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Plot range of Rt for continents
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library(data.table) | |
library(ggplot2) | |
cases <- fread('_nowcasts/covid-global/national-summary/cases.csv') | |
df <- fread('_nowcasts/covid-global/national-summary/rt.csv') | |
continents <- fread('_nowcasts/covid-global/data/continents_cnty.csv') | |
cases <- cases[, .(country, date, cases = median)] | |
dfcont <- merge(df, continents, by.x = "country", by.y = "country_name", all.x = TRUE) | |
dfcont <- merge(dfcont, cases, by = c("country", "date"), all.x = TRUE) | |
## Count cases by week remove if less than 50 in a week | |
dfcont$date <- as.Date(dfcont$date, format = "%Y-%m-%d") | |
dfcont[, week := week(dfcont$date)] | |
dfcont[, weekcases := sum(cases, na.rm = T), by = .(week, country) ] | |
dfcont <- dfcont[weekcases >=50,] | |
# Get min and max for each continent by date | |
range_cont <- dfcont[type == "nowcast", .(min = min(lower_90, na.rm = T), max = max(upper_90, na.rm = T)), by = .(Continent_Name, date)] | |
# PLot range | |
ggplot(range_cont) + | |
geom_hline(yintercept = 1, linetype = "dashed") + | |
geom_ribbon(aes(x = date, ymin = min, ymax = max, group = Continent_Name), alpha = 0.5) + | |
theme_minimal() + | |
theme(axis.text.x = element_text(angle = 90), | |
panel.grid.major = element_blank(), | |
panel.grid.minor = element_blank(), | |
axis.line = element_line(colour = "black") | |
) + | |
facet_wrap(. ~ Continent_Name, scales = "free_x") + | |
scale_y_continuous(breaks = c(0, 1,5,10,15)) + | |
scale_x_date(date_breaks = "2 week", limits = c(min(range_cont$date), max(range_cont$date)), | |
date_labels = "%b %d") + | |
ylab("Effective reproduction no") + | |
xlab("Date") | |
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Continent_Name | Continent_Code | country_name | Two_Letter_Country_Code | Three_Letter_Country_Code | Country_Number | |
---|---|---|---|---|---|---|
Europe | EU | AX | ALA | 248 | ||
Asia | AS | Afghanistan | AF | AFG | 4 | |
Europe | EU | AL | ALB | 8 | ||
Africa | AF | Algeria | DZ | DZA | 12 | |
Oceania | OC | AS | ASM | 16 | ||
Europe | EU | AD | AND | 20 | ||
Africa | AF | AO | AGO | 24 | ||
North America | NA | AI | AIA | 660 | ||
Antarctica | AN | AQ | ATA | 10 | ||
North America | NA | AG | ATG | 28 | ||
South America | SA | Argentina | AR | ARG | 32 | |
Europe | EU | AM | ARM | 51 | ||
Asia | AS | Armenia | AM | ARM | 51 | |
North America | NA | AW | ABW | 533 | ||
Oceania | OC | Australia | AU | AUS | 36 | |
Europe | EU | Austria | AT | AUT | 40 | |
Europe | EU | Azerbaijan | AZ | AZE | 31 | |
Asia | AS | AZ | AZE | 31 | ||
North America | NA | BS | BHS | 44 | ||
Asia | AS | Bahrain | BH | BHR | 48 | |
Asia | AS | Bangladesh | BD | BGD | 50 | |
North America | NA | BB | BRB | 52 | ||
Europe | EU | Belarus | BY | BLR | 112 | |
Europe | EU | Belgium | BE | BEL | 56 | |
North America | NA | BZ | BLZ | 84 | ||
Africa | AF | Benin | BJ | BEN | 204 | |
North America | NA | BM | BMU | 60 | ||
Asia | AS | BT | BTN | 64 | ||
South America | SA | Bolivia | BO | BOL | 68 | |
