ERF of waterborne microbes: Difference between revisions

Revision as of 09:13, 12 July 2019

This page is a knowledge crystal of subtype variable. The page identifier is Op_en7948
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Question

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

Answer

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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	0.011	0.024
2	rotavirus	rotavirus infection	ingestion	?	exact beta poisson	None	0.191	0.167
3	norovirus	norovirus infection	ingestion	?	exact beta poisson	None	0.055	0.04
4	cryptosporidium	cryptosporidium infection	ingestion	?	exact beta poisson	None	0.176	0.115
5	giardia	giardia infection	ingestion	?	exponential	None	0	0.0199
6	E.coli	E. coli infection	ingestion	?	exact beta poisson	None	9.16	0.157	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

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# This is code Op_en7948/ERF_micr2 on page [[ERF of waterborne microbes]]
# Note! This version has ERF and threshold in the same ovariable.

library(OpasnetUtils)

ERF_micr <- Ovariable("ERF_micr", ddata = "Op_en7948")
colnames(ERF_micr@data) <- gsub(" ", "_", colnames(ERF_micr@data))

objects.store(ERF_micr)
cat("Ovariable ERF_micr stored.\n")

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# 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)

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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

↑ Teunis, P., van den Brandhof, W., Nauta, M., Wagenaar, J., van den Kerkhof, H. and van Pelt, W. 2005. A reconsideration of the Campylobacter dose–response relation. Epidemiol. Infec. 133, 583-592. DOI: https://doi.org/10.1017/S0950268805003912
↑ Teunis, P. F. M. and Havelaar, A. 2000. "The beta Poisson dose‐response model is not a single hit model."Risk Analysis 20(4): 513-520. https://doi.org/10.1111/0272-4332.204048
↑ Teunis P.F.M., Moe, C.L., Liu, P., Miller, S.E., Lindesmith, L., Baric, R.S., Le Pendu, J., Calderon, R.L. 2008. Norwalk Virus: How Infectious is It? Journal of Medical Virology 80:1468-1476. https://doi.org/10.1002/jmv.21237
↑ Teunis, P.F.M., Chappell, C.L., Okhuysen, P.C. 2002. Cryptosporidium Dose Response Studies: Variation Between Isolates. Risk Analysis 22(1) 175-183 https://doi.org/10.1111/0272-4332.00014
↑ Teunis, P.F.M., van der Heijden, O.G., van der Giessen, J.W.B., Havelaar, A.H. 1996. The dose-response relation in human volunteers for gastro-intestinal pathogens. RIVM report No. 284550002. http://hdl.handle.net/10029/9966
↑ 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. https://doi.org/10.1111/j.0272-4332.2004.00441.x

[1] Teunis, P., van den Brandhof, W., Nauta, M., Wagenaar, J., van den Kerkhof, H. and van Pelt, W. 2005. A reconsideration of the Campylobacter dose–response relation. Epidemiol. Infec. 133, 583-592. DOI: https://doi.org/10.1017/S0950268805003912

[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): 513-520. https://doi.org/10.1111/0272-4332.204048

[3] Teunis P.F.M., Moe, C.L., Liu, P., Miller, S.E., Lindesmith, L., Baric, R.S., Le Pendu, J., Calderon, R.L. 2008. Norwalk Virus: How Infectious is It? Journal of Medical Virology 80:1468-1476. https://doi.org/10.1002/jmv.21237

[4] Teunis, P.F.M., Chappell, C.L., Okhuysen, P.C. 2002. Cryptosporidium Dose Response Studies: Variation Between Isolates. Risk Analysis 22(1) 175-183 https://doi.org/10.1111/0272-4332.00014

[5] Teunis, P.F.M., van der Heijden, O.G., van der Giessen, J.W.B., Havelaar, A.H. 1996. The dose-response relation in human volunteers for gastro-intestinal pathogens. RIVM report No. 284550002. http://hdl.handle.net/10029/9966

[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. https://doi.org/10.1111/j.0272-4332.2004.00441.x

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 44: / Line 44: @@
 |----
 | Campylobacter
-| <ref>P. Teunis, W. van den Brandhof, M. Nauta, J. Wagenaar, H. van den Kerkhof and W. van Pelt. (2005) A reconsideration of the Campylobacter dose–response relation. Epidemiol. Infec. 133, 583-592. DOI: https://doi.org/10.1017/S0950268805003912 </ref>
+| <ref>Teunis, P., van den Brandhof, W., Nauta, M., Wagenaar, J., van den Kerkhof, H. and van Pelt, W. 2005. A reconsideration of the Campylobacter dose–response relation. Epidemiol. Infec. 133, 583-592. DOI: https://doi.org/10.1017/S0950268805003912 </ref>
 |----
 | Rotavirus
-| <ref>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. </ref>
+| <ref>Teunis, P. F. M. and Havelaar, A. 2000. "The beta Poisson dose‐response model is not a single hit model."Risk Analysis 20(4): 513-520.  https://doi.org/10.1111/0272-4332.204048</ref>
 |----
 | Norovirus
-| <ref>Teunis et al. 2008 Norwalk Virus: How Infectious is It? Journal of Medical Virology 80:1468-1476.</ref>
+| <ref>Teunis P.F.M., Moe, C.L., Liu, P., Miller, S.E., Lindesmith, L., Baric, R.S., Le Pendu, J., Calderon, R.L. 2008. Norwalk Virus: How Infectious is It? Journal of Medical Virology 80:1468-1476. https://doi.org/10.1002/jmv.21237</ref>
 |----
 | Cryptosporidium
-| <ref>Teunis et al., 2002 Risk Analysis 22(1) 175-183 </ref>
+| <ref>Teunis, P.F.M., Chappell, C.L., Okhuysen, P.C. 2002. Cryptosporidium Dose Response Studies: Variation Between Isolates. Risk Analysis 22(1) 175-183  https://doi.org/10.1111/0272-4332.00014</ref>
 |----
 | Giardia
-| <ref>Teunis et al., 1996 RIVM report No. 284550002 " The dose-response relation in human volunteers for gastro-intestinal pathogens" </ref>
+| <ref>Teunis, P.F.M., van der Heijden, O.G., van der Giessen, J.W.B., Havelaar, A.H. 1996.  The dose-response relation in human volunteers for gastro-intestinal pathogens. RIVM report No. 284550002. http://hdl.handle.net/10029/9966 </ref>
 |----
 | E.coli O157:H7
-| <ref>Teunis, P., Takumi, K. and Shinagawa, K. (2004). "Dose response for infection by Escherichia coli O157:H7
+| <ref>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.</ref>
+from outbreak data." Risk Analysis 24(2): 401‐407. https://doi.org/10.1111/j.0272-4332.2004.00441.x</ref>
 |}

ERF of waterborne microbes: Difference between revisions

Revision as of 09:13, 12 July 2019

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Question

Answer

Rationale

Data

Calculations

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References

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