code for EU model running

desktop.ini

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+[LocalizedFileNames]
+preprocess_data_EU_old.R=@preprocess_data_EU_old.R,0

eu_model_init.R

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+
+
+runSimbinder = function(glhflows_input){
+  #3 times steps per day (8 hours), 40% chance of moving per time step
+  HPop_out =  runSim(HPop,pat_locator,glhflows_input,glhflows_input,movement_data, input_dates,recover_df, exposerate,exposepd,exposed_pop_inf_prop = 0, TSinday = 3,prob_move_per_TS=.4)
+  HPop_out
+}
+
+source("bearmod_fx_dev_EU_version.R")
+source("preprocess_data_EU.R")
+#Initial parameters
+NPat = length(patNames)
+patnInf = rep(0,NPat)
+patnExp = c(rep(0,NPat) )
+
+pat_locator$country = substr(pat_locator$patNames,1,2)
+
+r0vals = read.csv("pop_data_NPI_startDate_v2.csv")
+
+recprob = 1/4
+recrate = 1-exp(-1/4) #daily probability of recovery
+exposerate = 1 # This is set to 1 because we will set exposure rates on a NUTS3-level basis (ie. accounting for country-level heterogeneity in R0)
+
+pat_locator$ISO3 = countrycode(pat_locator$country,origin="eurostat",destination="iso3c")
+pat_locator$r0 = 0
+#define country-level R0
+for (i in 1:dim(pat_locator)[1]){
+  pat_locator$r0[i] = subset(r0vals,iso3c ==pat_locator$ISO3[i])$R0.ML
+}
+
+#read in cases on March 20 across Europe
+patinfdata = read.csv("nuts3_cases_320.csv",stringsAsFactors=F)
+
+#define cases based on cases on march 20 across all NUTS3 areas
+for (i in 1:length(patNames)){
+  patnInf[which(patinfdata$NUTS_ID == patNames[i])] = patinfdata$nuts3_cases[i]
+}
+library(viridis)
+
+
+#Repeat mobility data to add 6 months to the end of the  Google NUTS3 dataset
+movement_data$weekyr = paste("1",movement_data$V2+1,movement_data$V1,sep="-")
+movement_data=subset(movement_data,V2<52)
+movement_data$dateorig = as.Date(movement_data$weekyr,format="%w-%W-%Y")
+movement_data$date = movement_data$dateorig  + months(2)
+
+movement_data_add = subset(movement_data,date>"2019-03-08")
+movement_data_add$date = movement_data_add$date + months(3)
+movement_data = rbind(movement_data,movement_data_add)
+movement_data_add$date = movement_data_add$date + months(3)
+movement_data = rbind(movement_data,movement_data_add)
+#Because the Google NUTS3 dataset is from 2019, we will add one year to simulate 2020
+movement_data$date = movement_data$date + years(1)
+
+start_date = as.Date("2020-03-20")
+movement_data = subset(movement_data,date>(start_date - weeks(1)))
+end_date = as.Date("2020-03-20") + weeks(30)
+movement_data = subset(movement_data,date < end_date)
+input_dates=seq(start_date,end_date,by="days")
+recover_df = data.frame(date = input_dates,recrate = recprob)
+
+#This dataset records the relative movement in a given week, compared to a baseline, for 2020 (Recording reductions in movement due to COVID-19)
+glhflows = read.csv("glh flow data_NUTS3_EU.csv",stringsAsFactors=F)
+glhflows = glhflows[c("NUTS3fr","t1","change")]
+glhflows_fillin = expand.grid(NUTS3fr = pat_locator$patNames[!is.element(pat_locator$patNames,glhflows$NUTS3fr)], t1 = unique(glhflows$t1) )
+glhflows_fillin$change = 0 
+#for areas that did not have a reduction recorded, we used the mean value observed across all NUTS3 areas
+#note: t1 represents the first day of a given week -- ie. "01/03/2020" means the movement observed from March 1 to March 7
+for (date in levels(glhflows_fillin$t1)){
+  print(date)
+  glhflows_fillin$change[glhflows_fillin$t1 == date] = mean(glhflows$change[glhflows$t1 == date])
+}
+
+glhflows_all = rbind(glhflows,glhflows_fillin)
+glhflows_all = merge(glhflows_all,pat_locator[c("patNames","r0","country")],by.x="NUTS3fr",by.y="patNames")
+glhflows_all$change[is.na(glhflows_all$change)] = mean(subset(glhflows_all,t1 == "08/03/2020")$r0,na.rm=T)
+#new NUTS3-specific contact rate calculated by also accounting for locak R value
+glhflows_all$relative_contact = glhflows_all$change * glhflows_all$r0 * recrate 
+glhflows_all$relative_move = glhflows_all$change
+glhflows_all$date = dmy(glhflows_all$t1)
+#NUTS3 areas with no lockdown inherited the movement patterns from March 1
+glhflows_nolockdown = subset(glhflows_all,t1=="01/03/2020")
+
+
+
+glhflows_lockdown = subset(glhflows_all,t1=="22/03/2020")
+#We extended the lockdown effect one further week into April, to account for additional community uptake of lockdown
+glhflows_lockdown_extra = subset(glhflows_all,t1=="22/03/2020")
+glhflows_lockdown_extra$change =glhflows_lockdown_extra$change *.75
+#Both contact rates and movement reduced based on reductions in movement observed in the Google COVID-19 dataset
+glhflows_lockdown_extra$relative_contact = glhflows_lockdown_extra$change * glhflows_lockdown_extra$r0 * recrate 
+glhflows_lockdown_extra$relative_move = glhflows_lockdown_extra$change 
+

