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SARS-CoV-2.R
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organism<-"SARS-CoV-2"
source("Parameters and distributions.R")
#Matrix -------------------------------------------------
numevents<-8
eventsname<-c("Hamper to washer","Hand to face touch #1", "between face touch and end of washing cycle",
"Washer to dryer","Hand to face touch #2","Dry cycle","Dryer to folding area",
"Hand to face touch #3")
Conc.h<-matrix(nrow=numevents,ncol=iterations)
rownames(Conc.h)<-eventsname
Conc.l<-matrix(nrow=numevents, ncol=iterations)
rownames(Conc.l)<-eventsname
Dose<-matrix(nrow=numevents, ncol=iterations)
rownames(Dose)<-eventsname
Risk<-matrix(nrow=numevents, ncol=iterations)
rownames(Risk)<-eventsname
##Baseline scenario -----------------------------------------------------------------
#Event 1. Loading dirty clothes from hamper to washer
Conc.h[1,]<-Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-Conc.onecloth*exp(-Inact.s*Contact.time.laundry))}
Conc.l[1,]<-Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-Conc.i.hand*exp(-Inact.h*Contact.time.laundry))}
Dose[1,]<-0
Risk[1,]<-0
#Event 2. Hand to face contact #1
Conc.h[2,]<-(1-TE.face*Frac.HF)*(Conc.h[1,]*exp(-Inact.h*Contact.time.face.w))
Conc.l[2,]<-Conc.l[1,]/10^(Reduc.wash*Contact.time.face.w/Dur.wash)
Dose[2,]<-Conc.h[1,]*exp(-Inact.h*Contact.time.face.w)*TE.face*Frac.HF*T.handarea
Risk[2,]<-1-exp(-2.46E-3*Dose[2,])
#Event 3. Washing Laundry
Conc.h[3,]<-Conc.h[2,]*exp(-Inact.h*(Dur.wash-Contact.time.face.w))
Conc.l[3,]<-Conc.l[2,]/10^(Reduc.wash*(Dur.wash-Contact.time.face.w)/Dur.wash)
Dose[3,]<-Dose[2,]
Risk[3,]<-Risk[2,]
#Event 4. Loading washed clothes to dryer
Conc.h[4,]<-Conc.h[3,]*exp(-Inact.h*Contact.time.laundry)-{TE.wet*Frac.HS*
(Conc.h[3,]*exp(-Inact.h*Contact.time.laundry)-Conc.l[3,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l[4,]<-Conc.l[3,]*exp(-Inact.s*Contact.time.laundry)-{TE.wet*Frac.HS*T.handarea/Surface.area.laundry*
(Conc.l[3,]*exp(-Inact.s*Contact.time.laundry)-Conc.h[3,]*exp(-Inact.h*Contact.time.laundry))}
Dose[4,]<-Dose[3,]
Risk[4,]<-Risk[3,]
#Event 5. Hand to face contact #2
Conc.h[5,]<-(1-TE.face*Frac.HF)*(Conc.h[4,]*exp(-Inact.h*Contact.time.face.d))
Conc.l[5,]<-Conc.l[4,]/10^(Reduc.dry*Contact.time.face.d/Dur.dry)
Dose[5,]<-Dose[4,]+(Conc.h[4,]*exp(-Inact.h*Contact.time.face.d)*TE.face*Frac.HF*T.handarea)
Risk[5,]<- 1-exp(-2.46E-3*Dose[5,])
#Event 6. Drying Laundry
Conc.h[6,]<-Conc.h[5,]*exp(-Inact.h*(Dur.dry-Contact.time.face.d))
Conc.l[6,]<-Conc.l[5,]/10^(Reduc.dry*(Dur.dry-Contact.time.face.d)/Dur.dry)
Dose[6,]<-Dose[5,]
Risk[6,]<-Risk[5,]
#Event 7. Dryer to folding area
Conc.h[7,]<-Conc.h[6,]*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*
