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After installing SaviR, you are ready to use the following functions to read in the data and create visualizations. There are functions to create plots, maps, or tables by World Health Organization (WHO) Region, Department of State (DoS) Region, or globally.

Data: The Frankenstein Dataset

onetable - stored metadata with iso2 and iso3 codes, country names, WHO/DoS/World Bank regions, and UN population estimates
get_covid_df(sources = c("all", "WHO", "WHO+JHU", "WHO+Primary")) - COVID cases/deaths dataframe from WHO and other sources. calc_add_risk() - Add risk matrix calculations to dataframe (df)
get_vax() - Get vaccination data from Our World In Data (OWID)
get_combined_table(type = c("WHO", "Both", "legacy"), geometry=FALSE) - Combine all of the above into one large df, optionally add geometry

This snippet produces the master df with all the variables required for all of the following graphics.

# Load in data to create visuals
df_who <- get_combined_table("WHO") # China includes Taiwan, Hong Kong, and Macau data

# Data for visuals are typically as of Sunday of the current week
# but this can be determined dynamically using WHO data.
sunday_date <- df_who |>
  distinct(date, dow = weekdays(date)) |>
  arrange(desc(date)) |>
  filter(dow == "Sunday") |>
  slice(1) |>
  pull(date)

Plots

plot_epicurve(df, transparent = T)

When creating epi curves for the WHO regions, the “plot_epicurve” function should take in the df with only “WHO” observations in order to match the same curve on the WHO Coronavirus Dashboard. The individual epi curves for each region can be run simply by filtering for one WHO region in the df. The function will detect that the region column has only one region and will produce the epi curve accordingly.

When creating epi curves for the DoS regions, the plot_epicurve function should take in the df with “Both” observations. Similarly to the WHO epi curves, individual epi curves can also be produce by filtering to one DoS region.

# Epi Curves for WHO -- Global
epi_curve_global <- plot_epicurve(df_who, transparent = T)


epi_curve_global


# Epi Curves for DoS -- Global
state_epi_curve <- plot_epicurve(filter(df_who, date <= sunday_date),
                                 type = "cases", 
                                 by_cat = "State Region")
state_epi_curve

Inset plots

  • We can also pass inset = TRUE to plot an inset plot for the most recent weeks
    • By default, the inset for the case plot is slightly left and cener in the plot window
    • Deaths plot inset is slightly up and to the right
  • Looks at the past 9 weeks of data in the inset, or min(date) + weeks(1), whichever is later
inset_epi_curve <- df_who |>
  filter(date <= sunday_date) |>
  plot_epicurve(type = "cases", by_cat = "State Region", transparent = FALSE, inset = TRUE)

inset_epi_curve

# Regions
for (r in unique(na.omit(df_who$who_region))) {
  epi_curve_regional <- plot_epicurve(filter(df_who, who_region == r), transparent = F)


  print(epi_curve_regional)
}

plot_riskmatrix(df)

Note for labeling purposes, the labels variable should be added to the dataframe specifying the top 10 countries for weekly average incidence, week case percent change, and weekly total cases. Exclusion criteria: Countries with population less than 10 million and countries with weekly cases totals less than 100.

global_risk_matrix <- df_who %>%
  filter(date == sunday_date) %>%
  filter(population >= 10000000) %>% # Exclude population less than 10M
  filter(week_case >= 100) %>%
  mutate(
    rank_inc = dense_rank(desc(week_case_incidence)),
    rank_per = dense_rank(desc(percent_change_case)),
    rank_cas = dense_rank(desc(week_case))
  ) %>%
  mutate(labels = case_when(
    rank_inc %in% 1:10 ~ country,
    rank_per %in% 1:10 ~ country,
    rank_cas %in% 1:10 ~ country
  )) %>%
  plot_riskmatrix()


global_risk_matrix

global_vax_coverage <- df_who %>%
  filter(date <= sunday_date) %>%
  filter(date == max(date)) %>%
  filter(!is.na(state_region)) %>%
  plot_vaxcoverage(by_cat = "State Region")

global_vax_coverage

Maps

By default, get_combined_table() does not return geometry. This is preferable, since the size of the table is quite large and the geometry list column takes up a lot of space in memory. However, if we want to map these data, we can either call get_combined_table("Both", geometry = TRUE), or join with country_coords after filtering, like so:

