data2019nCoV: Data on the COVID-19 Outbreak

## Code to prepare `WHO_SR` dataset goes here.
## Package users ignore this code.

# SOURCE https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

devtools::load_all()
WHO_SR <- read.csv("data-raw/WHO_SR.csv")
WHO_SR$Date <- as.Date(WHO_SR$Date)

usethis::use_data(WHO_SR, overwrite = TRUE)

## Below creates alternately labelled object, for use by downstream outbreaks

library(tidyverse)
sarscov2_who_2019 <- WHO_SR

sarscov2_who_2019 <- rename(sarscov2_who_2019,
    situation_report = SituationReport,
    date = Date,

    cases_chn = China,
    cases_jpn = Japan,
    cases_kor = RepublicofKorea,
    cases_vnm = VietNam,
    cases_sgp = Singapore,
    cases_aus = Australia,
    cases_mys = Malaysia,
    cases_khm = Cambodia,
    cases_nzl = NewZealand,
    cases_brn = BruneiDarussalam,
    cases_mng = Mongolia,
    cases_pyf = FrenchPolynesia,
    cases_gum = Guam,
    cases_fji = Fiji,
    cases_ncl = NewCaledonia,
    cases_png = PapuaNewGuinea,
    cases_lao = LaoPeoplesDemocraticRepublic,
    cases_mnp = NorthernMarianaIslands,
    cases_region_westernpacific = Region.WesternPacific,

    cases_phl = Philippines,
    cases_tha = Thailand,
    cases_npl = Nepal,
    cases_lka = SriLanka,
    cases_ind = India,
    cases_idn = Indonesia,
    cases_btn = Bhutan,
    cases_mdv = Maldives,
    cases_bgd = Bangladesh,
    cases_tls = TimorLeste,
    cases_mmr = Myanmar,
    cases_region_southeastasia = Region.SouthEastAsia,

    cases_usa = UnitedStatesofAmerica,
    cases_can = Canada,
    cases_bra = Brazil,
    cases_mex = Mexico,
    cases_ecu = Ecuador,
    cases_dom = DominicanRepublic,
    cases_maf = SaintMartin,
    cases_blm = SaintBarthelemy,
    cases_arg = Argentina,
    cases_chl = Chile,
    cases_col = Colombia,
    cases_per = Peru,
    cases_cri = CostaRica,
    cases_guf = FrenchGuiana,
    cases_mtq = Martinique,
    cases_pry = Paraguay,
    cases_pan = Panama,
    cases_bol = Bolivia,
    cases_jam = Jamaica,
    cases_hnd = Honduras,
    cases_ury = Uruguay,
    cases_guy = Guyana,
    cases_vct = SaintVincentandtheGrenadines,
    cases_cub = Cuba,
    cases_jey = Jersey,
    cases_ven = Venezuela,
    cases_atg = AntiguaandBarbuda,
    cases_glp = Guadeloupe,
    cases_lca = SaintLucia,
    cases_gtm = Guatemala,
    cases_sur = Suriname,
    cases_tto = TrinidadandTobago,
    cases_pri = PuertoRico,
    cases_cym = CaymanIslands,
    cases_cuw = Curacao,
    cases_bhm = Bahamas,
    cases_abw = Aruba,
    cases_vir = UnitedStatesVirginIslands,
    cases_brb = Barbados,
    cases_msr = Montserrat,
    cases_slv = ElSalvador,
    cases_nic = Nicaragua,
    cases_sxm = SintMaarten,
    cases_bmu = Bermuda,
    cases_hti = Haiti,
    cases_blz = Belize,
    cases_dma = Dominica,
    cases_tca = TurksandCaicos,
    cases_kna = SaintKittsandNevis,
    cases_aia = Anguilla,
    cases_vgb = BritishVirginIslands,
    cases_grd = Grenada,
    cases_bes = BonaireSintEustatiusandSaba,
    cases_flk = FalklandIslands,
    cases_spm = SaintPierreandMiquelon,
    cases_region_americas = Region.Americas,