(Conc.h[6,]*exp(-Inact.h*Contact.time.laundry)-Conc.l[6,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l[7,]<-Conc.l[6,]*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*
T.handarea/Surface.area.laundry*(Conc.l[6,]*exp(-Inact.s*Contact.time.laundry)-Conc.h[6,]
*(exp(-Inact.h*Contact.time.laundry)))}
Dose[7,]<-Dose[6,]
Risk[7,]<-Risk[6,]
#Event 8. Hand to face Contact #3
Conc.h[8,]<-(1-TE.face*Frac.HF)*(Conc.h[7,]*exp(-Inact.h*Contact.time.face.f))
Conc.l[8,]<-Conc.l[7,]*exp(-Inact.s*Contact.time.face.f)
Dose[8,]<-Dose[7,]+(Conc.h[7,]*exp(-Inact.h*Contact.time.face.f)*TE.face*Frac.HF*T.handarea)
Risk[8,]<- 1-exp(-2.46E-3*Dose[8,])
#plotting
library(ggplot2)
library(ggpubr)
Conc.h.dataframe<-as.data.frame(t(Conc.h))
Conc.l.dataframe<-as.data.frame(t(Conc.l))
Dose.dataframe<-as.data.frame(t(Dose))
Risk.dataframe<-as.data.frame(t(Risk))
event<-rep(c(rep(1,iterations),rep(2,iterations),rep(3,iterations),rep(4,iterations),rep(5,iterations),rep(6,iterations),rep(7,iterations),rep(8,iterations)),4)
type<-c(rep("Hand",8*iterations),rep("Laundry",8*iterations),rep("Dose",8*iterations),rep("Risk",8*iterations))
value<-c(Conc.h.dataframe$`Hamper to washer`, Conc.h.dataframe$`Hand to face touch #1`,
Conc.h.dataframe$`between face touch and end of washing cycle`,Conc.h.dataframe $`Washer to dryer`,
Conc.h.dataframe $`Hand to face touch #2`, Conc.h.dataframe $`Dry cycle`,
Conc.h.dataframe $`Dryer to folding area`,Conc.h.dataframe $`Hand to face touch #3`,
Conc.l.dataframe$`Hamper to washer`, Conc.l.dataframe$`Hand to face touch #1`,
Conc.l.dataframe$`between face touch and end of washing cycle`,Conc.l.dataframe $`Washer to dryer`,
Conc.l.dataframe $`Hand to face touch #2`,
Conc.l.dataframe $`Dry cycle`,Conc.l.dataframe $`Dryer to folding area`,
Conc.l.dataframe $`Hand to face touch #3`,
Dose.dataframe$`Hamper to washer`, Dose.dataframe$`Hand to face touch #1`,
Dose.dataframe$`between face touch and end of washing cycle`,Dose.dataframe $`Washer to dryer`,
Dose.dataframe $`Hand to face touch #2`, Dose.dataframe $`Dry cycle`,Dose.dataframe $`Dryer to folding area`,
Dose.dataframe $`Hand to face touch #3`,
Risk.dataframe$`Hamper to washer`, Risk.dataframe$`Hand to face touch #1`,
Risk.dataframe$`between face touch and end of washing cycle`,Risk.dataframe $`Washer to dryer`,
Risk.dataframe $`Hand to face touch #2`, Risk.dataframe $`Dry cycle`,Risk.dataframe $`Dryer to folding area`,
Risk.dataframe $`Hand to face touch #3`)
data<-data.frame(event,type,value)
windows()
ggplot(data)+geom_violin(aes(x=event,y=value,fill=type, group=event),alpha=0.3,draw_quantiles = c(0.25,0.5,0.75))+
facet_wrap(~type,scales="free") +
scale_y_continuous(trans="log10")
##Hand washing scenario 1----------------------------------------------------
#Matrix
numevents<-8
eventsname<-c("Hamper to washer","Hand to face touch #1", "between face touch and end of washing cycle",
