-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathParameters and distributions.R
175 lines (139 loc) · 7.45 KB
/
Parameters and distributions.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
#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=2.03, 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=0.14, 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=0.91, 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=0.6, 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=0.6, 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)
}