iso2_csv.csv

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+Name,Code
+Afghanistan,AF
+Åland Islands,AX
+Albania,AL
+Algeria,DZ
+American Samoa,AS
+Andorra,AD
+Angola,AO
+Anguilla,AI
+Antarctica,AQ
+Antigua and Barbuda,AG
+Argentina,AR
+Armenia,AM
+Aruba,AW
+Australia,AU
+Austria,AT
+Azerbaijan,AZ
+Bahamas,BS
+Bahrain,BH
+Bangladesh,BD
+Barbados,BB
+Belarus,BY
+Belgium,BE
+Belize,BZ
+Benin,BJ
+Bermuda,BM
+Bhutan,BT
+"Bolivia, Plurinational State of",BO
+"Bonaire, Sint Eustatius and Saba",BQ
+Bosnia and Herzegovina,BA
+Botswana,BW
+Bouvet Island,BV
+Brazil,BR
+British Indian Ocean Territory,IO
+Brunei Darussalam,BN
+Bulgaria,BG
+Burkina Faso,BF
+Burundi,BI
+Cambodia,KH
+Cameroon,CM
+Canada,CA
+Cape Verde,CV
+Cayman Islands,KY
+Central African Republic,CF
+Chad,TD
+Chile,CL
+China,CN
+Christmas Island,CX
+Cocos (Keeling) Islands,CC
+Colombia,CO
+Comoros,KM
+Congo,CG
+"Congo, the Democratic Republic of the",CD
+Cook Islands,CK
+Costa Rica,CR
+Côte d'Ivoire,CI
+Croatia,HR
+Cuba,CU
+Curaçao,CW
+Cyprus,CY
+Czech Republic,CZ
+Denmark,DK
+Djibouti,DJ
+Dominica,DM
+Dominican Republic,DO
+Ecuador,EC
+Egypt,EG
+El Salvador,SV
+Equatorial Guinea,GQ
+Eritrea,ER
+Estonia,EE
+Ethiopia,ET
+Falkland Islands (Malvinas),FK
+Faroe Islands,FO
+Fiji,FJ
+Finland,FI
+France,FR
+French Guiana,GF
+French Polynesia,PF
+French Southern Territories,TF
+Gabon,GA
+Gambia,GM
+Georgia,GE
+Germany,DE
+Ghana,GH
+Gibraltar,GI
+Greece,GR
+Greenland,GL
+Grenada,GD
+Guadeloupe,GP
+Guam,GU
+Guatemala,GT
+Guernsey,GG
+Guinea,GN
+Guinea-Bissau,GW
+Guyana,GY
+Haiti,HT
+Heard Island and McDonald Islands,HM
+Holy See (Vatican City State),VA
+Honduras,HN
+Hong Kong,HK
+Hungary,HU
+Iceland,IS
+India,IN
+Indonesia,ID
+"Iran, Islamic Republic of",IR
+Iraq,IQ
+Ireland,IE
+Isle of Man,IM
+Israel,IL
+Italy,IT
+Jamaica,JM
+Japan,JP
+Jersey,JE
+Jordan,JO
+Kazakhstan,KZ
+Kenya,KE
+Kiribati,KI
+"Korea, Democratic People's Republic of",KP
+"Korea, Republic of",KR
+Kuwait,KW
+Kyrgyzstan,KG
+Lao People's Democratic Republic,LA
+Latvia,LV
+Lebanon,LB
+Lesotho,LS
+Liberia,LR
+Libya,LY
+Liechtenstein,LI
+Lithuania,LT
+Luxembourg,LU
+Macao,MO
+"Macedonia, the Former Yugoslav Republic of",MK
+Madagascar,MG
+Malawi,MW
+Malaysia,MY
+Maldives,MV
+Mali,ML
+Malta,MT
+Marshall Islands,MH
+Martinique,MQ
+Mauritania,MR
+Mauritius,MU
+Mayotte,YT
+Mexico,MX
+"Micronesia, Federated States of",FM
+"Moldova, Republic of",MD
+Monaco,MC
+Mongolia,MN
+Montenegro,ME
+Montserrat,MS
+Morocco,MA
+Mozambique,MZ
+Myanmar,MM
+Namibia,NA
+Nauru,NR
+Nepal,NP
+Netherlands,NL
+New Caledonia,NC
+New Zealand,NZ
+Nicaragua,NI
+Niger,NE
+Nigeria,NG
+Niue,NU
+Norfolk Island,NF
+Northern Mariana Islands,MP
+Norway,NO
+Oman,OM
+Pakistan,PK
+Palau,PW
+"Palestine, State of",PS
+Panama,PA
+Papua New Guinea,PG
+Paraguay,PY
+Peru,PE
+Philippines,PH
+Pitcairn,PN
+Poland,PL
+Portugal,PT
+Puerto Rico,PR
+Qatar,QA
+Réunion,RE
+Romania,RO
+Russian Federation,RU
+Rwanda,RW
+Saint Barthélemy,BL
+"Saint Helena, Ascension and Tristan da Cunha",SH
+Saint Kitts and Nevis,KN
+Saint Lucia,LC
+Saint Martin (French part),MF
+Saint Pierre and Miquelon,PM
+Saint Vincent and the Grenadines,VC
+Samoa,WS
+San Marino,SM
+Sao Tome and Principe,ST
+Saudi Arabia,SA
+Senegal,SN
+Serbia,RS
+Seychelles,SC
+Sierra Leone,SL
+Singapore,SG
+Sint Maarten (Dutch part),SX
+Slovakia,SK
+Slovenia,SI
+Solomon Islands,SB
+Somalia,SO
+South Africa,ZA
+South Georgia and the South Sandwich Islands,GS
+South Sudan,SS
+Spain,ES
+Sri Lanka,LK
+Sudan,SD
+Suriname,SR
+Svalbard and Jan Mayen,SJ
+Swaziland,SZ
+Sweden,SE
+Switzerland,CH
+Syrian Arab Republic,SY
+"Taiwan, Province of China",TW
+Tajikistan,TJ
+"Tanzania, United Republic of",TZ
+Thailand,TH
+Timor-Leste,TL
+Togo,TG
+Tokelau,TK
+Tonga,TO
+Trinidad and Tobago,TT
+Tunisia,TN
+Turkey,TR
+Turkmenistan,TM
+Turks and Caicos Islands,TC
+Tuvalu,TV
+Uganda,UG
+Ukraine,UA
+United Arab Emirates,AE
+United Kingdom,GB
+United States,US
+United States Minor Outlying Islands,UM
+Uruguay,UY
+Uzbekistan,UZ
+Vanuatu,VU
+"Venezuela, Bolivarian Republic of",VE
+Viet Nam,VN
+"Virgin Islands, British",VG
+"Virgin Islands, U.S.",VI
+Wallis and Futuna,WF
+Western Sahara,EH
+Yemen,YE
+Zambia,ZM
+Zimbabwe,ZW