Difference between revisions of "EU-kalat"

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(Initiate conc_pcddf)
(Initiate conc_pcddf for PFAS disease burden study)
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==== Initiate conc_pcddf for PFAS disease burden study ====
 
==== Initiate conc_pcddf for PFAS disease burden study ====
 +
 +
NOTE! This is not a probabilistic approach. Species and area-specific distributions should be created.
  
 
<rcode name="pcddf_mean" label="Initiate conc_pcddf (for developers only)" embed=1>
 
<rcode name="pcddf_mean" label="Initiate conc_pcddf (for developers only)" embed=1>
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library(OpasnetUtils)
 
library(OpasnetUtils)
 +
 +
conc_pcddf_raw <- Ovariable("conc_pcddf_raw", ddata="Op_en3104", subset="POPs")
  
 
conc_pcddf <- Ovariable(
 
conc_pcddf <- Ovariable(
 
   "conc_pcddf",
 
   "conc_pcddf",
   dependencies = data.frame(Name=c("TEF"),Ident=c("Op_en4017/initiate")), # [[Toxic equivalency factor]],
+
   dependencies = data.frame(Name=c("conc_pcddf_raw","TEF"),Ident=c(NA,"Op_en4017/initiate")), # [[Toxic equivalency factor]]
 
   formula = function(...) {
 
   formula = function(...) {
     df <- opbase.data("Op_en3104", subset="POPs") # [[EU-kalat]]
+
     df <- conc_pcddf_raw # [[EU-kalat]]
     df <- df[df$Matrix=="Muscle" & df$Catch_site %in% c("Baltic Sea", "Helsinki, Vanhankaupunginlahti Bay"),c(3,4,6,18)]
+
     df <- df[df$Matrix=="Muscle" & df$Catch_site %in% c("Baltic Sea", "Helsinki, Vanhankaupunginlahti Bay"),
     colnames(df) <- c("Compound","Fish","Area","Result")
+
            c(1,3,4,6,18)]
    df <- Ovariable("df",data=df, unit="pg/g fresh weight")
+
     colnames(df@output)[1:4] <- c("Sample","Compound","Fish","Area")
 +
#    df <- Ovariable("df",data=df, unit="pg/g fresh weight")
 
      
 
      
 
     out <- df * TEF
 
     out <- df * TEF
     out <- oapply(out,c("Fish","Area"),sum)
+
     out <- oapply(out,c("Sample","Fish","Area"),sum) # Sum over congeners
     out <- oapply(out,"Fish",mean)
+
     out <- oapply(out,"Fish",mean) # Average over samples
 
     return(out)
 
     return(out)
 
   },
 
   },
Line 477: Line 482:
 
)
 
)
  
objects.store(conc_pcddf)
+
objects.store(conc_pcddf, conc_pcddf_raw)
cat("Ovariable conc_pcddf stored.\n")
+
cat("Ovariables conc_pcddf, conc_pcddf_raw stored.\n")
 
</rcode>
 
</rcode>
  

Revision as of 17:00, 25 February 2021


EU-kalat is a study, where concentrations of PCDD/Fs, PCBs, PBDEs and heavy metals have been measured from fish

Question

The scope of EU-kalat study was to measure concentrations of persistent organic pollutants (POPs) including dioxin (PCDD/F), PCB and BDE in fish from Baltic sea and Finnish inland lakes and rivers. [1] [2] [3].

Answer

Dioxin concentrations in Baltic herring.

The original sample results can be acquired from Opasnet base. The study showed that levels of PCDD/Fs and PCBs depends especially on the fish species. Highest levels were on salmon and large sized herring. Levels of PCDD/Fs exceeded maximum level of 4 pg TEQ/g fw multiple times. Levels of PCDD/Fs were correlated positively with age of the fish.

Mean congener concentrations as WHO2005-TEQ in Baltic herring can be printed out with this link or by running the codel below.

+ Show code

Rationale

Data

Data was collected between 2009-2010. The study contains years, tissue type, fish species, and fat content for each concentration measurement. Number of observations is 285.

There is a new study EU-kalat 3, which will produce results in 2016.

Calculations

Preprocess

  • Preprocess model 22.2.2017 [4]
  • Model run 25.1.2017 [5]
  • Model run 22.5.2017 with new ovariables euRaw, euAll, euMain, and euRatio [6]
  • Model run 23.5.2017 with adjusted ovariables euRaw, eu, euRatio [7]
  • Model run 11.10.2017: Small herring and Large herring added as new species [8]
  • Model rerun 15.11.2017 because the previous stored run was lost in update [9]
  • Model run 21.3.2018: Small and large herring replaced by actual fish length [10]
  • Model run 26.3.2018 eu2 moved here [11]

See an updated version of preprocess code for eu on Health effects of Baltic herring and salmon: a benefit-risk assessment#Code for estimating TEQ from chinese PCB7

+ Show code

Bayes model for dioxin concentrations

  • Model run 28.2.2017 [12]
  • Model run 28.2.2017 with corrected survey model [13]
  • Model run 28.2.2017 with Mu estimates [14]
  • Model run 1.3.2017 [15]
  • Model run 23.4.2017 [16] produces list conc.param and ovariable concentration
  • Model run 24.4.2017 [17]
  • Model run 19.5.2017 without ovariable concentration [18] ⇤--#: . The model does not mix well, so the results should not be used for final results. --Jouni (talk) 19:37, 19 May 2017 (UTC) (type: truth; paradigms: science: attack)
----#: . Maybe we should just estimate TEQs until the problem is fixed. --Jouni (talk) 19:37, 19 May 2017 (UTC) (type: truth; paradigms: science: comment)
  • Model run 22.5.2017 with TEQdx and TEQpcb as the only Compounds [19]
  • Model run 23.5.2017 debugged [20] [21] [22]
  • Model run 24.5.2017 TEQdx, TECpcb -> PCDDF, PCB [23]
  • Model run 11.10.2017 with small and large herring [24] (removed in update)
  • Model run 12.3.2018: bugs fixed with data used in Bayes. In addition, redundant fish species removed and Omega assumed to be the same for herring and salmon. [25]
  • Model run 22.3.2018 [26] Model does not mix well. Thinning gives little help?
  • Model run 25.3.2018 with conc.param as ovariable [27]

+ Show code

Initiate conc_pcddf for PFAS disease burden study

NOTE! This is not a probabilistic approach. Species and area-specific distributions should be created.

+ Show code

Initiate conc_pcddf for Goherr

  • Model run 19.5.2017 [28]
  • Model run 23.5.2017 with bugs fixed [29]
  • Model run 12.10.2017: TEQ calculation added [30]
  • Model rerun 15.11.2017 because the previous stored run was lost in update [31]
  • 12.3.2018 adjusted to match the same Omega for all fish species [32]
  • 26.3.2018 includes length and time as parameters, lengt ovariable initiated here [33]

+ Show code

⇤--#: . These codes should be coherent with POPs in Baltic herring. --Jouni (talk) 12:14, 7 June 2017 (UTC) (type: truth; paradigms: science: attack)

See also

References

  1. A. Hallikainen, H. Kiviranta, P. Isosaari, T. Vartiainen, R. Parmanne, P.J. Vuorinen: Kotimaisen järvi- ja merikalan dioksiinien, furaanien, dioksiinien kaltaisten PCB-yhdisteiden ja polybromattujen difenyylieettereiden pitoisuudet. Elintarvikeviraston julkaisuja 1/2004. [1]
  2. E-R.Venäläinen, A. Hallikainen, R. Parmanne, P.J. Vuorinen: Kotimaisen järvi- ja merikalan raskasmetallipitoisuudet. Elintarvikeviraston julkaisuja 3/2004. [2]
  3. Anja Hallikainen, Riikka Airaksinen, Panu Rantakokko, Jani Koponen, Jaakko Mannio, Pekka J. Vuorinen, Timo Jääskeläinen, Hannu Kiviranta. Itämeren kalan ja muun kotimaisen kalan ympäristömyrkyt: PCDD/F-, PCB-, PBDE-, PFC- ja OT-yhdisteet. Eviran tutkimuksia 2/2011. ISSN 1797-2981 ISBN 978-952-225-083-4 [3]