External data file formats

These are the column headers for CSV-formatted external data files. The files should be UTF-8 encoded.

Missing values should be supplied as blank cells, not as NA or some other code.

Other columns can also be supplied, but will typically be ignored.

Contaminant data

The data file has one row for each measurement.

column name	type	mandatory	comments
country	character	yes	identifies the source of the data; for international assessments this is typically the country of origin, but for national assessments it could be a local monitoring authority must match country in station file no missing values
station_code	alphanumeric	yes	the station (code) where the sample was collected must match station_code in station file no missing values
station_name	alphanumeric	yes	the station (name) where the sample was collected; this is often more intuitive to a user than station_code must match station_name in station file no missing values
sample_latitude	numeric (decimal degrees)		need not match station_latitude in station file
sample_longitude	numeric (decimal degrees)		need not match station_longitude in station file
year	integer	yes	monitoring year doesn’t necessarily match date since a sampling season running from e.g. November 2021 to May 2022 might all be considered the 2022 monitoring year no missing values
date	date: use ISO 8601 standard e.g. 2023-06-28		sampling date
depth	numeric (m)		sediment: assumed to be a surface sediment sample with depth being the lower depth of the grab water: assumed to be a surface water sample with depth being the upper depth of the sample biota: not used, so can supply whatever is useful (or omit)
species	character	yes (biota)	latin name which must match a submitted_species in the species reference table
sex	character		see ICES reference codes for SEXCO required for EROD assessments desirable if sex is used to subdivide timeseries (see subseries)
n_individual	integer		number of pooled individuals in the sample required for imposex assessments
subseries	character		used to split up timeseries by e.g. sex or age for example: juvenile, adult_male, adult_female missing values indicate that all records in a timeseries will be considered together (no subdivision)
sample	alphanumeric	yes	links measurements made on the same individuals (biota), in the same sediment grab or in the same water sample no missing values
determinand	character	yes	must match values in determinand reference table most will be in ICES reference codes for PARAM but can provide own values no missing values
matrix	character	yes	see ICES reference codes for MATRX
basis	character	yes (biota & sediment)	W, D or L no missing values for chemical measurements in biota or sediment not mandatory for water where basis is always taken to be W
unit	character	yes	see ICES reference codes for MUNIT no missing values
value	numeric	yes	no missing values
censoring	character		typically D, Q or < indicating a value less than the limit of detection, less than the limit of quantification, or some other (non-specified) less than a missing value indicates that the measurement is not a less-than (i.e. is uncensored)
limit_detection	numeric		same unit as value
limit_quantification	numeric		same unit as value
uncertainty	numeric		analytical uncertainty in the measurement same unit as value
unit_uncertainty	character		SD, U2 or % if uncertainty is present, unit_uncertainty must also be present
method_pretreatment	character		use ICES reference codes for METPT
method_analysis	character		use ICES reference codes for METOA required for bile metabolite measurements
method_extraction	character		use ICES reference codes for METCX required for sediment normalisation (typically for metals)

Station data

The station file has one row for each station.

current_name	Type	mandatory	Comments
OSPAR_region	character		the regional columns can be called anything (and are optional) for OSPAR assessments, use OSPAR_region and OSPAR_subregion for HELCOM assessments use HELCOM_subbasin, HELCOM_L3 and HELCOM_L4 for other assessments any regional columns must be explicitly identified when calling read_data using the control argument
OSPAR_subregion	character		see above
country	character	yes	no missing values
station_code	alphanumeric	yes	no missing values
station_name	character	yes	no missing values
station_longname	character		typically a more intuitive name for the station than station_name
station_latitude	numeric (decimal degrees)	yes	no missing values
station_longitude	numeric (decimal degrees)	yes	no missing values
station_type	character		see ICES reference codes for MSTAT typically B (baseline), RH (representative) or IH (impacted)
waterbody_type	character		see ICES reference codes for WLTYP typically a code indicating transitional (estuarine) waters, coastal waters or open sea