North America | NA | BQ | BES | 535 | ||
Europe | EU | Bosnia and Herzegovina | BA | BIH | 70 | |
Africa | AF | BW | BWA | 72 | ||
Antarctica | AN | BV | BVT | 74 | ||
South America | SA | Brazil | BR | BRA | 76 | |
Asia | AS | IO | IOT | 86 | ||
North America | NA | VG | VGB | 92 | ||
Asia | AS | BN | BRN | 96 | ||
Europe | EU | Bulgaria | BG | BGR | 100 | |
Africa | AF | BF | BFA | 854 | ||
Africa | AF | BI | BDI | 108 | ||
Asia | AS | KH | KHM | 116 | ||
Africa | AF | Cameroon | CM | CMR | 120 | |
North America | NA | Canada | CA | CAN | 124 | |
Africa | AF | CV | CPV | 132 | ||
North America | NA | KY | CYM | 136 | ||
Africa | AF | Central African Republic | CF | CAF | 140 | |
Africa | AF | Chad | TD | TCD | 148 | |
South America | SA | Chile | CL | CHL | 152 | |
Asia | AS | China | CN | CHN | 156 | |
Asia | AS | CX | CXR | 162 | ||
Asia | AS | CC | CCK | 166 | ||
South America | SA | Colombia | CO | COL | 170 | |
Africa | AF | KM | COM | 174 | ||
Africa | AF | Democratic Republic of the Congo | CD | COD | 180 | |
Africa | AF | CG | COG | 178 | ||
Oceania | OC | CK | COK | 184 | ||
North America | NA | CR | CRI | 188 | ||
Africa | AF | Cote dIvoire | CI | CIV | 384 | |
Europe | EU | Croatia | HR | HRV | 191 | |
North America | NA | Cuba | CU | CUB | 192 | |
North America | NA | CW | CUW | 531 | ||
Europe | EU | CY | CYP | 196 | ||
Asia | AS | CY | CYP | 196 | ||
Europe | EU | Czechia | CZ | CZE | 203 | |
Europe | EU | Denmark | DK | DNK | 208 | |
Oceania | OC | XX | ||||
Africa | AF | Djibouti | DJ | DJI | 262 | |
North America | NA | DM | DMA | 212 | ||
North America | NA | Dominican Republic | DO | DOM | 214 | |
South America | SA | Ecuador | EC | ECU | 218 | |
Africa | AF | Egypt | EG | EGY | 818 | |
North America | NA | El Salvador | SV | SLV | 222 | |
Africa | AF | Equatorial Guinea | GQ | GNQ | 226 | |
Africa | AF | ER | ERI | 232 | ||
Europe | EU | Estonia | EE | EST | 233 | |
Africa | AF | ET | ETH | 231 | ||
South America | SA | FK | FLK | 238 | ||
Europe | EU | FO | FRO | 234 | ||
Oceania | OC | FJ | FJI | 242 | ||
Europe | EU | Finland | FI | FIN | 246 | |
Europe | EU | France | FR | FRA | 250 | |
South America | SA | GF | GUF | 254 | ||
Oceania | OC | PF | PYF | 258 | ||
Antarctica | AN | TF | ATF | 260 | ||
Africa | AF | Gabon | GA | GAB | 266 | |
Africa | AF | GM | GMB | 270 | ||
Europe | EU | GE | GEO | 268 | ||
Asia | AS | GE | GEO | 268 | ||
Europe | EU | Germany | DE | DEU | 276 | |
Africa | AF | Ghana | GH | GHA | 288 | |
Europe | EU | GI | GIB | 292 | ||
Europe | EU | Greece | GR | GRC | 300 | |
North America | NA | GL | GRL | 304 | ||
North America | NA | GD | GRD | 308 | ||
North America | NA | GP | GLP | 312 | ||
Oceania | OC | GU | GUM | 316 | ||
North America | NA | Guatemala | GT | GTM | 320 | |
Europe | EU | GG | GGY | 831 | ||
Africa | AF | Guinea | GN | GIN | 324 | |
Africa | AF | Guinea Bissau | GW | GNB | 624 | |
South America | SA | GY | GUY | 328 | ||
North America | NA | Haiti | HT | HTI | 332 | |
Antarctica | AN | HM | HMD | 334 | ||
Europe | EU | VA | VAT | 336 | ||
North America | NA | Honduras | HN | HND | 340 | |
