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00_data_2.R
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### Forecasting the geographic spread of Ebola Virus Disease in the Democratic Republic of the Congo during the 2018-2020 outbreak
### Alicia Rosello
### Expert elicitation results 2 - data input December 2019
## PREP
# packages
require(dplyr)
# paths
files<-"Outputs/"
plots<-"Plots/"
# bins
low_bins<-seq(from=0,to=48,by=2)
high_bins<-seq(from=2, to=50, by=2)
# ----------------------------------------------------------------
# forecast December 2019
HZ_considered<-c("MANDIMA", "MAMBASA", "BENI", "MABALAKO","KALUNGUTA", "GOMA")
# period considered
time_period<-"December 2019"
time_period_FR<-"Décembre 2019"
# number of responses
n_responses<-10
# response exp1 11-11-2019
chips_1<-c("4","4","4","4","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("4","4","4","4","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("10","4","3","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("4","4","4","4","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("10","4","3","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("18","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp1_KOMANDA<-c("4","4","4","4","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp1_OICHA<-c("4","4","4","4","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("11-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("1",length(HZ_considered)),
institution=rep("LSHTM",length(HZ_considered)),
last.in.field=rep("<2 weeks ago",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
# response exp2 12-11-2019
chips_1<-c("1","4","9","4","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("6","9","4","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("1","3","8","4","2","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("1","2","7","4","3","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("3","9","5","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("8","5","4","1","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp2_OICHA<-c("12","5","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp2_KOMANDA<-c("8","8","2","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("12-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("2",length(HZ_considered)),
institution=rep("WHO",length(HZ_considered)),
last.in.field=rep("<2 weeks ago",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp3 15-11-2019
chips_1<-c("6","6","4","3","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("7","6","6","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("5","5","5","4","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("3","6","4","5","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("10","10","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp3_LOLWA<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp3_OICHA<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp3_KOMANDA<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("15-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("3",length(HZ_considered)),
institution=rep("WHO",length(HZ_considered)),
last.in.field=rep(">2 weeks ago",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp4 15-11-2019
chips_1<-c("0","0","0","0","0","0","3","3","5","4","3","2","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("0","1","3","4","4","3","2","1","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("0","0","0","1","1","4","4","4","2","2","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("0","0","0","0","0","1","3","5","5","4","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("0","1","4","6","3","2","1","1","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("10","4","0","0","2","2","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp4_OICHA<-c("11","6","3","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp4_BUTEMBO<-c("11","9","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp4_KATWA<-c("10","10","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp4_MAKISO_KISANGANI<-c("10","7","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("15-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("4",length(HZ_considered)),
institution=rep("WHO",length(HZ_considered)),
last.in.field=rep("never",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp5 15-11-2019
chips_1<-c("14","6","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("16","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("0","3","11","6","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("0","0","0","2","7","8","3","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("18","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp5_OICHA<-c("19","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("15-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("5",length(HZ_considered)),
institution=rep("WHO",length(HZ_considered)),
last.in.field=rep("<2 weeks ago",length(HZ_considered)),
experience.ide=rep("<5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp6 20-11-2019
chips_1<-c("10","7","3","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("14","4","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("14","6","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("8","11","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("20-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("6",length(HZ_considered)),
institution=rep("MoH",length(HZ_considered)),
last.in.field=rep("<2 weeks ago",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp7 22-11-2019)
chips_1<-c("5","4","4","3","2","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("8","6","4","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("6","4","2","1","1","1","1","1","1","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("10","7","3","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("11","7","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("22-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("7",length(HZ_considered)),
institution=rep("LSHTM",length(HZ_considered)),
last.in.field=rep("<2 weeks ago",length(HZ_considered)),
experience.ide=rep("<5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp8 C22-11-2019)
chips_1<-c("2","4","6","3","2","1","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("7","4","3","2","1","1","1","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("0","0","1","2","3","3","3","3","3","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("0","0","0","0","0","0","1","1","1","2","3","4","3","2","1","1","1","0","0","0","0","0","0","0","0")
chips_5<-c("4","5","5","4","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("11","6","2","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp8_BUTEMBO<-c("10","10","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp8_KATWA<-c("10","10","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("22-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("8",length(HZ_considered)),
institution=rep("MSF",length(HZ_considered)),
last.in.field=rep(">2 weeks ago",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp9 22-11-2019)
chips_1<-c("9","8","3","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("10","8","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("10","8","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("8","8","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("20","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp9_KOMANDA<-c("14","6","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp9_OICHA<-c("8","8","4","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("22-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("9",length(HZ_considered)),
institution=rep("MSF",length(HZ_considered)),
last.in.field=rep(">2 weeks ago",length(HZ_considered)),
experience.ide=rep(">5 years",length(HZ_considered)))
df<-rbind(df, df1)
# response exp10 14-11-2019)
chips_1<-c("5","0","0","0","3","3","0","9","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_2<-c("10","2","2","0","0","6","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_3<-c("0","0","0","0","0","0","0","0","0","2","3","4","5","6","0","0","0","0","0","0","0","0","0","0","0")
chips_4<-c("0","0","0","0","0","0","0","0","0","2","3","4","5","6","0","0","0","0","0","0","0","0","0","0","0")
chips_5<-c("10","7","3","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_6<-c("14","6","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp10_OICHA<-c("10","10","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp10_KOMANDA<-c("11","9","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
chips_exp10_NYANKUNDE<-c("13","7","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0")
df1<-data.frame(HZ=rep(HZ_considered, each=length(chips_1)),
low_bin=rep(low_bins, length(HZ_considered)),
high_bin=rep(high_bins, length(HZ_considered)),
date=rep("14-11-2019", times=length(HZ_considered)),
chips=c(chips_1, chips_2, chips_3, chips_4, chips_5, chips_6),
expert=rep("10",length(HZ_considered)),
institution=rep("WHO",length(HZ_considered)),
