library(contactdata)Note that this package does not make any geopolitical statement and only provides the data as it has been published.
The data included in this package comes from two articles
Kiesha Prem, Alex R. Cook, Mark Jit, Projecting social contact matrices in 152 countries using contact surveys and demographic data, PLoS Comp. Biol. (2017), https://doi.org/10.1371/journal.pcbi.1005697.
and
Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies, CMMID COVID-19 Working Group, Alex R. Cook, Mark Jit, Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era, PLoS Comp. Biol. (2021), https://doi.org/10.1371/journal.pcbi.1009098.
and as indicated by the titles, not all regions were included.
The full list is available with the list_countries()
function:
(all_countries_2017 <- list_countries(data_source = 2017))
#> [1] "Albania" "Algeria" "Andorra"
#> [4] "Antigua & Barbuda" "Argentina" "Armenia"
#> [7] "Australia" "Austria" "Azerbaijan"
#> [10] "Bahamas" "Bahrain" "Bangladesh"
#> [13] "Belarus" "Belgium" "Belize"
#> [16] "Benin" "Bhutan" "Bolivia"
#> [19] "Bosnia" "Botswana" "Brazil"
#> [22] "Brunei" "Bulgaria" "Burkina Faso"
#> [25] "Cape Verde" "Cambodia" "Cameroon"
#> [28] "Canada" "Chile" "China"
#> [31] "Colombia" "Congo - Brazzaville" "Costa Rica"
#> [34] "Croatia" "Cyprus" "Czechia"
#> [37] "Denmark" "Dominican Republic" "Ecuador"
#> [40] "Egypt" "El Salvador" "Estonia"
#> [43] "Ethiopia" "Fiji" "Finland"
#> [46] "France" "Georgia" "Germany"
#> [49] "Ghana" "Greece" "Guatemala"
#> [52] "Guinea" "Guyana" "Haiti"
#> [55] "Honduras" "Hong Kong" "Hungary"
#> [58] "Iceland" "India" "Indonesia"
#> [61] "Iran" "Iraq" "Ireland"
#> [64] "Israel" "Italy" "Jamaica"
#> [67] "Japan" "Jordan" "Kazakhstan"
#> [70] "Kenya" "Kiribati" "Kuwait"
#> [73] "Kyrgyzstan" "Laos" "Latvia"
#> [76] "Lebanon" "Lesotho" "Liberia"
#> [79] "Lithuania" "Luxembourg" "Malaysia"
#> [82] "Maldives" "Malta" "Mauritania"
#> [85] "Mauritius" "Mexico" "Monaco"
#> [88] "Mongolia" "Montenegro" "Morocco"
#> [91] "Mozambique" "Namibia" "Nepal"
#> [94] "Netherlands" "New Zealand" "Nicaragua"
#> [97] "Niger" "Nigeria" "Oman"
#> [100] "Pakistan" "Panama" "Paraguay"
#> [103] "Peru" "Philippines" "Poland"
#> [106] "Portugal" "Qatar" "South Korea"
#> [109] "Romania" "Russia" "Rwanda"
#> [112] "St. Lucia" "Samoa" "São Tomé & Príncipe"
#> [115] "Saudi Arabia" "Senegal" "Serbia"
#> [118] "Seychelles" "Sierra Leone" "Singapore"
#> [121] "Slovakia" "Slovenia" "Solomon Islands"
#> [124] "South Africa" "Spain" "Sri Lanka"
#> [127] "Suriname" "Sweden" "Switzerland"
#> [130] "Syria" "Taiwan" "Tajikistan"
#> [133] "North Macedonia" "Thailand" "Timor-Leste"
#> [136] "Tonga" "Tunisia" "Turkey"
#> [139] "Uganda" "Ukraine" "United Arab Emirates"
#> [142] "UK" "Tanzania" "US"
#> [145] "Uruguay" "Uzbekistan" "Vanuatu"
#> [148] "Venezuela" "Vietnam" "Yemen"
#> [151] "Zambia" "Zimbabwe"
(all_countries_2020 <- list_countries(data_source = 2020))
#> [1] "Afghanistan" "Angola"
#> [3] "Albania" "United Arab Emirates"
#> [5] "Argentina" "Armenia"
#> [7] "Austria" "Azerbaijan"
#> [9] "Burundi" "Belgium"
#> [11] "Benin" "Burkina Faso"
#> [13] "Bangladesh" "Bulgaria"
#> [15] "Bahrain" "Bahamas"
#> [17] "Bosnia" "Belarus"