# Filter to only observations with date as of Sunday
# and join in geometry
df_who_mapping <- df_who %>%
  filter(date == sunday_date) %>%
  left_join(select(country_coords, id, geometry), by = "id")

map_burden(df, region, time_step)

The “map_burden” function takes in a pre-filtered data.frame and computes and displays average incidence for each country over the time period selected.
The region argument is optional, but it is used to specify a specific DoS/WHO region to zoom to, if desired.
time_step is used to specify the days used to average incidence over. This is always relative to the latest date in the data.frame.
bin_breaks and bin_colors can be used to over-ride sensible defaults for incidence cutpoints and color scheme, if desired.

burden_map_global <- df_who |>
  filter(date <= sunday_date) |>
  map_burden()


burden_map_global


for (r in unique(na.omit(df_who$who_region))) {
  burden_map_regional <- df_who |>
    filter(who_region == r, date <= sunday_date) |>
    map_burden(region = r)


  print(burden_map_regional)
}

and an example of how to produce a 14d map:

burden_map_global_14 <- df_who |>
  filter(date <= sunday_date) |>
  map_burden(time_step = 14)


burden_map_global_14

We can also over-ride the incidence cut-points, like so:

# same map with 0-1, 1-5, 5-10, 10+ breaks
burden_map_global_14_2 <- df_who |>
  filter(date <= sunday_date) |>
  map_burden(
    time_step = 14,
    bin_breaks = c(0, 1, 5, 10, Inf),
    bin_colors = c("0- <1" = "#f1e5a1", "1- <5" = "#e7b351", "5- <10" = "#d26230", "10+" = "#aa001e")
  )

burden_map_global_14_2

map_trend(df, region, time_step = 7)

The “map_trend” function requires a result column where weekly percent change is converted into factors using “cut”.

The default behavior is to visualize a global trend map, but passing a data frame filtered to a specific region and providing the region name as a region argument will change the bounding box accordingly.

A different time_step can be provided. The default assumes you are comparing two 7d periods, but this can be increased or decreased accordingly.

trend_map_global <- df_who |>
  filter(date <= sunday_date) |>
  map_trend()


trend_map_global

for (r in unique(na.omit(df_who$who_region))) {
  trend_map_reg <- df_who |>
  filter(date <= sunday_date) |>
    map_trend(region = r)

  print(trend_map_reg)
}

and an example producing the same with different time_step:

df_who |>
  filter(date <= sunday_date) |>
  map_trend(time_step = 14)

map_vaccinations(df, vac_type = c("People", "Fully"))

global_vax_map <- df_who_mapping %>%
  mutate(result = cut(people_vaccinated_per_hundred, breaks = c(0, 1, 3, 10, 30, Inf))) %>%
  group_by(country) %>%
  filter(!is.na(result)) %>%
  filter(date == max(date)) %>%
  ungroup() %>%
  map_vaccinations(., vac_type = "People")

global_vax_map

Tables

table_10mostcases(df, time_step = 7, region = NULL, data_as_of = NULL)

This function presents a top-10 table of countries based on cases reported in the past time_step.
The default is a 7 day period, but this can be adjusted. Additionally, you can tweak the title and data-as-of footnote using those variables respectively, or they will be inferred internally.

