Difference between revisions of "EU-kalat"

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(Initiate conc_pcddf for PFAS disease burden study)
(Initiate conc_poll)
Line 857: Line 857:
 
       mu <- tmp$conc_paramResult[tmp$Parameter=="mu_nd"]
 
       mu <- tmp$conc_paramResult[tmp$Parameter=="mu_nd"]
 
       tau <- tmp$conc_paramResult[tmp$Parameter=="tau_nd"][match(con,tmp$Compound[tmp$Parameter=="tau_nd"])]
 
       tau <- tmp$conc_paramResult[tmp$Parameter=="tau_nd"][match(con,tmp$Compound[tmp$Parameter=="tau_nd"])]
 +
      mulocat <- tmp$conc_paramResult[tmp$Parameter=="mulocat"]
 
       for(j in 1:length(con)) {
 
       for(j in 1:length(con)) {
         rnd <- exp(rnorm(1,mu[j],tau[j]))
+
         rnd <- exp(rnorm(1 , mu[j] + mulocat , tau[j]))
 
         out <- rbind(out,
 
         out <- rbind(out,
 
                     data.frame(tmp2[i,],Compound = con[j],Result = rnd)
 
                     data.frame(tmp2[i,],Compound = con[j],Result = rnd)

Revision as of 09:16, 13 March 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

Initiate euw data.frame

This code is similar to preprocess but is better and includes PFAS concentrations from op_fi:PFAS-yhdisteiden tautitaakka. It produces data.frame euw that is the EU-kalat + PFAS data in wide format and, for PFAS but not EU-kalat, a sampled value for measurements below the level of quantification.

+ Show code

Initiate conc_param using Bayesian approach

Bayesian approach for PCDDF, PCB, OT, PFAS.

  • Model run 2021-03-08 [28]
  • Model run 2021-03-08 [29] with the fish needed in PFAS assessment
  • Model run 2021-03-12 [30] using euw
  • Model run 2021-03-13 [31] with location parameter for PFAS

+ Show code

Initiate conc_poll

+ Show code

Initiate conc_pcddf for Goherr

  • Model run 19.5.2017 [32]
  • Model run 23.5.2017 with bugs fixed [33]
  • Model run 12.10.2017: TEQ calculation added [34]
  • Model rerun 15.11.2017 because the previous stored run was lost in update [35]
  • 12.3.2018 adjusted to match the same Omega for all fish species [36]
  • 26.3.2018 includes length and time as parameters, lengt ovariable initiated here [37]

+ 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]