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Copy pathParameters and distributions_hwash_impr.R
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Parameters and distributions_hwash_impr.R
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#File 1 Parameters and distributions
library (truncdist)
library(triangle)
iterations <- 50000
set.seed(100)
#Total hand area (cm^2)
T.handarea<-runif(iterations, min=445, max=535)
#Surface area of laundry
Surface.area.laundry<-runif(iterations, min=4.9*10^3, max=1.8*10^4)
Item.laundry<-runif(iterations, min=14, max=18)
#Fraction of hand surface(hand-surface, hand-face) (unitless)
Frac.HS <-runif(iterations,min=0.13, max=0.25)
Frac.HF <-runif(iterations, min=0.008, max=0.012)
#Duration (min) / Contact time
Dur.wash <- 50
Dur.dry <- 60
Contact.time.laundry<-runif(iterations, min=1/60, max=10/60)
Contact.time.face.w<-runif(iterations, min=1/60, max=50)
Contact.time.face.d<-runif(iterations, min=1/60, max=60)
Contact.time.face.f<-runif(iterations, min=1/60, max=60)
#Initial concentration on hand/face
Conc.i.hand<-0
Conc.i.face<-0
if(organism == "SARS-CoV-2") {
#Transfer efficiency
TE.dry <-rtrunc(iterations,"norm", mean=0.0003, sd=0.0002, a=0, b=1)
TE.wet <-rtriangle(n=iterations, a=0.00001, b=0.0001, c=0.00005)
TE.face<-rtrunc(iterations,"norm", mean=0.3390, sd=0.1318, a=0, b=1)
#Reduction, inactivation
Reduc.wash <-rtrunc(iterations,"norm", mean=3.0, sd=0.02, a=0, b=5.0)
Reduc.dry <-rtrunc(iterations, "norm", mean=3.0, sd=0.02, a=0, b=5.0)
Reduc.hwash<-runif(iterations, min=3, max=5.0)
Inact.h <-rtriangle(iterations, a=0.0056, b=0.0125, c=0.0084)
Inact.s <-rtriangle(iterations, a=0.000075, b=0.000125, c=0.0001)
#Initial concentration on laundry on Sunday
Viralload <-runif(iterations,min=3.3*10^6, max=2.35*10^9)
Freq.cough.day<-rtriangle(n=iterations, a=240, b=1872, c=864)
Volume.cough<-5.964*10^(-3)
Conversion.ratio<-runif(iterations, min=100, max=1000)
Conc.onecloth<-(Viralload*Volume.cough*Freq.cough.day)/(Conversion.ratio*Surface.area.laundry)
Conc.i.laundry<-(Conc.onecloth*exp(-Inact.s*6*24*60)+Conc.onecloth*exp(-Inact.s*5*24*60)+
Conc.onecloth*exp(-Inact.s*4*24*60)+Conc.onecloth*exp(-Inact.s*3*24*60)+
Conc.onecloth*exp(-Inact.s*2*24*60)+Conc.onecloth*exp(-Inact.s*1*24*60)+
Conc.onecloth)/Item.laundry
} else if (organism == "Rotavirus")
{
#Transfer efficiency
TE.dry <-rtrunc(iterations,"norm", mean=0.0003, sd=0.0002, a=0, b=1)
TE.wet <-rtriangle(n=iterations, a=0.00001, b=0.0001, c=0.00005)
TE.face<-rtrunc(iterations,"norm", mean=0.3390, sd=0.1318, a=0, b=1)
#Reduction, inactivation
Reduc.wash <-rtrunc(iterations,"norm", mean=5.0, sd=0.25, a=0, b=7.0)
Reduc.dry <-rtrunc(iterations, "norm", mean=6.9, sd=0.06, a=0, b=9.0)
Reduc.hwash<-runif(iterations, min=3, max=4.32)
Inact.h <-rtrunc(iterations, "norm", mean=0.0045, sd=0.000258, a=0, b=1)
Inact.s <-runif(iterations, min=0.0025, max=0.0042)
#Initial concentration on laundry on Sunday
Conc.feces <-runif(iterations,min=10^10, max=10^12)
Mass.feces <-runif(iterations, min=0.01, max=1)
Conc.onecloth<-Conc.feces*Mass.feces/(Surface.area.laundry)
Conc.i.laundry<-(Conc.onecloth*exp(-Inact.s*6*24*60)+Conc.onecloth*exp(-Inact.s*5*24*60)+
Conc.onecloth*exp(-Inact.s*4*24*60)+Conc.onecloth*exp(-Inact.s*3*24*60)+
Conc.onecloth*exp(-Inact.s*2*24*60)+Conc.onecloth*exp(-Inact.s*1*24*60)+
Conc.onecloth)/Item.laundry
#Dose response value
alpha<-2.53E-01
N50<-6.17E+00
beta<-N50/(2^(1/alpha)-1)
} else if(organism=="Norovirus"){
#Transfer efficiency