7-day Table

df_who |>
  filter(date <= sunday_date) |>
  table_10mostcases(data_as_of = format(sunday_date, "%B %d, %Y"))
10 Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
Brazil 91,120 577.7
Russia 55,802 −70.2
Greece 8,485 −54.4
United Kingdom 6,854 −27.3
Poland 5,750 −16.5
Italy 5,193 −61.2
New Zealand 3,809 −55.7
France 3,052 −41.0
Lithuania 2,759 −30.2
Norway 2,628 −50.6
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior

14-day Table

df_who |>
  filter(date <= sunday_date) |>
  table_10mostcases(time_step = 14)
10 Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 14 Days
% Change
Past 14 Days1
Russia 243,221 −33.5
Brazil 104,566 -
Greece 27,100 −52.7
Italy 18,593 −86.1
United Kingdom 16,281 −57.5
Poland 12,633 −85.8
New Zealand 12,403 −19.0
Czechia 10,030 −81.9
Malaysia 8,406 −24.2
France 8,225 −12.5
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 14 days to 14 days prior

By region

for (r in unique(na.omit(df_who$who_region))) {
  tab_out <- df_who |>
    filter(date <= sunday_date, who_region == r) |>
    table_10mostcases(region = r, data_as_of = format(Sys.Date(), "%B %d, %Y"))
  
  print(htmltools::tagList(tab_out))
}
10 (AMRO) Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
Brazil 91,120 577.7
Ecuador 1,143 465.8
Colombia 554 185.6
Argentina 492 −64.9
Guatemala 267 413.5
Costa Rica 246 215.4
Uruguay 155 −69.5
Panama 99 80.0
Chile 98 −97.7
Nicaragua 64 1,180.0
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
10 (EMRO) Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
Afghanistan 0 -
United Arab Emirates 0 -
Bahrain 0 -
Djibouti 0 -
Egypt 0 -
Iran 0 -
Iraq 0 -
Jordan 0 -
Kuwait 0 -
Lebanon 0 -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
10 (AFRO) Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
Mauritius 1,293 −4.7
South Africa 52 23.8
Madagascar 51 131.8
Ethiopia 22 −35.3
Niger 19 1,800.0
Algeria 18 −50.0
Mozambique 14 −69.6
Senegal 14 180.0
Gabon 12 1,100.0
Cote d’Ivoire 8 100.0
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
10 (EURO) Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
Russia 55,802 −70.2
Greece 8,485 −54.4
United Kingdom 6,854 −27.3
Poland 5,750 −16.5
Italy 5,193 −61.2
France 3,052 −41.0
Lithuania 2,759 −30.2
Norway 2,628 −50.6
Czechia 2,259 −70.9
Sweden 2,200 −52.6
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
10 (WPRO) Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
New Zealand 3,809 −55.7
Brunei Darussalam 135 −85.0
China 89 −79.7
American Samoa 0 -
Australia 0 -
Cook Islands 0 -
Fiji 0 -
Micronesia 0 -
Guam 0 -
Japan 0 -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
10 (SEARO) Countries/ Areas with Most New Cases
Country/ Area New Cases
Past 7 Days
% Change
Past 7 Days1
Thailand 1,884 −41.1
Indonesia 77 −74.2
Bangladesh 42 −26.3
India 34 −79.4
Bhutan 0 -
Sri Lanka 0 -
Maldives 0 -
Burma 0 -
Nepal 0 -
Korea (North) 0 -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Percent change in cases of most recent 7 days to 7 days prior

table_10incidence(df, time_step = 7, region = NULL, data_as_of = NULL)

Similar to the above, but computes top-10 countries baseed on incidence over past time_step.

7-day table

df_who |>
  filter(date <= sunday_date) |>
  table_10incidence(data_as_of = format(sunday_date, "%B %d, %Y"))
10 Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
Lithuania 14.3 −30.2
Mauritius 14.2 −4.7
Cyprus 12.9 −35.0
Greece 11.7 −54.4
New Zealand 10.5 −55.7
Luxembourg 10.5 −15.4
Croatia 7.7 −31.5
Norway 6.9 −50.6
Brazil 6.0 577.7
Estonia 5.6 −51.4
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior

14-day table

df_who |>
  filter(date <= sunday_date) |>
  table_10incidence(time_step = 14)
10 Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 14 Days2
Greece 18.6 −52.7
Lithuania 17.4 −78.9
New Zealand 17.1 −19.0
Brunei Darussalam 16.4 −33.7
Cyprus 16.3 −52.8
Mauritius 14.6 159.3
Russia 12.0 −33.5
Luxembourg 11.4 −60.4
Norway 10.5 −42.2
Croatia 9.5 −80.3
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Average daily incidence per 100,000 in past 14 days
2 Percent change in cases of most recent 14 days to 14 days prior