#> [19] "Belize" "Bolivia"
#> [21] "Brazil" "Barbados"
#> [23] "Brunei" "Bhutan"
#> [25] "Botswana" "Central African Republic"
#> [27] "Canada" "Switzerland"
#> [29] "Chile" "China"
#> [31] "Côte d’Ivoire" "Cameroon"
#> [33] "Congo - Kinshasa" "Congo - Brazzaville"
#> [35] "Colombia" "Comoros"
#> [37] "Cape Verde" "Costa Rica"
#> [39] "Cuba" "Cyprus"
#> [41] "Czechia" "Germany"
#> [43] "Djibouti" "Denmark"
#> [45] "Dominican Republic" "Algeria"
#> [47] "Ecuador" "Egypt"
#> [49] "Eritrea" "Spain"
#> [51] "Estonia" "Ethiopia"
#> [53] "Finland" "Fiji"
#> [55] "France" "Gabon"
#> [57] "UK" "Georgia"
#> [59] "Ghana" "Guinea"
#> [61] "Gambia" "Guinea-Bissau"
#> [63] "Equatorial Guinea" "Greece"
#> [65] "Guatemala" "Guyana"
#> [67] "Hong Kong" "Honduras"
#> [69] "Croatia" "Hungary"
#> [71] "Indonesia" "India"
#> [73] "Ireland" "Iran"
#> [75] "Iraq" "Iceland"
#> [77] "Israel" "Italy"
#> [79] "Jamaica" "Jordan"
#> [81] "Kazakhstan" "Kenya"
#> [83] "Kyrgyzstan" "Cambodia"
#> [85] "South Korea" "Kuwait"
#> [87] "Laos" "Liberia"
#> [89] "Libya" "St. Lucia"
#> [91] "Sri Lanka" "Lesotho"
#> [93] "Lithuania" "Luxembourg"
#> [95] "Latvia" "Macao"
#> [97] "Morocco" "Moldova"
#> [99] "Madagascar" "Maldives"
#> [101] "Mexico" "North Macedonia"
#> [103] "Mali" "Malta"
#> [105] "Myanmar" "Montenegro"
#> [107] "Mongolia" "Mozambique"
#> [109] "Mauritania" "Mauritius"
#> [111] "Malawi" "Malaysia"
#> [113] "Namibia" "Niger"
#> [115] "Nigeria" "Nicaragua"
#> [117] "Netherlands" "Norway"
#> [119] "Nepal" "New Zealand"
#> [121] "Oman" "Pakistan"
#> [123] "Panama" "Peru"
#> [125] "Philippines" "Papua New Guinea"
#> [127] "Poland" "Puerto Rico"
#> [129] "North Korea" "Portugal"
#> [131] "Paraguay" "Palestine"
#> [133] "Qatar" "Romania"
#> [135] "Russia" "Rwanda"
#> [137] "Saudi Arabia" "Sudan"
#> [139] "Senegal" "Singapore"
#> [141] "Solomon Islands" "Sierra Leone"
#> [143] "El Salvador" "Serbia"
#> [145] "South Sudan" "São Tomé & Príncipe"
#> [147] "Suriname" "Slovakia"
#> [149] "Slovenia" "Sweden"
#> [151] "Eswatini" "Syria"
#> [153] "Chad" "Togo"
#> [155] "Thailand" "Tajikistan"
#> [157] "Turkmenistan" "Timor-Leste"
#> [159] "Tonga" "Trinidad & Tobago"
#> [161] "Tunisia" "Turkey"
#> [163] "Tanzania" "Uganda"
#> [165] "Ukraine" "Uruguay"
#> [167] "US" "Uzbekistan"
#> [169] "St. Vincent & Grenadines" "Venezuela"
#> [171] "Vietnam" "Vanuatu"
#> [173] "Samoa" "Yemen"
#> [175] "South Africa" "Zambia"
#> [177] "Zimbabwe"Below is a map that may help you find out which countries are absent from the dataset:
library(ggplot2)
wrld <- map_data("world")
wrld$region <- countrycode::countryname(wrld$region)
#> Warning in countrycode_convert(sourcevar = sourcevar, origin = origin, destination = dest, : Some values were not matched unambiguously: Ascension Island, Azores, Barbuda, Canary Islands, Chagos Archipelago, Grenadines, Heard Island, Madeira Islands, Micronesia, Saba, Saint Martin, Siachen Glacier, Sint Eustatius, Virgin Islands
wrld$included <- "Not included"
wrld$included[wrld$region %in% all_countries_2020] <- "2020"
wrld$included[wrld$region %in% all_countries_2017] <- "2017 & 2020"
ggplot(wrld, aes(long, lat, group = group, fill = included)) +
geom_polygon() +
coord_equal() +
theme_bw()