"Washer to dryer","Hand to face touch #2","Dry cycle","Dryer to folding area",
"Hand to face touch #3")
Conc.h.1<-matrix(nrow=numevents,ncol=iterations)
rownames(Conc.h.1)<-eventsname
Conc.l.1<-matrix(nrow=numevents, ncol=iterations)
rownames(Conc.l.1)<-eventsname
Dose.1<-matrix(nrow=numevents, ncol=iterations)
rownames(Dose.1)<-eventsname
Risk.1<-matrix(nrow=numevents, ncol=iterations)
rownames(Risk.1)<-eventsname
#Event 1. Loading dirty clothes from hamper to washer
Conc.h.1[1,]<-Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-Conc.onecloth*exp(-Inact.s*Contact.time.laundry))}
Conc.l.1[1,]<-Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-Conc.i.hand*exp(-Inact.h*Contact.time.laundry))}
Dose.1[1,]<-0
Risk.1[1,]<-0
#Event 2. Hand washing + Hand to face contact #1
Conc.h.1[2,]<-(1-TE.face*Frac.HF)*{(Conc.h.1[1,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.w)}
Conc.l.1[2,]<-Conc.l.1[1,]/10^(Reduc.wash*Contact.time.face.w/Dur.wash)
Dose.1[2,]<-(Conc.h.1[1,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.w)*TE.face*Frac.HF*T.handarea
Risk.1[2,]<-1-exp(-2.46E-3*Dose.1[2,])
#Event 3. Washing Laundry
Conc.h.1[3,]<-Conc.h.1[2,]*exp(-Inact.h*(Dur.wash-Contact.time.face.w))
Conc.l.1[3,]<-Conc.l.1[2,]/10^(Reduc.wash*(Dur.wash-Contact.time.face.w)/Dur.wash)
Dose.1[3,]<-Dose.1[2,]
Risk.1[3,]<-Risk.1[2,]
#Event 4. Loading washed clothes to dryer
Conc.h.1[4,]<-Conc.h.1[3,]*exp(-Inact.h*Contact.time.laundry)-{TE.wet*Frac.HS*
(Conc.h.1[3,]*exp(-Inact.h*Contact.time.laundry)-Conc.l.1[3,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l.1[4,]<-Conc.l.1[3,]*exp(-Inact.s*Contact.time.laundry)-{TE.wet*Frac.HS*T.handarea/Surface.area.laundry*
(Conc.l.1[3,]*exp(-Inact.s*Contact.time.laundry)-Conc.h.1[3,]*exp(-Inact.h*Contact.time.laundry))}
Dose.1[4,]<-Dose.1[3,]
Risk.1[4,]<-Risk.1[3,]
#Event 5. Hand to face contact #2
Conc.h.1[5,]<-(1-TE.face*Frac.HF)*(Conc.h.1[4,]*exp(-Inact.h*Contact.time.face.d))
Conc.l.1[5,]<-Conc.l.1[4,]/10^(Reduc.dry*Contact.time.face.d/Dur.dry)
Dose.1[5,]<-Dose.1[4,]+(Conc.h.1[4,]*exp(-Inact.h*Contact.time.face.d)*TE.face*Frac.HF*T.handarea)
Risk.1[5,]<- 1-exp(-2.46E-3*Dose.1[5,])
#Event 6. Drying Laundry
Conc.h.1[6,]<-Conc.h.1[5,]*exp(-Inact.h*(Dur.dry-Contact.time.face.d))
Conc.l.1[6,]<-Conc.l.1[5,]/10^(Reduc.dry*(Dur.dry-Contact.time.face.d)/Dur.dry)
Dose.1[6,]<-Dose.1[5,]
Risk.1[6,]<-Risk.1[5,]
#Event 7. Dryer to folding area
Conc.h.1[7,]<-Conc.h.1[6,]*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.h.1[6,]*exp(-Inact.h*Contact.time.laundry)-Conc.l.1[6,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l.1[7,]<-Conc.l.1[6,]*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.l.1[6,]*exp(-Inact.s*Contact.time.laundry)-Conc.h.1[6,]*exp(-Inact.h*Contact.time.laundry))}
Dose.1[7,]<-Dose.1[6,]
Risk.1[7,]<-Risk.1[6,]
#Event 8. Hand to face Contact #3
Conc.h.1[8,]<-(1-TE.face*Frac.HF)*(Conc.h.1[7,]*exp(-Inact.h*Contact.time.face.f))
Conc.l.1[8,]<-Conc.l.1[7,]*exp(-Inact.s*Contact.time.face.f)
Dose.1[8,]<-Dose.1[7,]+(Conc.h.1[7,]*exp(-Inact.h*Contact.time.face.f)*TE.face*Frac.HF*T.handarea)
Risk.1[8,]<- 1-exp(-2.46E-3*Dose.1[8,])
#plotting
library(ggplot2)
library(ggpubr)
Conc.h.1.dataframe<-as.data.frame(t(Conc.h.1))
Conc.l.1.dataframe<-as.data.frame(t(Conc.l.1))
Dose.1.dataframe<-as.data.frame(t(Dose.1))
Risk.1.dataframe<-as.data.frame(t(Risk.1))
event<-rep(c(rep(1,iterations),rep(2,iterations),rep(3,iterations),rep(4,iterations),rep(5,iterations),rep(6,iterations),rep(7,iterations),rep(8,iterations)),4)
type<-c(rep("Hand",8*iterations),rep("Laundry",8*iterations),rep("Dose",8*iterations),rep("Risk",8*iterations))
value<-c(Conc.h.1.dataframe$`Hamper to washer`, Conc.h.1.dataframe$`Hand to face touch #1`,
Conc.h.1.dataframe$`between face touch and end of washing cycle`,Conc.h.1.dataframe $`Washer to dryer`,
Conc.h.1.dataframe $`Hand to face touch #2`, Conc.h.1.dataframe $`Dry cycle`,
Conc.h.1.dataframe $`Dryer to folding area`,Conc.h.1.dataframe $`Hand to face touch #3`,
Conc.l.1.dataframe$`Hamper to washer`, Conc.l.1.dataframe$`Hand to face touch #1`,
Conc.l.1.dataframe$`between face touch and end of washing cycle`,Conc.l.1.dataframe $`Washer to dryer`,
Conc.l.1.dataframe $`Hand to face touch #2`,
Conc.l.1.dataframe $`Dry cycle`,Conc.l.1.dataframe $`Dryer to folding area`,
Conc.l.1.dataframe $`Hand to face touch #3`,
Dose.1.dataframe$`Hamper to washer`, Dose.1.dataframe$`Hand to face touch #1`,
Dose.1.dataframe$`between face touch and end of washing cycle`,Dose.1.dataframe $`Washer to dryer`,
Dose.1.dataframe $`Hand to face touch #2`, Dose.1.dataframe $`Dry cycle`,Dose.1.dataframe $`Dryer to folding area`,
Dose.1.dataframe $`Hand to face touch #3`,
Risk.1.dataframe$`Hamper to washer`, Risk.1.dataframe$`Hand to face touch #1`,
Risk.1.dataframe$`between face touch and end of washing cycle`,Risk.1.dataframe $`Washer to dryer`,
Risk.1.dataframe $`Hand to face touch #2`, Risk.1.dataframe $`Dry cycle`,Risk.1.dataframe $`Dryer to folding area`,
Risk.1.dataframe $`Hand to face touch #3`)
data<-data.frame(event,type,value)
windows()
ggplot(data)+geom_violin(aes(x=event,y=value,fill=type, group=event),alpha=0.3,draw_quantiles = c(0.25,0.5,0.75))+
facet_wrap(~type,scales="free") +
scale_y_continuous(trans="log10")
##Hand washing scenario 2----------------------------------------------------
#Matrix
numevents<-8
eventsname<-c("Hamper to washer","Hand to face touch #1", "between face touch and end of washing cycle",
"Washer to dryer","Hand to face touch #2","Dry cycle","Dryer to folding area",
"Hand to face touch #3")
Conc.h.2<-matrix(nrow=numevents,ncol=iterations)
rownames(Conc.h.2)<-eventsname