By Region

for (r in unique(na.omit(df_who$who_region))) {
  tab_out <- df_who %>%
    filter(date <= sunday_date, who_region == r) |>
    table_10incidence(region = r, data_as_of = format(Sys.Date(), "%B %d, %Y"))

  print(htmltools::tagList(tab_out))
}
10 (AMRO) Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
Brazil 6.0 577.7
Turks and Caicos Islands 4.1 85.7
Ecuador 0.9 465.8
Costa Rica 0.7 215.4
Uruguay 0.6 −69.5
British Virgin Islands 0.5 -
Panama 0.3 80.0
Guatemala 0.2 413.5
Argentina 0.2 −64.9
Colombia 0.2 185.6
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior
10 (EMRO) Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
Afghanistan 0.0 -
United Arab Emirates 0.0 -
Bahrain 0.0 -
Djibouti 0.0 -
Egypt 0.0 -
Iran 0.0 -
Iraq 0.0 -
Jordan 0.0 -
Kuwait 0.0 -
Lebanon 0.0 -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior
10 (AFRO) Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
Mauritius 14.2 −4.7
Gabon 0.1 1,100.0
Madagascar 0.0 131.8
Mauritania 0.0 500.0
South Africa 0.0 23.8
Senegal 0.0 180.0
South Sudan 0.0 33.3
Niger 0.0 1,800.0
Zimbabwe 0.0 33.3
Mozambique 0.0 −69.6
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior
10 (EURO) Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
Lithuania 14.3 −30.2
Cyprus 12.9 −35.0
Greece 11.7 −54.4
Luxembourg 10.5 −15.4
Croatia 7.7 −31.5
Norway 6.9 −50.6
Estonia 5.6 −51.4
Russia 5.5 −70.2
Slovenia 4.2 −56.5
Czechia 3.1 −70.9
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior
10 (WPRO) Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
New Zealand 10.5 −55.7
Brunei Darussalam 4.3 −85.0
China 0.0 −79.7
American Samoa 0.0 -
Australia 0.0 -
Cook Islands 0.0 -
Fiji 0.0 -
Micronesia 0.0 -
Guam 0.0 -
Japan 0.0 -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior
10 (SEARO) Countries/ Areas with Highest Incidence
Country/ Area Incidence
Per 100,0001
% Change
Past 7 Days2
Thailand 0.4 −41.1
Indonesia 0.0 −74.2
Bangladesh 0.0 −26.3
India 0.0 −79.4
Bhutan 0.0 -
Sri Lanka 0.0 -
Maldives 0.0 -
Burma 0.0 -
Nepal 0.0 -
Korea (North) 0.0 -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of March 11, 2025
1 Average daily incidence per 100,000 in past 7 days
2 Percent change in cases of most recent 7 days to 7 days prior

table_10percentchange(df, time_step = 7, second_time_step = 28, region = NULL, data_as_of = NULL)

Works similarly to the above, but selects top 10 countries based on percent change over time_step.
There’s an additional argument second_time_step that specifies a second (normally longer) period to compute a percent change over.
The default visualization is using weekly change and 4 week change.

This table is usually filtered to only countries over a certain population size, but this should be handled
externally.

Global table (7d and 28d pct change)

df_who %>%
  filter(date <= sunday_date, population >= 10000000) |>
  table_10percentchange(data_as_of = format(sunday_date, "%B %d, %Y"))
10 Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
Niger 1,800.0 900.0
Venezuela 933.3 -
Nigeria 600.0 700.0
Brazil 577.7 -
Ecuador 465.8 −61.9
Guatemala 413.5 553.8
Colombia 185.6 −85.5
Senegal 180.0 −70.9
Madagascar 131.8 27.9
Cote d'Ivoire 100.0 −33.3
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior

Global table (14d and 28d pct change)

df_who %>%
  filter(date <= sunday_date, population >= 10000000) |>
  table_10percentchange(time_step = 14)
10 Countries/ Areas with
Highest Percent Change In Past 14 Days
Country/ Area % Change
Past 14 Days1
% Change
Past 28 Days2
Mozambique 2,900.0 −21.5
Guatemala 1,419.0 553.8
Madagascar 421.4 27.9
Angola 400.0 −96.8
Kenya 375.0 64.3
Congo DR 100.0 −97.4
Niger 100.0 900.0
South Africa 64.9 9.4
Algeria 58.8 −30.7
Zimbabwe 55.6 −76.8
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 14 days to 14 days prior
2 Percent change in cases of most recent 28 days to 28 days prior

Regional Tables

for (r in unique(na.omit(df_who$who_region))) {
  tab_out <- df_who %>%
    filter(date <= sunday_date, population >= 100000, who_region == r) |> # Exclude population less than 100,000
    table_10percentchange(region = r, data_as_of = format(sunday_date, "%B %d, %Y")) 
    
  print(htmltools::tagList(tab_out))
}
10 (AMRO) Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
Nicaragua 1,180.0 19.0
Venezuela 933.3 -
Brazil 577.7 -
Ecuador 465.8 −61.9
Guatemala 413.5 553.8
El Salvador 250.0 −24.4
Costa Rica 215.4 −74.5
Barbados 200.0 −69.4
Colombia 185.6 −85.5
Panama 80.0 −67.8
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior
10 (EMRO) Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
Afghanistan - -
United Arab Emirates - -
Bahrain - -
Djibouti - -
Egypt - -
Iran - -
Iraq - -
Jordan - -
Kuwait - -
Lebanon - -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior
10 (AFRO) Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
Niger 1,800.0 900.0
Gabon 1,100.0 -
Nigeria 600.0 700.0
Mauritania 500.0 −71.4
Senegal 180.0 −70.9
Madagascar 131.8 27.9
Cote d’Ivoire 100.0 −33.3
South Sudan 33.3 1,433.3
Zimbabwe 33.3 −76.8
South Africa 23.8 9.4
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior
10 (EURO) Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
North Macedonia 37.5 68.4
Ukraine 26.2 137.7
Azerbaijan 0.0 −51.1
Luxembourg −15.4 24.0
Poland −16.5 392.4
Ireland −18.2 −42.9
United Kingdom −27.3 −35.0
Romania −27.6 −16.3
Lithuania −30.2 332.8
Croatia −31.5 339.5
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior
10 (WPRO) Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
New Zealand −55.7 −83.7
China −79.7 −86.8
Brunei Darussalam −85.0 −54.5
Australia - -
Fiji - -
Micronesia - -
Guam - -
Japan - -
Cambodia - −97.5
Kiribati - -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior
10 (SEARO) Countries/ Areas with
Highest Percent Change In Past 7 Days
Country/ Area % Change
Past 7 Days1
% Change
Past 28 Days2
Bangladesh −26.3 −94.7
Thailand −41.1 −69.3
Indonesia −74.2 −60.4
India −79.4 −85.0
Bhutan - -
Sri Lanka - −74.1
Maldives - -
Burma - −72.1
Nepal - -
Korea (North) - -
Data Source: WHO Coronavirus Disease (COVID-19) Dashboard
Data as of February 23, 2025
1 Percent change in cases of most recent 7 days to 7 days prior
2 Percent change in cases of most recent 28 days to 28 days prior

table_10vaccinations(df, type = c("Global", "Region"), run_date)

The “table_10vaccinations” function takes looks for a country, value1 (people vaccinated per hundred), and a value2 (daily vaccinations per hundred) column. Note as vaccination reporting has gaps, the df must be sliced by country and the most recent date with people_vaccinated_per_hundred value (if there is one).