    cases_fin = Finland,
    cases_hrv = Croatia,
    cases_aut = Austria,
    cases_dnk = Denmark,
    cases_est = Estonia,
    cases_geo = Georgia,
    cases_grc = Greece,
    cases_mkd = NorthMacedonia,
    cases_nor = Norway,
    cases_rou = Romania,
    cases_che = Switzerland,
    cases_blr = Belarus,
    cases_ltu = Lithuania,
    cases_nld = Netherlands,
    cases_smr = SanMarino,
    cases_aze = Azerbaijan,
    cases_irl = Ireland,
    cases_mco = Monaco,
    cases_cze = Czechia,
    cases_isl = Iceland,
    cases_arm = Armenia,
    cases_kaz = Kazakhstan,
    cases_lux = Luxembourg,
    cases_prt = Portugal,
    cases_and = Andorra,
    cases_lva = Latvia,
    cases_pol = Poland,
    cases_ukr = Ukraine,
    cases_uzb = Uzbekistan,
    cases_lie = Liechtenstein,
    cases_bih = BosniaHerzegovina,
    cases_hun = Hungary,
    cases_svn = Slovenia,
    cases_gib = Gibraltar,
    cases_isr = Israel,
    cases_fra = France,
    cases_deu = Germany,
    cases_ita = Italy,
    cases_rus = RussianFederation,
    cases_esp = Spain,
    cases_swe = Sweden,
    cases_gbr = UnitedKingdom,
    cases_bel = Belgium,
    cases_srb = Serbia,
    cases_svk = Slovakia,
    cases_vat = HolySee,
    cases_mlt = Malta,
    cases_bgr = Bulgaria,
    cases_mda = RepublicofMoldova,
    cases_fro = FaroeIslands,
    cases_alb = Albania, 
    cases_cyp = Cyprus,
    cases_ggy = Guernsey,
    cases_tur = Turkey,
    cases_kgz = Kyrgyzstan,
    cases_grl = Greenland,
    cases_mne = Montenegro,
    cases_kosovo = Kosovo,
    cases_imn = IsleofMan,
    cases_region_european = Region.European,

    cases_are = UnitedArabEmirates,
    cases_egy = Egypt,
    cases_irn = Iran,
    cases_lbn = Lebanon,
    cases_kwt = Kuwait,
    cases_afg = Afghanistan,
    cases_bhr = Bahrain,
    cases_irq = Iraq,
    cases_omn = Oman,
    cases_pak = Pakistan,
    cases_qat = Qatar,
    cases_jor = Jordan,
    cases_mar = Morocco,
    cases_sau = SaudiArabia,
    cases_tun = Tunisia,
    cases_pse = OccupiedPalestinianTerritory,
    cases_sdn = Sudan,
    cases_som = Somalia,
    cases_dji = Djibouti,
    cases_syr = SyrianArabRepublic,
    cases_lby = Libya,
    cases_yem = Yemen,
    cases_region_easternmediterranean = Region.EasternMediterranean,

    cases_dza = Algeria,
    cases_nga = Nigeria,
    cases_sen = Senegal,
    cases_cmr = Cameroon,
    cases_zaf = SouthAfrica,
    cases_tgo = Togo,
    cases_bfa = BurkinaFaso,
    cases_cod = DemocraticRepublicoftheCongo,
    cases_civ = CotedIvoire,
    cases_eth = Ethiopia,
    cases_gab = Gabon,
    cases_gha = Ghana,
    cases_gin = Guinea,
    cases_ken = Kenya,
    cases_nam = Namibia,
    cases_caf = CentralAfricanRepublic,
    cases_cog = Congo,
    cases_gnq = EquatorialGuinea,
    cases_swz = Eswatini,
    cases_mrt = Mauritania,
    cases_myt = Mayotte,
    cases_rwa = Rwanda,
    cases_syc = Seychelles,
    cases_ben = Benin,
    cases_lbr = Liberia,
    cases_tza = UnitedRepublicofTanzania,
    cases_mus = Mauritius,
    cases_zmb = Zambia,
    cases_gmb = Gambia,
    cases_tcd = Chad,
    cases_ner = Niger,
    cases_reu = Reunion,
    cases_cpv = CaboVerde,
    cases_zwe = Zimbabwe,
    cases_mdg = Madagascar,
    cases_ago = Angola,
    cases_eri = Eritrea,
    cases_uga = Uganda,
    cases_moz = Mozambique,
    cases_gnb = GuineaBissau,
    cases_mli = Mali,
    cases_bwa = Botswana,
    cases_bdi = Burundi,
    cases_sle =	SierraLeone,
    cases_mwi = Malawi,
    cases_ssd = SouthSudan,
    cases_stp = SaoTomeandPrincipe,


