ERF of waterborne microbes: Difference between revisions

Latest revision as of 08:59, 6 February 2022

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(-)
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	sapovirus	sapovirus infection	ingestion	?	exact beta poisson	None	0.055	0.04
5	cryptosporidium	cryptosporidium infection	ingestion	?	exact beta poisson	None	0.176	0.115
6	giardia	giardia infection	ingestion	?	exponential	None	0	0.0199
7	E.coli O157:H7	E.coli O157:H7 infection	ingestion	?	exact beta poisson	None	9.16	0.157	E. coli O157:H7 strain

Probability of illness, given infection(probability)
Obs	Response	Illness	Subgroup	Result
1	giardia infection	gastroenteritis		1
2	cryptosporidium infection	gastroenteritis		0.71
3	cryptosporidium infection	death	Age:0-4	0.00000070645
4	cryptosporidium infection	death	Age:5-9	0
5	cryptosporidium infection	death	Age:10-14	0
6	cryptosporidium infection	death	Age:15-64	0.000014839
7	cryptosporidium infection	death	Age:65-79	0.0011644
8	cryptosporidium infection	death	Age:80+	0.0011644
9	norovirus infection	gastroenteritis		0.7
10	norovirus infection	death	Age:0-4	0.000002058
11	norovirus infection	death	Age:5-9	0
12	norovirus infection	death	Age:10-14	0
13	norovirus infection	death	Age:15-64	0
14	norovirus infection	death	Age:65-79	0.000168
15	norovirus infection	death	Age:80+	0.000168
16	sapovirus infection	gastroenteritis		0.7
17	sapovirus infection	death	Age:0-4	0.000002058
18	sapovirus infection	death	Age:5-9	0
19	sapovirus infection	death	Age:10-14	0
20	sapovirus infection	death	Age:15-64	0
21	sapovirus infection	death	Age:65-79	0.000168
22	sapovirus infection	death	Age:80+	0.000168
23	rotavirus infection	gastroenteritis		0.5
24	rotavirus infection	death	Age:0-4	0.00001917
25	rotavirus infection	death	Age:5-9	0
26	rotavirus infection	death	Age:10-14	0
27	rotavirus infection	death	Age:15-64	0
28	rotavirus infection	death	Age:65-79	0
29	rotavirus infection	death	Age:80+	0
30	campylobacter infection	gastroenteritis		0.323
31	campylobacter infection	clinical Guillian-Barré syndrome		0.000066
32	campylobacter infection	residual Guillian Barré syndrome		0.000066
33	campylobacter infection	reactive arthritis		0.0066
34	campylobacter infection	death		0.000131
35	E.coli O157:H7 infection	gastroenteritis		0.4346
36	E.coli O157:H7 infection	hemorrhagic colitis		0.3854
37	E.coli O157:H7 infection	haemolytic uraemic syndrome		0.0082
38	E.coli O157:H7 infection	end stage renal disease		0.0009676
39	E.coli O157:H7 infection	death		0.00062238

⇤--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)

----arg2087: . The ERF and Threshold numbers in the tables correspond to parameters called alpha and beta respectively in the papers cited below in the cases of campylo, rota, noro and crypto. The equations alpha and beta are used in in the papers don't (seem to) match the equations below. At least for campylo the equations are significantly more complicated. For giardia the value in ERF does seem to be used in the paper it's from in the way the exponential equation shows. In the paper it's marked as r, the probability of infection. The equation in the paper uses "mean number per portion" where Dose is in this equation. E.coli is the biggest mystery: I wasn't able to find the numbers in the table above from the paper sited for it at all. --Heta (talk) 10:32, 12 July 2019 (UTC) (type: truth; paradigms: science: comment)

In these equations, Param1 and Param2 are in ERF and Threshold, 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] ^[2]
Rotavirus	^[3] ^[2]
Norovirus	^[4]
Sapovirus	^[5]
Cryptosporidium	^[6]^[2]
Giardia	^[7]
E.coli O157:H7	^[8]

Calculations

+ Show code - Hide code

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

library(OpasnetUtils)

objects.latest("Op_en2031", code_name="subgrouping") # [[ERF]] subgrouping

P_illness <- Ovariable("P_illness", ddata = "Op_en7948", subset="Probability of illness, given infection")
P_illness@data <- subgrouping(P_illness@data)

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

+ Show code - Hide code

# 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", subset="ERF")
colnames(ERF_micr@data) <- gsub(" ", "_", colnames(ERF_micr@data))

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

+ 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

↑ 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
↑ ^2.0 ^2.1 ^2.2 WHO Guidelines for drinking-water quality 2017. ISBN 978-92-4-154995-0 [1]
↑ 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., 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

[WHO-2] 2.0 ^2.1 ^2.2 WHO Guidelines for drinking-water quality 2017. ISBN 978-92-4-154995-0 [1]

[3] 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

[4] 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

[5] 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

[6] 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

[7] 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

[8] 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]

[7]

[8]

@@ Line 23: / Line 23: @@
 === Data ===
-<t2b index="Exposure agent,Response,Exposure,Exposure unit,ER function,Scaling,Observation" locations="Threshold,ERF" desc="Description" unit="-">
+<t2b name="ERF" 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|
+campylobacter|campylobacter infection|ingestion|?|beta poisson approximation|None|0.011|0.024|
-rotavirus|rotavirus infection|ingestion|?|exact beta poisson|None|0.167|0.191|
+rotavirus|rotavirus infection|ingestion|?|exact beta poisson|None|0.191|0.167|
-norovirus|norovirus infection|ingestion|?|exact beta poisson|None|0.04|0.055|
+norovirus|norovirus infection|ingestion|?|exact beta poisson|None|0.055|0.04|
-cryptosporidium|cryptosporidium infection|ingestion|?|exact beta poisson|None|0.115|0.176|
+sapovirus|sapovirus infection|ingestion|?|exact beta poisson|None|0.055|0.04|
-giardia|giardia infection|ingestion|?|exponential|None|0.0199|0|
+cryptosporidium|cryptosporidium infection|ingestion|?|exact beta poisson|None|0.176|0.115|
-E.coli|E. coli infection|ingestion|?|exact beta poisson|None|0.157|9.16|E. coli O157:H7 strain
+giardia|giardia infection|ingestion|?|exponential|None|0|0.0199|
+E.coli O157:H7|E.coli O157:H7 infection|ingestion|?|exact beta poisson|None|9.16|0.157|E. coli O157:H7 strain
+</t2b>
+<t2b name="Probability of illness, given infection" index="Response, Illness, Subgroup" obs="Result" unit="probability">
+giardia infection|gastroenteritis||1
+cryptosporidium infection|gastroenteritis||0.71
+cryptosporidium infection|death|Age:0-4|0.00000070645
+cryptosporidium infection|death|Age:5-9|0
+cryptosporidium infection|death|Age:10-14|0
+cryptosporidium infection|death|Age:15-64|0.000014839
+cryptosporidium infection|death|Age:65-79|0.0011644
+cryptosporidium infection|death|Age:80+|0.0011644
+norovirus infection|gastroenteritis||0.7
+norovirus infection|death|Age:0-4|0.000002058
+norovirus infection|death|Age:5-9|0
+norovirus infection|death|Age:10-14|0
+norovirus infection|death|Age:15-64|0
+norovirus infection|death|Age:65-79|0.000168
+norovirus infection|death|Age:80+|0.000168
+sapovirus infection|gastroenteritis||0.7
+sapovirus infection|death|Age:0-4|0.000002058
+sapovirus infection|death|Age:5-9|0
+sapovirus infection|death|Age:10-14|0
+sapovirus infection|death|Age:15-64|0
+sapovirus infection|death|Age:65-79|0.000168
+sapovirus infection|death|Age:80+|0.000168
+rotavirus infection|gastroenteritis||0.5
+rotavirus infection|death|Age:0-4|0.00001917
+rotavirus infection|death|Age:5-9|0
+rotavirus infection|death|Age:10-14|0
+rotavirus infection|death|Age:15-64|0
+rotavirus infection|death|Age:65-79|0
+rotavirus infection|death|Age:80+|0
+campylobacter infection|gastroenteritis||0.323
+campylobacter infection|clinical Guillian-Barré syndrome||0.000066
+campylobacter infection|residual Guillian Barré syndrome||0.000066
+campylobacter infection|reactive arthritis||0.0066
+campylobacter infection|death||0.000131
+E.coli O157:H7 infection|gastroenteritis||0.4346
+E.coli O157:H7 infection|hemorrhagic colitis||0.3854
+E.coli O157:H7 infection|haemolytic uraemic syndrome||0.0082
+E.coli O157:H7 infection|end stage renal disease||0.0009676
+E.coli O157:H7 infection|death||0.00062238
 </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)}}
+:{{argument|relat1=comment|id=arg2087|type=truth|content=The ERF and Threshold numbers in the tables correspond to parameters called alpha and beta respectively in the papers cited below in the cases of campylo, rota, noro and crypto. The equations alpha and beta are used in in the papers don't (seem to) match the equations below. At least for campylo the equations are significantly more complicated. For giardia the value in ERF does seem to be used in the paper it's from in the way the exponential equation shows. In the paper it's marked as r, the probability of infection. The equation in the paper uses "mean number per portion" where Dose is in this equation. ''E.coli'' is the biggest mystery: I wasn't able to find the numbers in the table above from the paper sited for it at all. |sign=--[[User:Heta|Heta]] ([[User talk:Heta|talk]]) 10:32, 12 July 2019 (UTC)}}
-In these equations, Param1 and Param2 are in Threshold and ERF columns, respectively.
+In these equations, Param1 and Param2 are in ERF and Threshold, respectively.
 * Beta Poisson approximation: 1-(1+Dose/Param2)^-Param1
 * Exact beta Poisson: 1-exp(-(Param1/(Param1+Param2))*Dose)
@@ Line 44: / Line 89: @@
 |----
 | Campylobacter
-| <ref>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. </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> <ref name="WHO">WHO Guidelines for drinking-water quality 2017. ISBN 978-92-4-154995-0 [https://apps.who.int/iris/bitstream/handle/10665/254637/9789241549950-eng.pdf?sequence=1]</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> <ref name="WHO"/>
 |----
 | 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>
+|----
+| Sapovirus
+| <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><ref name="WHO"/>
 |----
 | 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
+| ''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>
 |}
 === Calculations ===
-<rcode name="ERF_micr" label="Initiate ovariables ERF_micr, threshold_micr" embed)1>
+<rcode name="P_illness" label="Initiate P_illness" embed=1>
+# This is code Op_en7948/P_illness on page [[ERF of waterborne microbes]]
+library(OpasnetUtils)
+objects.latest("Op_en2031", code_name="subgrouping") # [[ERF]] subgrouping
+P_illness <- Ovariable("P_illness", ddata = "Op_en7948", subset="Probability of illness, given infection")
+P_illness@data <- subgrouping(P_illness@data)
+objects.store(P_illness)
+cat("Ovariable P_illness stored.\n")
+</rcode>
+<rcode name="ERF_micr2" label="Initiate ovariable ERF_micr" embed=1>
+# 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", subset="ERF")
+colnames(ERF_micr@data) <- gsub(" ", "_", colnames(ERF_micr@data))
+objects.store(ERF_micr)
+cat("Ovariable ERF_micr stored.\n")
+</rcode>
+<rcode name="ERF_micr" label="Initiate ovariables ERF_micr, threshold_micr" embed=1>
 # This is code Op_en7948/ERF_micr on page [[ERF of waterborne microbes]]

ERF of waterborne microbes: Difference between revisions

Latest revision as of 08:59, 6 February 2022

Contents

Question

Answer

Rationale

Data

Calculations

See also

References

Navigation menu