df_who %>%
  filter(date <= sunday_date) %>%
  filter(population > 1000000) %>%
  group_by(country) %>%
  filter(!is.na(people_vaccinated_per_hundred)) %>%
  filter(date == max(date)) %>%
  ungroup() %>%
  select(country = who_country, value1 = people_vaccinated_per_hundred, value2 = daily_vaccinations_per_hundred) %>%
  arrange(desc(value1)) %>%
  head(10) %>%
  table_10vaccinations(., run_date = format(sunday_date, "%B %d, %Y"))
Top 10 Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
United Arab Emirates 105.8 NA
Qatar 105.8 NA
Cuba 96.3 NA
Portugal 95.3 NA
Chile 92.3 NA
Nicaragua 92.2 NA
Viet Nam 91.9 NA
China 91.9 NA
Singapore 91.5 NA
Cambodia 91.3 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 1 million were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated
for (r in unique(na.omit(df_who$who_region))) {
  tab_out <- df_who %>%
    filter(date <= sunday_date) %>%
    filter(population > 100000) %>% # Exclude population less than 100,000
    filter(who_region == r) %>%
    group_by(country) %>%
    filter(!is.na(people_vaccinated_per_hundred)) %>%
    arrange(date) %>%
    top_n(1, date) %>%
    distinct(id, .keep_all = T) %>%
    select(country = who_country, value1 = people_vaccinated_per_hundred, value2 = daily_vaccinations_per_hundred) %>%
    arrange(desc(value1)) %>%
    head(10) %>%
    table_10vaccinations(., type = r, run_date = format(sunday_date, "%B %d, %Y"))

  print(htmltools::tagList(tab_out))
}
10 (AMRO) Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
Cuba 96.3 NA
Chile 92.3 NA
Nicaragua 92.2 NA
Argentina 91.2 NA
Canada 90.3 NA
Peru 89.8 NA
Costa Rica 89.6 NA
Brazil 88.1 NA
Uruguay 88.0 NA
Ecuador 85.2 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 100,000 were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated
10 (EMRO) Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
United Arab Emirates 105.8 NA
Qatar 105.8 NA
Bahrain 84.3 NA
Kuwait 81.0 NA
Iran 73.6 NA
Saudi Arabia 71.3 NA
Oman 71.1 NA
Pakistan 70.2 NA
Morocco 66.8 NA
Tunisia 58.4 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 100,000 were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated
10 (AFRO) Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
Mauritius 86.5 NA
Seychelles 82.6 NA
Rwanda 79.0 NA
Botswana 74.2 NA
Liberia 73.6 NA
Mozambique 69.4 NA
Sierra Leone 66.0 NA
Guinea 62.9 NA
Sao Tome and Principe 61.7 NA
Cabo Verde 60.1 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 100,000 were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated
10 (EURO) Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
Portugal 95.3 NA
Malta 89.8 NA
Spain 86.9 NA
Italy 86.3 NA
Iceland 83.0 NA
Ireland 81.9 NA
Finland 81.7 NA
Denmark 80.7 NA
France 80.6 NA
Norway 80.0 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 100,000 were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated
10 (WPRO) Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
Brunei Darussalam 100.5 NA
Viet Nam 91.9 NA
China 91.9 NA
Singapore 91.5 NA
Cambodia 91.3 NA
Korea (South) 86.4 NA
Samoa 86.1 NA
Australia 84.9 NA
Japan 84.5 NA
New Zealand 83.0 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 100,000 were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated
10 (SEARO) Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
Nepal 91.3 NA
Bhutan 89.3 NA
Bangladesh 88.5 NA
Thailand 79.5 NA
Sri Lanka 78.5 NA
Maldives 76.2 NA
Burma 74.5 NA
Indonesia 74.0 NA
India 72.5 NA
Timor-Leste 66.1 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 100,000 were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated

table_10vaccinations(df, vac_type = c("Partial", "Fully"), type = "Global", run_date = "Enter a date")