    cases_region_african = Region.African,

    cases_internationalconveyance = InternationalConveyance,

    cases_global = Global.confirmed,
    deaths_global = Global.deaths,

    suspected_chn = China.suspected,
    severe_chn = China.severe,

    deaths_chn = China.deaths,
    deaths_phl = Philippines.deaths,
    deaths_jpn = Japan.deaths,
    deaths_fra = France.deaths,
    deaths_kor = RepublicofKorea.deaths,
    deaths_irn = Iran.deaths,
    deaths_ita = Italy.deaths, 
    deaths_aus = Australia.deaths,
    deaths_tha = Thailand.deaths,
    deaths_usa = UnitedStatesofAmerica.deaths,
    deaths_irq = Iraq.deaths,
    deaths_esp = Spain.deaths,
    deaths_che = Switzerland.deaths,
    deaths_gbr = UnitedKingdom.deaths,
    deaths_bel = Belgium.deaths,
    deaths_swe = Sweden.deaths,
    deaths_dnk = Denmark.deaths,
    deaths_hun = Hungary.deaths, 
    deaths_bhr = Bahrain.deaths,
    deaths_sdn = Sudan.deaths,
    deaths_ecu = Ecuador.deaths,
    deaths_gtm = Guatemala.deaths,
    deaths_cym = CaymanIslands.deaths,
    deaths_nld = Netherlands.deaths,
    deaths_smr = SanMarino.deaths,
    deaths_arg = Argentina.deaths,
    deaths_egy = Egypt.deaths,
    deaths_deu = Germany.deaths,
    deaths_idn = Indonesia.deaths,
    deaths_lbn = Lebanon.deaths,
    deaths_mar = Morocco.deaths,
    deaths_pan = Panama.deaths,
    deaths_can = Canada.deaths,
    deaths_dza = Algeria.deaths,
    deaths_bgr = Bulgaria.deaths,
    deaths_irl = Ireland.deaths,
    deaths_grc = Greece.deaths,
    deaths_aut = Austria.deaths, 
    deaths_pol = Poland.deaths,
    deaths_ind = India.deaths,
    deaths_guy = Guyana.deaths,
    deaths_nor = Norway.deaths,
    deaths_lux = Luxembourg.deaths,
    deaths_alb = Albania.deaths,
    deaths_ukr = Ukraine.deaths,
    deaths_mys = Malaysia.deaths,
    deaths_prt = Portugal.deaths,
    deaths_svn = Slovenia.deaths,
    deaths_tur = Turkey.deaths,
    deaths_bra = Brazil.deaths,
    deaths_cub = Cuba.deaths,
    deaths_bgd = Bangladesh.deaths,
    deaths_pak = Pakistan.deaths, 
    deaths_mex = Mexico.deaths,
    deaths_cri = CostaRica.deaths,
    deaths_jam = Jamaica.deaths,
    deaths_isr = Israel.deaths,
    deaths_isl = Iceland.deaths,
    deaths_srb = Serbia.deaths,
    deaths_hrv = Croatia.deaths,
    deaths_ltu = Lithuania.deaths,
    deaths_mda = RepublicofMoldova.deaths,
    deaths_tun = Tunisia.deaths,
    deaths_per = Peru.deaths,
    deaths_dom = DominicanRepublic.deaths,
    deaths_sgp = Singapore.deaths,
    deaths_fin = Finland.deaths,
    deaths_bih = BosniaHerzegovina.deaths,
    deaths_are = UnitedArabEmirates.deaths,
    deaths_chl = Chile.deaths,
    deaths_pry = Paraguay.deaths,
    deaths_pri = PuertoRico.deaths,
    deaths_cuw = Curacao.deaths,
    deaths_cod = DemocraticRepublicoftheCongo.deaths,
    deaths_gum = Guam.deaths,
    deaths_cze = Czechia.deaths,
    deaths_rou = Romania.deaths,
    deaths_mkd = NorthMacedonia.deaths,
    deaths_kosovo = Kosovo.deaths,
    deaths_and = Andorra.deaths,
    deaths_col = Colombia.deaths,
    deaths_zwe = Zimbabwe.deaths,
