ERF of waterborne microbes: Difference between revisions

Revision as of 12:54, 11 July 2019

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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: Difference between revisions(-)
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

⇤--arg5268: . This is old code 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.

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@@ Line 22: / Line 22: @@
 === Data ===
+<t2b index="Exposure agent,Response,Exposure,Exposure unit,ER function,Scaling,Observation" locations="Threshold,ERF" desc="Description" unit="-">
+campylobacter|campylobacter infection|ingestion|?|Beta Poisson approximation|None|0.024|0.011|
+rotavirus|rotavirus infection|ingestion|?|Exact beta Poisson|None|0.167|0.191|
+norovirus|norovirus infection|ingestion|?|Exact beta Poisson|None|0.04|0.055|
+cryptosporidium|cryptosporisium infection|ingestion|?|Exact beta Poisson|None|0.115|0.176|
+giardia|giardia infection|ingestion|?|Exponential|None|0.0199|0|
+E.coli|E. coli infection|ingestion|?|Exact beta Poisson|None|0.157|9.16|E. coli O157:H7 strain
+</t2b>
+{{argument|relat1=attack|id=arg6688|type=truth|content=Find out the units of the parameters to understand the functions precisely.|sign=--[[User:Jouni|Jouni]] ([[User talk:Jouni|talk]]) 12:54, 11 July 2019 (UTC)}}
+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)
 {| {{prettytable}}
@@ Line 47: / Line 63: @@
 |}
+=== Calculations ===
-<t2b index = "Pathogen,Parameter" locations = "Function type,Function,Rname,Unit,Param1,Param2" unit = "-">
+{{argument|relat1=attack|id=arg5268|type=truth|content=This is old code and does not work with the new ERF table.|sign=--[[User:Jouni|Jouni]] ([[User talk:Jouni|talk]]) 12:54, 11 July 2019 (UTC)}}
-Campylobacter|Beta Poisson approximation|1-(1+Dose/Param2)^-Param1|f.beta.poisson.approx|No unit|0.024|0.011
-Rotavirus|Exact beta Poisson|1-exp(-(Param1/(Param1+Param2))*Dose)|f.exact.beta.poisson|No unit|0.167|0.191
-Norovirus|Exact beta Poisson|1-exp(-(Param1/(Param1+Param2))*Dose)|f.exact.beta.poisson|No unit|0.04|0.055
-Cryptosporidium|Exact beta Poisson|1-exp(-(Param1/(Param1+Param2))*Dose)|f.exact.beta.poisson|No unit|0.115|0.176
-Giardia|Exponential|1-exp(-Param1*Dose)|f.exponential|No unit|0.0199|0
-E.coli O157:H7|Exact beta Poisson|1-exp(-(Param1/(Param1+Param2))*Dose)|f.exact.beta.poisson|No unit|0.157|9.16
-</t2b>
-=== Calculations ===
 <rcode