last.in.field=rep("<2 weeks ago",length(HZ_considered)),
experience.ide=rep("<5 years",length(HZ_considered)))
df<-rbind(df, df1)
## aggregate results
df$chips<-as.numeric(as.character(df$chips))
# probabilities
df$p<-df$chips/20
# how many chips per HZ placed?
df%>%group_by(HZ)%>%summarise(sum.chips=sum(chips))
# total chips all experts
all.experts<-df%>%group_by(HZ,low_bin)%>%summarise(chips.all.experts=sum(chips))
# probabilities per HZ
all.experts$p.all.experts<-all.experts$chips.all.experts/(n_responses*20)
# merge
df<-merge(df, all.experts, by=c("HZ","low_bin"))
# add expert and date into one col
df$expert.date<-paste("expert",df$expert, df$date)
# output
write.csv(df, file=paste0(files, "results_", gsub(" ", "_", time_period), ".csv"))
# factor level for experts
df$expert.date<-as.factor(df$expert.date)
df$expert.date = factor(df$expert.date,levels(df$expert.date)[c(1,3:10,2)])
## add expert info on all other health zones
df_additional_HZ_OICHA<-data.frame(HZ="OICHA",
low_bin=rep(low_bins,7),
high_bin=rep(high_bins,7),
chips=c(chips_exp1_OICHA,chips_exp2_OICHA,chips_exp3_OICHA,
chips_exp4_OICHA, chips_exp5_OICHA, chips_exp9_OICHA,
chips_exp10_OICHA),
expert=c(rep("1", length(chips_exp1_OICHA)),
rep("2", length(chips_exp1_OICHA)),
rep("3", length(chips_exp1_OICHA)),
rep("4", length(chips_exp1_OICHA)),
rep("5", length(chips_exp1_OICHA)),
rep("9", length(chips_exp1_OICHA)),
rep("10", length(chips_exp1_OICHA))))
df_additional_HZ_KOMANDA<-data.frame(HZ="KOMANDA",
low_bin=rep(low_bins,5),
high_bin=rep(high_bins,5),
chips=c(chips_exp1_KOMANDA,chips_exp2_KOMANDA,chips_exp3_KOMANDA,
chips_exp9_KOMANDA,chips_exp10_KOMANDA),
expert=c(rep("1", length(chips_exp1_OICHA)),
rep("2", length(chips_exp1_OICHA)),
rep("3", length(chips_exp1_OICHA)),
rep("9", length(chips_exp1_OICHA)),
rep("10", length(chips_exp1_OICHA))))
df_additional_HZ_BUTEMBO<-data.frame(HZ="BUTEMBO",
low_bin=rep(low_bins,2),
high_bin=rep(high_bins,2),
chips=c(chips_exp4_BUTEMBO, chips_exp8_BUTEMBO),
expert=c(rep("4", length(chips_exp4_BUTEMBO)),
rep("8", length(chips_exp8_BUTEMBO))))
df_additional_HZ_KATWA<-data.frame(HZ="KATWA",
low_bin=rep(low_bins,2),
high_bin=rep(high_bins,2),
chips=c(chips_exp4_KATWA, chips_exp8_KATWA),
expert=c(rep("4", length(chips_exp4_KATWA)),
rep("8", length(chips_exp8_KATWA))))
df_additional_HZ_LOLWA<-data.frame(HZ="LOLWA",
low_bin=rep(low_bins,1),
high_bin=rep(high_bins,1),
chips=c(chips_exp3_LOLWA),
expert=c(rep("3", length(chips_exp3_LOLWA))))
df_additional_HZ_MAKISO_KISANGANI<-data.frame(HZ="MAKISO_KISANGANI",
low_bin=rep(low_bins,1),
high_bin=rep(high_bins,1),
chips=c(chips_exp4_MAKISO_KISANGANI),
expert=c(rep("4", length(chips_exp4_MAKISO_KISANGANI))))
df_additional_HZ_NYANKUNDE<-data.frame(HZ="NYANKUNDE",
low_bin=rep(low_bins,1),
high_bin=rep(high_bins,1),
chips=c(chips_exp10_NYANKUNDE),
expert=c(rep("10", length(chips_exp10_NYANKUNDE))))
df_additional_HZ<-rbind(df_additional_HZ_OICHA,
df_additional_HZ_KOMANDA,
df_additional_HZ_BUTEMBO,
df_additional_HZ_KATWA,
df_additional_HZ_LOLWA,
df_additional_HZ_MAKISO_KISANGANI,
df_additional_HZ_NYANKUNDE)
df_additional_HZ$chips<-as.numeric(as.character(df_additional_HZ$chips))
df_additional_HZ$p<-df_additional_HZ$chips/20
experts<-df%>%group_by(expert,date, institution, last.in.field, experience.ide, expert.date)%>%summarise(n=n())%>%select(-n)
df_additional_HZ<-merge(df_additional_HZ, experts, by="expert")
# save dataset extra HZ
write.csv(df_additional_HZ, file=paste0(files, "results_", gsub(" ", "_", time_period), "_additional_HZ.csv"))
# # total chips all experts
# all.experts<-df_additional_HZ%>%group_by(HZ,low_bin)%>%summarise(chips.all.experts=sum(chips))
# # probabilities per HZ all experts
# all.experts_OICHA<-all.experts%>%filter(HZ=="OICHA")
# all.experts_OICHA$p.all.experts<-all.experts_OICHA$chips.all.experts/(20*length(unique(df_additional_HZ_OICHA$expert)))
# all.experts_KOMANDA<-all.experts%>%filter(HZ=="KOMANDA")
# all.experts_KOMANDA$p.all.experts<-all.experts_KOMANDA$chips.all.experts/(20*length(unique(df_additional_HZ_KOMANDA$expert)))
# all.experts<-rbind(all.experts_OICHA, all.experts_KOMANDA)
# # merge
# df_additional_HZ<-merge(df_additional_HZ, all.experts, by=c("HZ","low_bin"))
# # same order of rows as df
# df_additional_HZ<-df_additional_HZ[,names(df)]
#
# # bind OICHA and KOMANDA with other dataset
# df_all<-rbind(df, df_additional_HZ)
#
# # save dataset all
# write.csv(df, file=paste0(files, "results_", gsub(" ", "_", time_period), "_with_additional_HZ_3ormore_experts.csv"))