    deaths_gha = Ghana.deaths,
    deaths_cyp = Cyprus.deaths,
    deaths_sau = SaudiArabia.deaths,
    deaths_cmr = Cameroon.deaths,
    deaths_mus = Mauritius.deaths,
    deaths_mne = Montenegro.deaths,
    deaths_rus = RussianFederation.deaths,
    deaths_est = Estonia.deaths,
    deaths_tto = TrinidadandTobago.deaths,
    deaths_mtq = Martinique.deaths,
    deaths_nga = Nigeria.deaths,
    deaths_arm = Armenia.deaths,
    deaths_ken = Kenya.deaths,
    deaths_ner = Niger.deaths,
    deaths_bfa = BurkinaFaso.deaths,
    deaths_gab = Gabon.deaths,
    deaths_hnd = Honduras.deaths,
    deaths_afg = Afghanistan.deaths,
    deaths_pse = OccupiedPalestinianTerritory.deaths,
    deaths_aze = Azerbaijan.deaths, 
    deaths_brn = BruneiDarussalam.deaths,
    deaths_kaz = Kazakhstan.deaths,
    deaths_uzb = Uzbekistan.deaths,
    deaths_jey = Jersey.deaths,
    deaths_jor = Jordan.deaths,
    deaths_glp = Guadeloupe.deaths, 
    deaths_nic = Nicaragua.deaths,
    deaths_cpv = CaboVerde.deaths,
    deaths_gmb = Gambia.deaths,
    deaths_zaf = SouthAfrica.deaths,
    deaths_nzl = NewZealand.deaths,
    deaths_qat = Qatar.deaths,
    deaths_lka = SriLanka.deaths,
    deaths_syr = SyrianArabRepublic.deaths,
    deaths_tgo = Togo.deaths,
    deaths_bol = Bolivia.deaths,
    deaths_maf = SaintMartin.deaths,
    deaths_ggy = Guernsey.deaths,
    deaths_mmr = Myanmar.deaths,
    deaths_omn = Oman.deaths,
    deaths_ury = Uruguay.deaths,
    deaths_ago = Angola.deaths,
    deaths_tza = UnitedRepublicofTanzania.deaths,
    deaths_blr = Belarus.deaths,
    deaths_slv = ElSalvador.deaths,
    deaths_sen = Senegal.deaths,
    deaths_cog = Congo.deaths,
    deaths_bwa = Botswana.deaths,
    deaths_myt = Mayotte.deaths,
    deaths_mnp = NorthernMarianaIslands.deaths,
    deaths_imn = IsleofMan.deaths,
    deaths_kgz = Kyrgyzstan.deaths,
    deaths_lby = Libya.deaths,
    deaths_sxm = SintMaarten.deaths,
    deaths_bhm = Bahamas.deaths,
    deaths_mli = Mali.deaths,
    deaths_zmb = Zambia.deaths,
    deaths_civ = CotedIvoire.deaths,
    deaths_lva = Latvia.deaths,
    deaths_gib = Gibraltar.deaths,
    deaths_mrt = Mauritania.deaths,
    deaths_lie = Liechtenstein.deaths,
    deaths_geo = Georgia.deaths,
    deaths_kwt = Kuwait.deaths,
    deaths_lbr = Liberia.deaths,
    deaths_tca = TurksandCaicos.deaths,
    deaths_eth = Ethiopia.deaths,
    deaths_svk = Slovakia.deaths,
    deaths_vir = UnitedStatesVirginIslands.deaths,
    deaths_sur = Suriname.deaths,
    deaths_brb = Barbados.deaths,
    deaths_hti = Haiti.deaths,
    deaths_blz = Belize.deaths,
    deaths_ben = Benin.deaths, 
    deaths_bmu = Bermuda.deaths,
    deaths_mwi = Malawi.deaths,
    deaths_mlt = Malta.deaths,
    deaths_som = Somalia.deaths,
    deaths_atg = AntiguaandBarbuda.deaths,
    deaths_dji = Djibouti.deaths,
    deaths_mco = Monaco.deaths,
    deaths_swz = Eswatini.deaths,
    deaths_gin = Guinea.deaths,
    deaths_vgb = BritishVirginIslands.deaths,
    deaths_guf = FrenchGuiana.deaths,
    deaths_bdi = Burundi.deaths,