TE.dry <-rtrunc(iterations,"norm", mean=0.0003, sd=0.0002, a=0, b=1)
TE.wet <-rtriangle(n=iterations, a=0.00001, b=0.0001, c=0.00005)
TE.face<-rtrunc(iterations,"norm", mean=0.3390, sd=0.1318, a=0, b=1)
#Reduction, inactivation (cold, cotton)
Reduc.wash <-rtrunc(iterations,"norm", mean=2.4, sd=0.62, a=0, b=4.0)
Reduc.dry <-rtrunc(iterations, "norm", mean=6.1, sd=0.10, a=0, b=8.0)
Reduc.hwash<-runif(iterations, min=3, max=3.78)
Inact.h <-runif(iterations, min=0.0002, max=0.0118)
Inact.s <-runif(iterations, min=0.0008, max=0.0016)
#Initial concentration on laundry on Sunday
Viralload <-runif(iterations,min=10^7.71, max=10^10.94)
Mass.feces <-runif(iterations, min=0.01, max=1)
Conversion.ratio<-runif(iterations, min=100, max=1000)
Conc.onecloth<-Viralload*Mass.feces/(Surface.area.laundry*Conversion.ratio)
Conc.i.laundry<-(Conc.onecloth*exp(-Inact.s*6*24*60)+Conc.onecloth*exp(-Inact.s*5*24*60)+
Conc.onecloth*exp(-Inact.s*4*24*60)+Conc.onecloth*exp(-Inact.s*3*24*60)+
Conc.onecloth*exp(-Inact.s*2*24*60)+Conc.onecloth*exp(-Inact.s*1*24*60)+
Conc.onecloth)/Item.laundry
} else if(organism=="Salmonella"){
#Transfer efficiency
TE.dry <-rtrunc(iterations,"norm", mean=0.068, sd=0.070, a=0, b=1)
TE.wet <-rtriangle(n=iterations, a=0.00001, b=0.0001, c=0.00003)
TE.face<-rtrunc(iterations,"norm", mean=0.3397, sd=0.1604, a=0, b=1)
#Reduction, inactivation
Reduc.wash <-rtrunc(iterations,"norm", mean=3.4, sd=0.39, a=0, b=5.0)
Reduc.dry <-rtrunc(iterations, "norm", mean=7.3, sd=0.42, a=0, b=9.0)
Reduc.hwash<-runif(iterations, min=3, max=5.8)
Inact.h <-runif(iterations, min=0.0275, max=0.0533)
Inact.s <-runif(iterations, min=0.0013, max=0.0015)
#Initial concentration on laundry on Sunday
Conc.feces <-runif(iterations,min=10^6, max=10^10)
Mass.feces <-runif(iterations, min=0.01, max=1)
Conc.onecloth<-Conc.feces*Mass.feces/Surface.area.laundry
Conc.i.laundry<-(Conc.onecloth*exp(-Inact.s*6*24*60)+Conc.onecloth*exp(-Inact.s*5*24*60)+
Conc.onecloth*exp(-Inact.s*4*24*60)+Conc.onecloth*exp(-Inact.s*3*24*60)+
Conc.onecloth*exp(-Inact.s*2*24*60)+Conc.onecloth*exp(-Inact.s*1*24*60)+
Conc.onecloth)/Item.laundry
#Dose response value
alpha<-2.1E-01
N50<-4.98E+01
beta<-N50/(2^(1/alpha)-1)
} else { #E.coli
#Transfer efficiency
TE.dry <-rtrunc(iterations,"norm", mean=0.068, sd=0.070, a=0, b=1)
TE.wet <-rtriangle(n=iterations, a=0.00001, b=0.0001, c=0.00003)
TE.face<-rtrunc(iterations,"norm", mean=0.3397, sd=0.1604, a=0, b=1)
#Reduction, inactivation (cold, cotton)
Reduc.wash <-rtrunc(iterations,"norm", mean=3.5, sd=0.96, a=0, b=6.0)
Reduc.dry <-rtrunc(iterations, "norm", mean=8.0, sd=0.93, a=0, b=10.0)
Reduc.hwash<-runif(iterations, min=3, max=5.8)
Inact.h <-runif(iterations, min=0.05, max=0.0753)
Inact.s <-runif(iterations, min=0.0015, max=0.023)
#Reduction (various options)
Reduc.wash.terry <-rtrunc(iterations, "norm", mean=2.1, sd=0.21, a=0, b=4)
Reduc.wash.terry.w<- rtrunc(iterations, "norm", mean=2.1, sd=0.11, a=0, b=4.0)
Reduc.dry.line<-rtrunc(iterations, "norm", mean=5.2, sd=0.55, a=0, b=7.0)
#Initial concentration on laundry on Sunday
Conc.feces <-runif(iterations,min=10^7, max=10^9)
Mass.feces <-runif(iterations, min=0.01, max=1)
Conc.onecloth<-Conc.feces*Mass.feces/Surface.area.laundry
Conc.i.laundry<-(Conc.onecloth*exp(-Inact.s*6*24*60)+Conc.onecloth*exp(-Inact.s*5*24*60)+
Conc.onecloth*exp(-Inact.s*4*24*60)+Conc.onecloth*exp(-Inact.s*3*24*60)+
Conc.onecloth*exp(-Inact.s*2*24*60)+Conc.onecloth*exp(-Inact.s*1*24*60)+
Conc.onecloth)/Item.laundry
#Dose response value
alpha<-1.55E-01
N50<-2.11E+06
beta<-N50/(2^(1/alpha)-1)
}