Asia | AS | HK | HKG | 344 | ||
Europe | EU | Hungary | HU | HUN | 348 | |
Europe | EU | Iceland | IS | ISL | 352 | |
Asia | AS | India | IN | IND | 356 | |
Asia | AS | Indonesia | ID | IDN | 360 | |
Asia | AS | Iran | IR | IRN | 364 | |
Asia | AS | Iraq | IQ | IRQ | 368 | |
Asia | AS | XE | ||||
Europe | EU | Ireland | IE | IRL | 372 | |
Europe | EU | IM | IMN | 833 | ||
Asia | AS | Israel | IL | ISR | 376 | |
Europe | EU | Italy | IT | ITA | 380 | |
North America | NA | JM | JAM | 388 | ||
Asia | AS | Japan | JP | JPN | 392 | |
Europe | EU | JE | JEY | 832 | ||
Asia | AS | JO | JOR | 400 | ||
Europe | EU | Kazakhstan | KZ | KAZ | 398 | |
Asia | AS | KZ | KAZ | 398 | ||
Africa | AF | Kenya | KE | KEN | 404 | |
Oceania | OC | KI | KIR | 296 | ||
Asia | AS | South Korea | KP | PRK | 408 | |
Asia | AS | KR | KOR | 410 | ||
Asia | AS | Kuwait | KW | KWT | 414 | |
Asia | AS | Kyrgyzstan | KG | KGZ | 417 | |
Asia | AS | LA | LAO | 418 | ||
Europe | EU | Latvia | LV | LVA | 428 | |
Asia | AS | Lebanon | LB | LBN | 422 | |
Africa | AF | LS | LSO | 426 | ||
Africa | AF | LR | LBR | 430 | ||
Africa | AF | LY | LBY | 434 | ||
Europe | EU | LI | LIE | 438 | ||
Europe | EU | Lithuania | LT | LTU | 440 | |
Europe | EU | Luxembourg | LU | LUX | 442 | |
Asia | AS | MO | MAC | 446 | ||
Europe | EU | North Macedonia | MK | MKD | 807 | |
Africa | AF | MG | MDG | 450 | ||
Africa | AF | MW | MWI | 454 | ||
Asia | AS | Malaysia | MY | MYS | 458 | |
Asia | AS | Maldives | MV | MDV | 462 | |
Africa | AF | ML | MLI | 466 | ||
Europe | EU | MT | MLT | 470 | ||
Oceania | OC | MH | MHL | 584 | ||
North America | NA | MQ | MTQ | 474 | ||
Africa | AF | MR | MRT | 478 | ||
Africa | AF | MU | MUS | 480 | ||
Africa | AF | YT | MYT | 175 | ||
North America | NA | Mexico | MX | MEX | 484 | |
Oceania | OC | FM | FSM | 583 | ||
Europe | EU | Moldova | MD | MDA | 498 | |
Europe | EU | MC | MCO | 492 | ||
Asia | AS | Mongolia | MN | MNG | 496 | |
Europe | EU | ME | MNE | 499 | ||
North America | NA | MS | MSR | 500 | ||
Africa | AF | Morocco | MA | MAR | 504 | |
Africa | AF | MZ | MOZ | 508 | ||
Asia | AS | MM | MMR | 104 | ||
Africa | AF | NA | NAM | 516 | ||
Oceania | OC | NR | NRU | 520 | ||
Asia | AS | Nepal | NP | NPL | 524 | |
North America | NA | AN | ANT | 530 | ||
Europe | EU | Netherlands | NL | NLD | 528 | |
Oceania | OC | NC | NCL | 540 | ||
Oceania | OC | New Zealand | NZ | NZL | 554 | |
North America | NA | NI | NIC | 558 | ||
Africa | AF | Niger | NE | NER | 562 | |
Africa | AF | Nigeria | NG | NGA | 566 | |
Oceania | OC | NU | NIU | 570 | ||
Oceania | OC | NF | NFK | 574 | ||
Oceania | OC | MP | MNP | 580 | ||
Europe | EU | Norway | NO | NOR | 578 | |
Asia | AS | Oman | OM | OMN | 512 | |
Asia | AS | Pakistan | PK | PAK | 586 | |
Oceania | OC | PW | PLW | 585 | ||
Asia | AS | Palestine | PS | PSE | 275 | |
North America | NA | Panama | PA | PAN | 591 | |
Oceania | OC | PG | PNG | 598 | ||
South America | SA | Paraguay | PY | PRY | 600 | |
South America | SA | Peru | PE | PER | 604 | |
Asia | AS | Philippines | PH | PHL | 608 | |
Oceania | OC | PN | PCN | 612 | ||