    deaths_region_westernpacific = Region.WesternPacific.deaths,
    deaths_region_european = Region.European.deaths,
    deaths_region_southeastasia = Region.SouthEastAsia.deaths,
    deaths_region_easternmediterranean = Region.EasternMediterranean.deaths,
    deaths_region_americas = Region.Americas.deaths,
    deaths_region_african = Region.African.deaths,

    deaths_internationalconveyance = InternationalConveyance.deaths,

    critical_chn = China.critical,
    clinical_chn_hubei = Hubei.clinicaldx,
    cases_outside_chn = Cases.nonChina,
    countries_outside_chn = Countries.nonChina,
    deaths_outside_chn = Deaths.nonChina,
    cases_outside_chn_wuhan_travel_history = Cases.nonChina.WuhanTravel,
    cases_outside_chn_chn_travel_history = Cases.nonChina.ChinaTravel,

    risk_chn = RA.China,
    risk_regional = RA.Regional,
    risk_global = RA.Global,

    cases_health_care_workers = HealthCareWorkers,
    cases_chn_wuhan = China.WuhanCity,

    cases_chn_hubei = China.Hubei,
    cases_chn_guangdong = China.Guangdong,
    cases_chn_beijing = China.Beijing,
    cases_chn_shanghai = China.Shanghai,
    cases_chn_chongqing = China.Chongqing,
    cases_chn_zhejiang = China.Zhejiang,
    cases_chn_jiangxi = China.Jiangxi,
    cases_chn_sichuan = China.Sichuan,
    cases_chn_tianjin = China.Tianjin,
    cases_chn_henan = China.Henan,
    cases_chn_hunan = China.Hunan,
    cases_chn_shandong = China.Shandong,
    cases_chn_yunnan = China.Yunnan,
    cases_chn_taiwan = China.Taiwan,
    cases_chn_taipei = China.Taipei,
    cases_chn_hkg = China.HongKongSAR,
    cases_chn_mac = China.Macao,
    cases_chn_unspecified = China.Unspecified,
    cases_chn_anhui = China.Anhui,
    cases_chn_jiangsu = China.Jiangsu,
    cases_chn_fujian = China.Fujian,
    cases_chn_shaanxi = China.Shaanxi,
    cases_chn_guangxi = China.Guangxi,
    cases_chn_hebei = China.Hebei,
    cases_chn_heilongjiang = China.Heilongjiang,
    cases_chn_liaoning = China.Liaoning,
    cases_chn_hainan = China.Hainan,
    cases_chn_shanxi = China.Shanxi,
    cases_chn_gansu = China.Gansu,
    cases_chn_guizhou = China.Guizhou,
    cases_chn_ningxia = China.Ningxia,
    cases_chn_mng = China.InnerMongolia,
    cases_chn_xinjiang = China.Xinjiang,
    cases_chn_jilin = China.Jilin,
    cases_chn_qinghai = China.Qinghai,
    cases_chn_xizang = China.Xizang,

    deaths_chn_hubei = China.Hubei.deaths,
    deaths_chn_guangdong = China.Guangdong.deaths,
    deaths_chn_beijing = China.Beijing.deaths,
    deaths_chn_shanghai = China.Shanghai.deaths,
    deaths_chn_chongqing = China.Chongqing.deaths,
    deaths_chn_zhejiang = China.Zhejiang.deaths,
    deaths_chn_jiangxi = China.Jiangxi.deaths,
    deaths_chn_sichuan = China.Sichuan.deaths,
    deaths_chn_tianjin = China.Tianjin.deaths,
    deaths_chn_henan = China.Henan.deaths,
    deaths_chn_hunan = China.Hunan.deaths,
    deaths_chn_shandong = China.Shandong.deaths,
    deaths_chn_yunnan = China.Yunnan.deaths,
    deaths_chn_taipei = China.Taipei.deaths,
    deaths_chn_hkg = China.HongKongSAR.deaths,
    deaths_chn_mac = China.Macao.deaths,
    deaths_chn_anhui = China.Anhui.deaths,
    deaths_chn_jiangsu = China.Jiangsu.deaths,
    deaths_chn_fujian = China.Fujian.deaths,
    deaths_chn_shaanxi = China.Shaanxi.deaths,
    deaths_chn_guangxi = China.Guangxi.deaths,
    deaths_chn_hebei = China.Hebei.deaths,
    deaths_chn_heilongjiang = China.Heilongjiang.deaths,
    deaths_chn_liaoning = China.Liaoning.deaths,
    deaths_chn_hainan = China.Hainan.deaths,
    deaths_chn_shanxi = China.Shanxi.deaths,
    deaths_chn_gansu = China.Gansu.deaths,
    deaths_chn_guizhou = China.Guizhou.deaths,
    deaths_chn_ningxia = China.Ningxia.deaths,
    deaths_chn_mng = China.InnerMongolia.deaths,
    deaths_chn_xinjiang = China.Xinjiang.deaths,
    deaths_chn_jilin = China.Jilin.deaths,
    deaths_chn_qinghai = China.Qinghai.deaths,
    deaths_chn_xizang = China.Xizang.deaths
  )

usethis::use_data(sarscov2_who_2019, overwrite = TRUE)

# Once the data in the CSV is updated, run the above code, update the package 
# version, followed by:

devtools::document()
devtools::build_vignettes()
devtools::check()

save(sarscov2_who_2019, file = "sarscov2_who_2019.RData", version = 2)