Conc.l.2<-matrix(nrow=numevents, ncol=iterations)
rownames(Conc.l.2)<-eventsname
Dose.2<-matrix(nrow=numevents, ncol=iterations)
rownames(Dose.2)<-eventsname
Risk.2<-matrix(nrow=numevents, ncol=iterations)
rownames(Risk.2)<-eventsname
#Event 1. Loading dirty clothes from hamper to washer
Conc.h.2[1,]<-Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-Conc.onecloth*exp(-Inact.s*Contact.time.laundry))}
Conc.l.2[1,]<-Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-Conc.i.hand*exp(-Inact.h*Contact.time.laundry))}
Dose.2[1,]<-0
Risk.2[1,]<-0
#Event 2. Hand to face contact #1
Conc.h.2[2,]<-(1-TE.face*Frac.HF)*(Conc.h.2[1,]*exp(-Inact.h*Contact.time.face.w))
Conc.l.2[2,]<-Conc.l.2[1,]/10^(Reduc.wash*Contact.time.face.w/Dur.wash)
Dose.2[2,]<-Conc.h.2[1,]*exp(-Inact.h*Contact.time.face.w)*TE.face*Frac.HF*T.handarea
Risk.2[2,]<-1-exp(-2.46E-3*Dose.2[2,])
#Event 3. Washing Laundry
Conc.h.2[3,]<-Conc.h.2[2,]*exp(-Inact.h*(Dur.wash-Contact.time.face.w))
Conc.l.2[3,]<-Conc.l.2[2,]/10^(Reduc.wash*(Dur.wash-Contact.time.face.w)/Dur.wash)
Dose.2[3,]<-Dose.2[2,]
Risk.2[3,]<-Risk.2[2,]
#Event 4. Loading washed clothes to dryer
Conc.h.2[4,]<-Conc.h.2[3,]*exp(-Inact.h*Contact.time.laundry)-{TE.wet*Frac.HS*
(Conc.h.2[3,]*exp(-Inact.h*Contact.time.laundry)-Conc.l.2[3,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l.2[4,]<-Conc.l.2[3,]*exp(-Inact.s*Contact.time.laundry)-{TE.wet*Frac.HS*T.handarea/Surface.area.laundry*
(Conc.l.2[3,]*exp(-Inact.s*Contact.time.laundry)-Conc.h.2[3,]*exp(-Inact.h*Contact.time.laundry))}
Dose.2[4,]<-Dose.2[3,]
Risk.2[4,]<-Risk.2[3,]
#Event 5. Hand Washing + Hand to face contact #2
Conc.h.2[5,]<-(1-TE.face*Frac.HF)*{(Conc.h.2[4,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.d)}
Conc.l.2[5,]<-Conc.l.2[4,]/10^(Reduc.dry*Contact.time.face.d/Dur.dry)
Dose.2[5,]<-Dose.2[4,]+((Conc.h.2[4,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.d)*TE.face*Frac.HF*T.handarea)
Risk.2[5,]<- 1-exp(-2.46E-3*Dose.2[5,])
#Event 6. Drying Laundry
Conc.h.2[6,]<-Conc.h.2[5,]*exp(-Inact.h*(Dur.dry-Contact.time.face.d))
Conc.l.2[6,]<-Conc.l.2[5,]/10^(Reduc.dry*(Dur.dry-Contact.time.face.d)/Dur.dry)
Dose.2[6,]<-Dose.2[5,]
Risk.2[6,]<-Risk.2[5,]
#Event 7. Dryer to folding area
Conc.h.2[7,]<-Conc.h.2[6,]*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.h.2[6,]*exp(-Inact.h*Contact.time.laundry)-Conc.l.2[6,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l.2[7,]<-Conc.l.2[6,]*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.l.2[6,]*exp(-Inact.s*Contact.time.laundry)-Conc.h.2[6,]*exp(-Inact.h*Contact.time.laundry))}
Dose.2[7,]<-Dose.2[6,]
Risk.2[7,]<-Risk.2[6,]
#Event 8. Hand to face Contact #3
Conc.h.2[8,]<-(1-TE.face*Frac.HF)*(Conc.h.2[7,]*exp(-Inact.h*Contact.time.face.f))
Conc.l.2[8,]<-Conc.l.2[7,]*exp(-Inact.s*Contact.time.face.f)
Dose.2[8,]<-Dose.2[7,]+(Conc.h.2[7,]*exp(-Inact.h*Contact.time.face.f)*TE.face*Frac.HF*T.handarea)
Risk.2[8,]<- 1-exp(-2.46E-3*Dose.2[8,])
#plotting
library(ggplot2)
library(ggpubr)
Conc.h.2.dataframe<-as.data.frame(t(Conc.h.2))
Conc.l.2.dataframe<-as.data.frame(t(Conc.l.2))
Dose.2.dataframe<-as.data.frame(t(Dose.2))
Risk.2.dataframe<-as.data.frame(t(Risk.2))
event<-rep(c(rep(1,iterations),rep(2,iterations),rep(3,iterations),rep(4,iterations),rep(5,iterations),rep(6,iterations),rep(7,iterations),rep(8,iterations)),4)
type<-c(rep("Hand",8*iterations),rep("Laundry",8*iterations),rep("Dose",8*iterations),rep("Risk",8*iterations))
value<-c(Conc.h.2.dataframe$`Hamper to washer`, Conc.h.2.dataframe$`Hand to face touch #1`,
Conc.h.2.dataframe$`between face touch and end of washing cycle`,Conc.h.2.dataframe $`Washer to dryer`,
Conc.h.2.dataframe $`Hand to face touch #2`, Conc.h.2.dataframe $`Dry cycle`,
Conc.h.2.dataframe $`Dryer to folding area`,Conc.h.2.dataframe $`Hand to face touch #3`,
Conc.l.2.dataframe$`Hamper to washer`, Conc.l.2.dataframe$`Hand to face touch #1`,
Conc.l.2.dataframe$`between face touch and end of washing cycle`,Conc.l.2.dataframe $`Washer to dryer`,
Conc.l.2.dataframe $`Hand to face touch #2`,
Conc.l.2.dataframe $`Dry cycle`,Conc.l.2.dataframe $`Dryer to folding area`,
Conc.l.2.dataframe $`Hand to face touch #3`,
Dose.2.dataframe$`Hamper to washer`, Dose.2.dataframe$`Hand to face touch #1`,
Dose.2.dataframe$`between face touch and end of washing cycle`,Dose.2.dataframe $`Washer to dryer`,
Dose.2.dataframe $`Hand to face touch #2`, Dose.2.dataframe $`Dry cycle`,Dose.2.dataframe $`Dryer to folding area`,
Dose.2.dataframe $`Hand to face touch #3`,
Risk.2.dataframe$`Hamper to washer`, Risk.2.dataframe$`Hand to face touch #1`,
Risk.2.dataframe$`between face touch and end of washing cycle`,Risk.2.dataframe $`Washer to dryer`,
Risk.2.dataframe $`Hand to face touch #2`, Risk.2.dataframe $`Dry cycle`,Risk.2.dataframe $`Dryer to folding area`,
Risk.2.dataframe $`Hand to face touch #3`)
data<-data.frame(event,type,value)
windows()
ggplot(data)+geom_violin(aes(x=event,y=value,fill=type, group=event),alpha=0.3,draw_quantiles = c(0.25,0.5,0.75))+
facet_wrap(~type,scales="free") +
scale_y_continuous(trans="log10")
##Hand washing scenario 3----------------------------------------------------
#Matrix
numevents<-8
eventsname<-c("Hamper to washer","Hand to face touch #1", "between face touch and end of washing cycle",
"Washer to dryer","Hand to face touch #2","Dry cycle","Dryer to folding area",
"Hand to face touch #3")
Conc.h.3<-matrix(nrow=numevents,ncol=iterations)
rownames(Conc.h.3)<-eventsname
Conc.l.3<-matrix(nrow=numevents, ncol=iterations)
rownames(Conc.l.3)<-eventsname
Dose.3<-matrix(nrow=numevents, ncol=iterations)
rownames(Dose.3)<-eventsname
Risk.3<-matrix(nrow=numevents, ncol=iterations)
rownames(Risk.3)<-eventsname
#Event 1. Loading dirty clothes from hamper to washer
Conc.h.3[1,]<-Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.i.hand*exp(-Inact.h*Contact.time.laundry)-Conc.onecloth*exp(-Inact.s*Contact.time.laundry))}
Conc.l.3[1,]<-Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.i.laundry*exp(-Inact.s*Contact.time.laundry)-Conc.i.hand*exp(-Inact.h*Contact.time.laundry))}
Dose.3[1,]<-0
Risk.3[1,]<-0
#Event 2. Hand washing + Hand to face contact #1
Conc.h.3[2,]<-(1-TE.face*Frac.HF)*{(Conc.h.3[1,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.w)}
Conc.l.3[2,]<-Conc.l.3[1,]/10^(Reduc.wash*Contact.time.face.w/Dur.wash)
Dose.3[2,]<-(Conc.h.3[1,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.w)*TE.face*Frac.HF*T.handarea
Risk.3[2,]<-1-exp(-2.46E-3*Dose.3[2,])
#Event 3. Washing Laundry
Conc.h.3[3,]<-Conc.h.3[2,]*exp(-Inact.h*(Dur.wash-Contact.time.face.w))
Conc.l.3[3,]<-Conc.l.3[2,]/10^(Reduc.wash*(Dur.wash-Contact.time.face.w)/Dur.wash)
Dose.3[3,]<-Dose.3[2,]
Risk.3[3,]<-Risk.3[2,]
#Event 4. Loading washed clothes to dryer
Conc.h.3[4,]<-Conc.h.3[3,]*exp(-Inact.h*Contact.time.laundry)-{TE.wet*Frac.HS*
(Conc.h.3[3,]*exp(-Inact.h*Contact.time.laundry)-Conc.l.3[3,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l.3[4,]<-Conc.l.3[3,]*exp(-Inact.s*Contact.time.laundry)-{TE.wet*Frac.HS*T.handarea/Surface.area.laundry*
(Conc.l.3[3,]*exp(-Inact.s*Contact.time.laundry)-Conc.h.3[3,]*exp(-Inact.h*Contact.time.laundry))}
Dose.3[4,]<-Dose.3[3,]
Risk.3[4,]<-Risk.3[3,]
#Event 5. Hand Washing + Hand to face contact #2
Conc.h.3[5,]<-(1-TE.face*Frac.HF)*{(Conc.h.3[4,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.d)}
Conc.l.3[5,]<-Conc.l.3[4,]/10^(Reduc.dry*Contact.time.face.d/Dur.dry)
Dose.3[5,]<-Dose.3[4,]+((Conc.h.3[4,]/10^Reduc.hwash)*exp(-Inact.h*Contact.time.face.d)*TE.face*Frac.HF*T.handarea)
Risk.3[5,]<- 1-exp(-2.46E-3*Dose.3[5,])
#Event 6. Drying Laundry
Conc.h.3[6,]<-Conc.h.3[5,]*exp(-Inact.h*(Dur.dry-Contact.time.face.d))
Conc.l.3[6,]<-Conc.l.3[5,]/10^(Reduc.dry*(Dur.dry-Contact.time.face.d)/Dur.dry)
Dose.3[6,]<-Dose.3[5,]
Risk.3[6,]<-Risk.3[5,]
#Event 7. Dryer to folding area
Conc.h.3[7,]<-Conc.h.3[6,]*exp(-Inact.h*Contact.time.laundry)-{TE.dry*Frac.HS*(Conc.h.3[6,]*exp(-Inact.h*Contact.time.laundry)-Conc.l.3[6,]*exp(-Inact.s*Contact.time.laundry))}
Conc.l.3[7,]<-Conc.l.3[6,]*exp(-Inact.s*Contact.time.laundry)-{TE.dry*Frac.HS*T.handarea/Surface.area.laundry*(Conc.l.3[6,]*exp(-Inact.s*Contact.time.laundry)-Conc.h.3[6,]*exp(-Inact.h*Contact.time.laundry))}
Dose.3[7,]<-Dose.3[6,]
Risk.3[7,]<-Risk.3[6,]
#Event 8. Hand to face Contact #3
Conc.h.3[8,]<-(1-TE.face*Frac.HF)*(Conc.h.3[7,]*exp(-Inact.h*Contact.time.face.f))
Conc.l.3[8,]<-Conc.l.3[7,]*exp(-Inact.s*Contact.time.face.f)
Dose.3[8,]<-Dose.3[7,]+(Conc.h.3[7,]*exp(-Inact.h*Contact.time.face.f)*TE.face*Frac.HF*T.handarea)
Risk.3[8,]<- 1-exp(-2.46E-3*Dose.3[8,])
#plotting
library(ggplot2)
library(ggpubr)
Conc.h.3.dataframe<-as.data.frame(t(Conc.h.3))
Conc.l.3.dataframe<-as.data.frame(t(Conc.l.3))
Dose.3.dataframe<-as.data.frame(t(Dose.3))
Risk.3.dataframe<-as.data.frame(t(Risk.3))
event<-rep(c(rep(1,iterations),rep(2,iterations),rep(3,iterations),rep(4,iterations),rep(5,iterations),rep(6,iterations),rep(7,iterations),rep(8,iterations)),4)
type<-c(rep("Hand",8*iterations),rep("Laundry",8*iterations),rep("Dose",8*iterations),rep("Risk",8*iterations))
value<-c(Conc.h.3.dataframe$`Hamper to washer`, Conc.h.3.dataframe$`Hand to face touch #1`,
Conc.h.3.dataframe$`between face touch and end of washing cycle`,Conc.h.3.dataframe $`Washer to dryer`,
Conc.h.3.dataframe $`Hand to face touch #2`, Conc.h.3.dataframe $`Dry cycle`,
Conc.h.3.dataframe $`Dryer to folding area`,Conc.h.3.dataframe $`Hand to face touch #3`,
Conc.l.3.dataframe$`Hamper to washer`, Conc.l.3.dataframe$`Hand to face touch #1`,
Conc.l.3.dataframe$`between face touch and end of washing cycle`,Conc.l.3.dataframe $`Washer to dryer`,
Conc.l.3.dataframe $`Hand to face touch #2`,
Conc.l.3.dataframe $`Dry cycle`,Conc.l.3.dataframe $`Dryer to folding area`,
Conc.l.3.dataframe $`Hand to face touch #3`,
Dose.3.dataframe$`Hamper to washer`, Dose.3.dataframe$`Hand to face touch #1`,
Dose.3.dataframe$`between face touch and end of washing cycle`,Dose.3.dataframe $`Washer to dryer`,
Dose.3.dataframe $`Hand to face touch #2`, Dose.3.dataframe $`Dry cycle`,Dose.3.dataframe $`Dryer to folding area`,
Dose.3.dataframe $`Hand to face touch #3`,
Risk.3.dataframe$`Hamper to washer`, Risk.3.dataframe$`Hand to face touch #1`,
Risk.3.dataframe$`between face touch and end of washing cycle`,Risk.3.dataframe $`Washer to dryer`,
Risk.3.dataframe $`Hand to face touch #2`, Risk.3.dataframe $`Dry cycle`,Risk.3.dataframe $`Dryer to folding area`,
Risk.3.dataframe $`Hand to face touch #3`)
data<-data.frame(event,type,value)
windows()
ggplot(data)+geom_violin(aes(x=event,y=value,fill=type, group=event),alpha=0.3,draw_quantiles = c(0.25,0.5,0.75))+
facet_wrap(~type,scales="free") +
scale_y_continuous(trans="log10")
#Sensitivity Analysis---------------------------------------------------
spear.SARS<-data.frame(T.handarea, Surface.area.laundry, Frac.HS, Frac.HF,Item.laundry, Dur.wash, Dur.dry,
Contact.time.laundry, Contact.time.face.w, Contact.time.face.d, Contact.time.face.f,
Reduc.wash, Reduc.dry, Reduc.hwash, TE.dry, TE.wet, TE.face,Freq.cough.day,Volume.cough,
Conversion.ratio, Viralload, Conc.onecloth, Inact.h, Inact.s, Risk.3[8,])
spear.anal<-cor(spear.SARS,method="spearman")
View(spear.anal)
library(openxlsx)
write.xlsx(spear.anal, sheetName="SARS", file="Sensitivity.sars1.xlsx")