ERF of waterborne microbes

This page is a knowledge crystal of subtype variable. The page identifier is Op_en7948
Moderator:Heta (see all)

Upload data {{#opasnet_base_link:Op_en7948}}

Question

What are the dose-response functions of pathogens in drinking water?

Answer

+ Show code - Hide code

library(OpasnetUtils)

objects.latest("Op_en7948", code_name = "variable")

oprint(AnnosVaste)

Rationale

Data

ERF of waterborne microbes(-)
Obs	Exposure agent	Response	Exposure	Exposure unit	ER function	Scaling	Threshold	ERF	Description
1	campylobacter	campylobacter infection	ingestion	?	beta poisson approximation	None	0.024	0.011
2	rotavirus	rotavirus infection	ingestion	?	exact beta poisson	None	0.167	0.191
3	norovirus	norovirus infection	ingestion	?	exact beta poisson	None	0.04	0.055
4	cryptosporidium	cryptosporisium infection	ingestion	?	exact beta poisson	None	0.115	0.176
5	giardia	giardia infection	ingestion	?	exponential	None	0.0199	0
6	E.coli	E. coli infection	ingestion	?	exact beta poisson	None	0.157	9.16	E. coli O157:H7 strain

⇤--arg6688: . Find out the units of the parameters to understand the functions precisely. --Jouni (talk) 12:54, 11 July 2019 (UTC) (type: truth; paradigms: science: attack)

In these equations, Param1 and Param2 are in Threshold and ERF columns, respectively.

Beta Poisson approximation: 1-(1+Dose/Param2)^-Param1
Exact beta Poisson: 1-exp(-(Param1/(Param1+Param2))*Dose)
Exponential: 1-exp(-Param1*Dose)

Pathogen	Reference
Campylobacter	^[1]
Rotavirus	^[2]
Norovirus	^[3]
Cryptosporidium	^[4]
Giardia	^[5]
E.coli O157:H7	^[6]

Calculations

+ Show code - Hide code

# This is code Op_en7948/ERF_micr on page [[ERF of waterborne microbes]]

library(OpasnetUtils)

d <- opbase.data("Op_en7948")[-1]

colnames(d) <- gsub(" ", "_", colnames(d))
d$Result <- ifelse(d$Result == "", "0", as.character(d$Result))

ERF_micr <- Ovariable("ERF_micr", data = d[d$Observation == "ERF", colnames(d) != "Observation"])

threshold_micr <- Ovariable("threshold_micr", data = d[d$Observation == "Threshold", colnames(d) != "Observation"])

objects.store(ERF_micr, threshold_micr)
cat("Ovariables ERF_micr, threshold_micr stored.\n")

⇤--arg5268: . The code below is old and does not work with the new ERF table. --Jouni (talk) 12:54, 11 July 2019 (UTC) (type: truth; paradigms: science: attack)

+ Show code - Hide code

library(OpasnetUtils)

f.exact.beta.poisson <- function(Dose, Param1, Param2, ...) 1 - exp(-(Param1 / (Param1 + Param2)) * Dose)
f.beta.poisson.approx <- function(Dose, Param1, Param2, ...) 1 - (1 + Dose / Param2)^(-Param1)
f.exponential <- function(Dose, Param1, ...) 1 - exp(-Param1 * Dose)
f.alt.exponential <- function(Dose, Param1, Param2, ...) 1 - (1 + (Dose / Param1))^(Param2)

EFR <- Ovariable("ERF", data = tidy(opbase.data("Op_fi2653")))

objects.store(ERF, f.exact.beta.poisson, f.beta.poisson.approx, f.exponential, f.alt.exponential)

cat("Ovariable ERF and functions f.exact.beta.poisson, f.beta.poisson.approx, f.exponential and f.alt.exponential saved.\n")

oprint(ERF)

References

↑ Campylobacter (Teunis et al. 2005) Exact Beta-Poisson model Low Dose Approximation:Dose Response relationship for Campylobacter from model fit results presented by Teunis et al. (2005) Epidemiol. Infec. 133, 583-592.
↑ Teunis, P. F. M. and Havelaar, A. (2000). "The beta Poisson dose‐response model is not a single hit model."Risk Analysis 20(4): 511‐518.
↑ Teunis et al. 2008 Norwalk Virus: How Infectious is It? Journal of Medical Virology 80:1468-1476.
↑ Teunis et al., 2002 Risk Analysis 22(1) 175-183
↑ Teunis et al., 1996 RIVM report No. 284550002 " The dose-response relation in human volunteers for gastro-intestinal pathogens"
↑ Teunis, P., Takumi, K. and Shinagawa, K. (2004). "Dose response for infection by Escherichia coli O157:H7 from outbreak data." Risk Analysis 24(2): 401‐407.

[1] Campylobacter (Teunis et al. 2005) Exact Beta-Poisson model Low Dose Approximation:Dose Response relationship for Campylobacter from model fit results presented by Teunis et al. (2005) Epidemiol. Infec. 133, 583-592.

[2] Teunis, P. F. M. and Havelaar, A. (2000). "The beta Poisson dose‐response model is not a single hit model."Risk Analysis 20(4): 511‐518.

[3] Teunis et al. 2008 Norwalk Virus: How Infectious is It? Journal of Medical Virology 80:1468-1476.

[4] Teunis et al., 2002 Risk Analysis 22(1) 175-183

[5] Teunis et al., 1996 RIVM report No. 284550002 " The dose-response relation in human volunteers for gastro-intestinal pathogens"

[6] Teunis, P., Takumi, K. and Shinagawa, K. (2004). "Dose response for infection by Escherichia coli O157:H7 from outbreak data." Risk Analysis 24(2): 401‐407.

[1]

[2]

[3]

[4]

[5]

[6]

ERF of waterborne microbes

Contents

Question

Answer

Rationale

Data

Calculations

See also

References

Navigation menu