df_who %>%
  filter(date <= sunday_date) %>%
  filter(population > 1000000) %>%
  group_by(country) %>%
  filter(!is.na(people_fully_vaccinated_per_hundred)) %>%
  filter(date == max(date)) %>%
  ungroup() %>%
  select(country = who_country, value1 = people_fully_vaccinated_per_hundred, value2 = daily_vaccinations_per_hundred) %>%
  arrange(desc(value1)) %>%
  head(10) %>%
  table_10vaccinations(., run_date = format(sunday_date, "%B %d, %Y"))
Top 10 Countries/ Areas with Highest
Vaccination per 100 People
1,2
Country/ Area People Vaccinated
per 100 People3
Daily Vaccines
Administered
per 100 People4
Qatar 105.8 NA
United Arab Emirates 103.7 NA
Singapore 90.8 NA
Chile 90.3 NA
Cuba 89.7 NA
China 89.5 NA
Nicaragua 88.0 NA
Cambodia 87.6 NA
Viet Nam 87.5 NA
Portugal 86.8 NA
Data as of February 23, 2025
1 Countries with population size less than or equal to 1 million were excluded
2 People vaccinated per 100 people represents total population (all ages)
3 Number of people out of 100 who received at least one vaccine dose; does not represent percent of population that completed primary vaccination series
4 Vaccine doses administered per day (7 day rolling average); does not represent number of people vaccinated

table_countriesofconcern(df, df_vaccinations_manufacturers, country_list)

c_list <- c("United Kingdom","Denmark","Portugal","South Africa","Kenya","Zambia","United States of America")
c_list_iso <- parse_country(c_list, to = "iso3c")

df_who_latest <- df_who %>%
  group_by(id) %>%
  filter(date == max(date)) %>%
  ungroup()

vax_man <- get_vax_manufacturers()

table_countriesofconcern(df_who_latest, vax_man, c_list_iso)

Country

Denmark

United Kingdom

Kenya

Portugal

United States of America

South Africa

Zambia

Date

2025-02-23

2025-02-23

2025-02-23

2025-02-23

2025-02-23

2025-02-23

2025-02-23

New Cases 7 Day Average
(7 Day Average Case Incidence per 100,000)

149.1
(2.54)

979.1
(1.45)

0.9
(0)

72.7
(0.71)

0
(0)

7.4
(0.01)

0
(0)

7 Day Cases

1,044

6,854

6

509

0

52

0

Previous 7 Day Cases

1,827

9,427

13

808

0

42

0

% Change in Cases from Previous 7 Days

-42.9%

-27.3%

-53.8%

-37%

23.8%

New Deaths 7 Day Average
(7 Day Average Death Incidence per 100,000)

0
(0)

0
(0)

0
(0)

5.1
(0.05)

800.3
(0.24)

0
(0)

0
(0)

7 Day Deaths

0

0

0

36

5,602

0

0

Previous 7 Day Deaths

2

0

0

21

4,164

0

0

% Change in Deaths from Previous 7 Days

-100%

71%

35%

Most Recent Date for Vaccinations

2023-09-29

2022-09-11

2023-04-02

2023-09-29

2023-05-09

2023-09-24

2023-06-25

People Vaccinated Per 100 People

80.69

79.71

26.83

95.34

81.39

40.42

58.51

People who completed primary
vaccination series per 100 People

80.11

75.19

20.53

86.75

69.47

35.13

46.03

Total Vaccinations Per 100 People

254.24

224.04

43.96

275.03

203.81

69.79

67.21

Vaccines in Use

Johnson&Johnson, Moderna, Oxford/AstraZeneca, Pfizer/BioNTech

Moderna, Oxford/AstraZeneca, Pfizer/BioNTech

Johnson&Johnson, Moderna, Oxford/AstraZeneca, Pfizer/BioNTech, Sinopharm/Beijing

Covaxin, Johnson&Johnson, Moderna, Novavax, Oxford/AstraZeneca, Pfizer/BioNTech, Sanofi/GSK, Sinopharm/Beijing, Sinovac

Johnson&Johnson, Moderna, Novavax, Pfizer/BioNTech

Johnson&Johnson, Pfizer/BioNTech

Johnson&Johnson, Oxford/AstraZeneca, Sinopharm/Beijing

% Delta since January 1, 2022

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% Omicron since January 1, 2022

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