [7]:
cases = fetch_cases() # Get a DataFrame where each row is the country, and columns cumulative case numbers
cases = cases.groupby(cases.index).sum() # Merge the rows for different regions as we want the numbers for an entire country

/tmp/ipykernel_3403315/1570404713.py:2: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.
  cases = cases.groupby(cases.index).sum() # Merge the rows for different regions as we want the numbers for an entire country
In [8]:
cases_germany = cases.loc['Germany'][2:] # First 2 entries are lat/lon so we only take the subsequent ones
cases_germany.tail()
Out[8]:
1/21/23    37668384.0
1/22/23    37668384.0
1/23/23    37684456.0
1/24/23    37701193.0
1/25/23    37715000.0
Name: Germany, dtype: float64
In [9]:
yesterday = datetime.datetime.now() - datetime.timedelta(days=1)
x_days_ago = yesterday - datetime.timedelta(days=period)
In [10]:
period_mask = (
    (yesterday > pd.to_datetime(cases_germany.index)) &
    (pd.to_datetime(cases_germany.index) > x_days_ago)
) # Mask for dates between today and x days ago
In [11]:
cases_in_period_per_day_germany = cases_germany[period_mask].diff() # Apply the period mask and get the diff to get the daily new cases
cases_in_period_per_day_germany
Out[11]:
1/12/23        NaN
1/13/23    10609.0
1/14/23        0.0
1/15/23        0.0
1/16/23    17222.0
1/17/23    15450.0
1/18/23    12001.0
1/19/23     9710.0
1/20/23     8866.0
1/21/23        0.0
1/22/23        0.0
1/23/23    16072.0
1/24/23    16737.0
1/25/23    13807.0
Name: Germany, dtype: float64
In [12]:
cases_in_period_per_day_germany.plot() # We can easily look at new cases per day
Out[12]:
<AxesSubplot: >
In [13]:
population = get_population().population
In [14]:
population_germany = population.loc['Germany'] # Get the population of Germany
population_germany
Out[14]:
83155031.0
In [15]:
incidence_rate_germany = cases_in_period_per_day_germany.sum() / population_germany * 100_000
incidence_rate_germany # By convention this is total cases over period / population * 100_000
Out[15]:
144.87878670864785
In [ ]: