Contaminant_indicators

Creating indicator data (levels/trends) for contaminants in biota on the Norwegian coast, based on both HI (previously NIFES) and NIVA data

• This is the source for the following blue mussel indicators (North Sea, Norwegian Sea and Barents Sea, resp.):

  • https://miljostatus.miljodirektoratet.no/tema/hav-og-kyst/havindikatorer/nordsjoen-skagerrak/forurensende-stoffer/forurensning-i-blaskjell-i-nordsjoen/
  • https://miljostatus.miljodirektoratet.no/tema/hav-og-kyst/havindikatorer/norskehavet/forurensende-stoffer/miljogifter-i-blaskjell-langs-kysten-av-norskehavet/
  • https://miljostatus.miljodirektoratet.no/tema/hav-og-kyst/havindikatorer/barentshavet/forurensende-stoffer/forurensning-i-blaskjell-langs-kysten-av-nordland-troms-og-finnmark/

• ...and for the following cod indicators (North Sea, Norwegian Sea and Barents Sea, resp.):

  • https://miljostatus.miljodirektoratet.no/tema/hav-og-kyst/havindikatorer/nordsjoen-skagerrak/forurensende-stoffer/forurensning-i-torsk-i-nordsjoen/
  • https://miljostatus.miljodirektoratet.no/tema/hav-og-kyst/havindikatorer/norskehavet/forurensende-stoffer/forurensning-i-kysttorsk-i-norskehavet/
  • https://miljostatus.miljodirektoratet.no/tema/hav-og-kyst/havindikatorer/barentshavet/forurensende-stoffer/forurensning-i-torsk-i-barentshavet/

• Created data (csv) are saved in the 'Data_export' folder and manually re-saved as Excel

• Note that results use

  • limits from Input_data/Grenseverdier_fra_Sylvia.xlsx
  • trend functions from 00_Trend_functions.R
    Copied to K:\Avdeling\Mar\NOG\JMGdata\Kart\Indikatorer

Overview of excel files produced on K (last versions only)

- Cod (North Sea, Norwegian Sea and Barents Sea, resp.):    
    - "K:\Avdeling\Mar\NOG\JMGdata\Kart\Indikatorer\2020\Grunnlagsdata\GaduMor_2020data_ver02.xlsx"
    - "K:\Avdeling\Mar\NOG\JMGdata\Kart\Indikatorer\2021\Norskehavet torsk\GaduMor_2021data_Norw_Sea_ver06.xlsx"
    - "K:\Avdeling\Mar\NOG\JMGdata\Kart\Indikatorer\2019\Grunnlagsdata\GaduMor_2020_withNIFES_ver06.xlsx"  

- Blue mussel (North Sea, Norwegian Sea and Barents Sea, resp.):  
    - "K:\Avdeling\Mar\NOG\JMGdata\Kart\Indikatorer\2020\Grunnlagsdata\MytiEdu_Snegl_2020_ver4.xlsx"
    - "K:\Avdeling\Mar\NOG\JMGdata\Kart\Indikatorer\2021\Norskehavet blåskjell\MytiEdu_Snegl_2020_ver6.xlsx"  
    - Barents Sea: ?

- Codes in excel sheets (see script 14 in various versions)   
    - trend: 0 = no trend calculated, 1 = zero time trend, 2 = up, 3 = down
    - Proref: Klasse 1-4 = Conc/PROREF ratio is <1, 1-2, 2-10, >10  
    - EQS and Mattrygghet: 1 = below, 2 = above  

Norskehavet - data until 2018, analysis 2019

• Script 01-04
  • Data kysttorsk NH nov. 2018.xlsx
  • GaduMor_2018_withNIFES_ver4.xlsx
• Final result:
  • 'Forurensning i blåskjell langs kysten av Norskehavet_rev3001_2019.docx' (from mail form Norman 30.01.2019)

Barentshavet - data until 2019, analysis 2020

• Script 11-14 marked "2020"
  • Cd Pb torsk lever 2006-2019 HI.xlsx
  • Kvikksølv torskefilet Bhav 2006-2019.xlsx
  • POPs torskelever Bhav 2006-2019.xlsx

Nordsjøen - data until 2019, analysis 2021

• scripts 05, 11, 12, 13, 14 marked "2021"
• For cod, we use
  • HI data (prepared using scripts 11 and 12)
  • NIVA data (prepared using script 13)
  • HI + NIVA cod data are combined in script 14
• For blue mussel and snails (only NIVA data) we use script 05

Norwegian Sea (Norskehavet) cod - data until 2020 (for HI, these data)

• script 11, 12, 14 marked '2021_NorwSea'
• script 13 marked '2021'
• Overview:
  • 11: Prepares HI data by adding lat-long, Træna (data in 2018 only) is combined with Vikna to form Helgeland
  • 12: HI data (Lofoten, Helgeland, Møre) medians and trends (using the same regression function as Milkys)
  • 13: Gets NIVA data trends (10 year trend, directly from the big excel sheet from Milkys) + medians
  • 14: Combines HI indicators (11 + 12) with NIVA indicators (13), adds Proref, EQS, food limit

Norwegian Sea (Norskehavet) blue mussel - data until 2020

• only NIVA data - script 05 modified and halfway generalized
  • 05_Bluemussel_snail_NIVA_data_2021.Rmd - contains all parts of the procedure

Barentshavet - data until 2022, analysis 2023

• Script 11-14 marked "2022"
  • Cd Pb torsk lever 2006-2022 HI.xlsx
  • Kvikksølv torskefilet Bhav 2006-2022.xlsx
  • POPs torskelever Bhav 2006-2022 inkl. PBDE HI.xlsx
• Script 11: read excel files from HI (IMR, formerly NIFES)
• Script 12: trends/levels for HI data (copy "12_Trends_NIFES_data_2020.Rmd" to new script with 2022 in the name)
• Script 13: trends/levels for NIVA data (copy "13_Get_NIVA_data_2021.Rmd" to new script with 2022 in the name)
• Script 14: combine trends/levels from HI and NIVA