Europe | EU | Poland | PL | POL | 616 | |
Europe | EU | Portugal | PT | PRT | 620 | |
North America | NA | Puerto Rico | PR | PRI | 630 | |
Asia | AS | Qatar | QA | QAT | 634 | |
Africa | AF | RE | REU | 638 | ||
Europe | EU | Romania | RO | ROU | 642 | |
Europe | EU | Russia | RU | RUS | 643 | |
Asia | AS | RU | RUS | 643 | ||
Africa | AF | RW | RWA | 646 | ||
North America | NA | BL | BLM | 652 | ||
Africa | AF | SH | SHN | 654 | ||
North America | NA | KN | KNA | 659 | ||
North America | NA | LC | LCA | 662 | ||
North America | NA | MF | MAF | 663 | ||
North America | NA | PM | SPM | 666 | ||
North America | NA | VC | VCT | 670 | ||
Oceania | OC | WS | WSM | 882 | ||
Europe | EU | SM | SMR | 674 | ||
Africa | AF | ST | STP | 678 | ||
Asia | AS | Saudi Arabia | SA | SAU | 682 | |
Africa | AF | Senegal | SN | SEN | 686 | |
Europe | EU | Serbia | RS | SRB | 688 | |
Africa | AF | SC | SYC | 690 | ||
Africa | AF | SL | SLE | 694 | ||
Asia | AS | Singapore | SG | SGP | 702 | |
North America | NA | SX | SXM | 534 | ||
Europe | EU | Slovakia | SK | SVK | 703 | |
Europe | EU | SI | SVN | 705 | ||
Oceania | OC | SB | SLB | 90 | ||
Africa | AF | Somalia | SO | SOM | 706 | |
Africa | AF | South Africa | ZA | ZAF | 710 | |
Antarctica | AN | GS | SGS | 239 | ||
Africa | AF | SS | SSD | 728 | ||
Europe | EU | Spain | ES | ESP | 724 | |
Asia | AS | XS | ||||
Asia | AS | Sri Lanka | LK | LKA | 144 | |
Africa | AF | Sudan | SD | SDN | 736 | |
South America | SA | SR | SUR | 740 | ||
Europe | EU | SJ | SJM | 744 | ||
Africa | AF | SZ | SWZ | 748 | ||
Europe | EU | Sweden | SE | SWE | 752 | |
Europe | EU | Switzerland | CH | CHE | 756 | |
Asia | AS | SY | SYR | 760 | ||
Asia | AS | TW | TWN | 158 | ||
Asia | AS | TJ | TJK | 762 | ||
Africa | AF | United Republic of Tanzania | TZ | TZA | 834 | |
Asia | AS | Thailand | TH | THA | 764 | |
Asia | AS | TL | TLS | 626 | ||
Africa | AF | TG | TGO | 768 | ||
Oceania | OC | TK | TKL | 772 | ||
Oceania | OC | TO | TON | 776 | ||
North America | NA | TT | TTO | 780 | ||
Africa | AF | Tunisia | TN | TUN | 788 | |
Europe | EU | Turkey | TR | TUR | 792 | |
Asia | AS | TR | TUR | 792 | ||
Asia | AS | TM | TKM | 795 | ||
North America | NA | TC | TCA | 796 | ||
Oceania | OC | TV | TUV | 798 | ||
Africa | AF | UG | UGA | 800 | ||
Europe | EU | Ukraine | UA | UKR | 804 | |
Asia | AS | United Arab Emirates | AE | ARE | 784 | |
Europe | EU | United Kingdom | GB | GBR | 826 | |
Asia | AS | XD | ||||
Oceania | OC | UM | UMI | 581 | ||
North America | NA | UM | UMI | 581 | ||
North America | NA | United States of America | US | USA | 840 | |
North America | NA | VI | VIR | 850 | ||
South America | SA | Uruguay | UY | URY | 858 | |
Asia | AS | Uzbekistan | UZ | UZB | 860 | |
Oceania | OC | VU | VUT | 548 | ||
South America | SA | Venezuela | VE | VEN | 862 | |
Asia | AS | Zambia | VN | VNM | 704 | |
Oceania | OC | WF | WLF | 876 | ||
Africa | AF | EH | ESH | 732 | ||
Asia | AS | YE | YEM | 887 | ||
Africa | AF | Zambia | ZM | ZMB | 894 | |
Africa | AF | ZW | ZWE | 716 | ||
Europe | EU | Kosovo |
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