The file biota_regional_data.csv contains summary measures of status and trends for contaminants and biological effects in biota. The summary measures are used to construct the National Performance Framework Clean Seas Indicator 2020. They are also used to make regional assessments of status and trends in Scottish waters for selected contaminant and biological effect groups. The summary measures are obtained from timeseries models fitted to the contaminant and biological effect data in biota_data.csv which in turn are based on data extracted from the MERMAN database on 30 March 2022. Details of the modelling procedures can be found in the method help files for contaminants, PAH metabolites, imposex and other biological effects.

The file biota_regional_data.csv is UTF-8-BOM encoded so can be read directly into Excel, or into R using the function read.csv with the argument fileEncoding = “UTF-8-BOM”.

The data mostly relate to chemical concentrations and the variable descriptions are written with that in mind. Any differences are usually related to imposex time series and these are detailed in the notes accompanying each variable.

The variables in the file are:

series
Description: timeseries identifier
Unit:
Type: categorical
Levels: 1057
Note: links to the timeseries data in biota_data.csv

biogeographic_region
Description: biogeographic region where the monitoring station is located
Unit:
Type: categorical
Levels: Northern North Sea, Irish Sea, Minches & Western Scotland, Scottish Continental Shelf
Note: these regions are the Scottish component of the biogeographic regions used for Charting Progress 2 and for UK MS reporting purposes. There are 5 regions in Scottish waters, but there are no stations in the Atlantic North-West Approaches because it is difficult to sample. The Northern North Sea, Minches and Western Scotland and Irish Sea (Clyde & Solway) are used in the Clean Seas Indicator. The Scottish Continental Shelf is not used in the Indicator because it is difficult to get sufficient spatial coverage for regional assessments for both biota and sediment.

station
Description: monitoring station
Unit:
Type: categorical
Levels: 76
Note:

latitude
Description: station latitude
Unit: decimal degrees
Type: continuous
Range: 54.75, 60.78
Note: this is a nominal position: sampling occurs in a pre-defined area broadly centred on this position

longitude
Description: station longitude
Unit: decimal degrees
Type: continuous
Range: -6.38, -0.62
Note: this is a nominal position: sampling occurs in a pre-defined area broadly centred on this position

MSTAT
Description: type of monitoring station
Unit:
Type: categorical
Levels: RH, IH
Note: reference (RH) or impacted (IH)

last_year
Description: last year of the timeseries
Unit: y
Type: discrete
Range: 2014, 2019
Note: only timeseries with some data in the last six monitoring years are included in the assessment (i.e. 2014-2019 for the 2020 assessment)

species
Description: species
Unit:
Type: categorical
Levels: 5
Note:

• Limanda limanda: AphiaID = 127139
• Mytilus edulis: AphiaID = 140480
• Nucella lapillus: AphiaID = 140403
• Platichthys flesus: AphiaID = 127141
• Pleuronectes platessa: AphiaID = 127143

sex
Description: sex
Unit:
Type: categorical
Levels: F, M
Note: only provided for EROD where separate time series are assessed for females (F) and males (M)

matrix
Description: sample matrix (tissue)
Unit:
Type: categorical
Levels: BI, LI, LIS9, MU, SB
Note: see ICES reference codes for MATRX

determinand_group
Description: contaminant or biological effect group
Unit:
Type: categorical
Levels: Metals, PAH parent compounds, PAH metabolites, Polybrominated diphenyl ethers, Polychlorinated biphenyls, Imposex, Biological effects (other)
Note:

determinand
Description: contaminant or biological effect
Unit:
Type: categorical
Levels: 46
Note: see ICES reference codes for PARAM

metoa
Description: method of chemical analysis
Unit:
Type: categorical
Levels: FLM-SS
Notes:

• see ICES reference codes for METOA
• only provided for PAH metabolites where the assessment concentrations depend on the method of analysis

basis
Description: basis of the assessment
Unit:
Type: discrete
Levels: dry weight (D), lipid weight (L) or wet weight (W)
Note:

unit
Description: unit of measurement
Unit:
Type: discrete
Levels: pmol/min/mg protein, st, ug/kg, ug/ml
Note:

mean_last_year
Description: the fitted mean concentration (or equivalent for biological effects) in last_year
Unit: see unit column
Type: continuous
Range: 0, 287602
Note:

BAC_type
Description: the name of the Background Assessment Concentration (BAC) or equivalent
Unit:
Type: categorical
Levels: BAC
Note:

BAC_value
Description: the value of the BAC (or equivalent)
Unit: see unit column
Type: continuous
Range: 0.065, 63000
Note: more details can be found in the help files on assessment criteria for contaminants in biota and biological effects

status_BAC
Description: the log ratio of mean_last_year to the BAC
Unit: dimensionless
Type: continuous
Range: -2.8, 6.65
Notes:

• contaminants, PAH metabolites and EROD: status_BAC = log(mean_last_year / BAC_value), with a value above / below 0 indicating that the fitted mean concentration in the last monitoring year is above / below the BAC; the standard error is given by status_se
• imposex: status_BAC = sqrt(mean_last_year / BAC_value), with a value above / below 1 indicating that the estimated mean VDS in the last monitoring year is above / below the BAC; the standard error is given by status_se / sqrt(BAC_value)

EAC_type
Description: the name of the Environmenal Assessment Criterion (EAC) or equivalent
Unit:
Type: categorical
Levels: EAC, FEQG, QSsp
Notes:

• EAC = Environmental Assessment Criterion
• FEQG = Federal Environmental Quality Guideline
• QSsp = Quality Standard secondary poisoning
• the Maximum Permissible Concentration (MPC) used for the Clean Seas Indicator is a health threshold; see HAC_type

EAC_value
Description: the value of the EAC (or equivalent)
Unit: see unit column
Type: continuous
Range: 2, 2400
Note: more details can be found in the help files on assessment criteria for contaminants in biota and biological effects

status_EAC
Description: the log ratio of mean_last_year to the EAC
Unit: dimensionless
Type: continuous
Range: -8.1, 2.7
Notes:

• contaminants, PAH metabolites and EROD: status_EAC = log(mean_last_year / EAC_value), with a value above / below 0 indicating that the fitted mean concentration in the last monitoring year is above / below the EAC; the standard error is given by status_se
• imposex: status_EAC = sqrt(mean_last_year / EAC_value), with a value above / below 1 indicating that the estimated mean VDS in the last monitoring year is above / below the EAC; the standard error is given by status_se / sqrt(EAC_value)

HAC_type
Description: the name of the (human) Health Assessment Criterion (HAC)
Unit:
Type: categorical
Levels: MPC, QShh
Notes:

• MPC = Maximum Permissible Concentration
• QShh = Quality Standard human health
• there are no HAC for biological effects (as one might expect)

HAC_value
Description: the value of the HAC
Unit: see unit column
Type: continuous
Range: 30.5, 9146
Note: more details can be found in the help file on assessment criteria for contaminants in biota

status_HAC
Description: the log ratio of mean_last_year to the HAC
Unit: dimensionless
Type: continuous
Range: -4.1, 0.91
Note: status_HAC = log(mean_last_year / HAC_value), with a value above / below 0 indicating that the fitted mean concentration in the last monitoring year is above / below the HAC; the standard error is given by status_se

status_profile
Description: the log of mean_last_year standardised to a common basis
Unit: log unit
Type: continuous
Range: -1.5, 6.44
Note: these values are used to investigate concentration profiles of selected PAH parent compounds, Polybrominated diphenyl ethers and Polychlorinated biphenyls, and have been standardised to the basis given in basis_profile

basis_profile
Description: the basis of status_profile
Unit:
Type: categorical
Levels: dry weight (D) or lipid weight (L)
Note:

status_se
Description: the standard error of log mean_last_year
Unit:
Type: continuous
Range: 0.025, 2.06
Notes:

• contaminants, PAH metabolites and EROD: this is the also the standard error of status_BAC, status_EAC, status_HAC and status_profile
• imposex: this is the standard error of sqrt(mean_last_year)

trend
Description: the estimated yearly change in log concentration in the last 20 years
Unit:
Type: continuous
Range: -45, 62
Notes:

• contaminants, PAH metabolites and EROD: trend can loosely be interpreted as the percentage annual change in concentration in the last 20 years assuming the trend in concentration is log-linear; values below / above 0 indicate a decreasing / increasing trend
• imposex: trend is the estimated odds ratio of the VDS of an individual being above the EAC in one year relative to the previous year; values below / above 1 indicate a decreasing / increasing trend

trend_se
Description: the standard error of trend
Unit:
Type: continuous
Range: 0.014, 33.1
Note: