Skip to contents

Add stations to contaminant data from an ICES extraction

Source: R/import_functions.R
add_stations.Rd

Adds the station name and station code to the contaminant data from an ICES extraction. This is done by either matching the station names submitted with the data to the station dictionary, or by matching the sample coordinates to the station dictionary, or a combination of both.

Usage

add_stations(data, stations, info)

Arguments

data

A data frame with the contaminant data from an ICES extraction

stations

A data frame with the ICES station dictionary

info

A HARSAT information list which must contain the elements purpose, compartment, and add_stations. The latter is a list of control parameters supplied through control_default or control_modify which control how the station matching is achieved. See details.

Value

A data frame containing the contaminant data augmented by variables containing the station code and the station name

Details

info$add_stations is a list of control parameters that modify the station matching process. The default values depend on info$purpose and are given at the end of this section. The elements of info$add_stations are:

  • method: a string specifying whether the stations are matched by "name", "coordinates", or "both". If info$purpose is "custom", method is restricted to either "name" (the default) or "coordinates". If info$purpose is "OSPAR", "HELCOM" or "AMAP", then method is set to "both" by default and stations are matched by name or coordinates according to rules specified by OSPAR, HELCOM or AMAP data providers. Currently, stations are matched by name for Denmark, France (biota and water - all years; sediment 2009 onwards), Germany (biota HELCOM - all years; biota OSPAR, biota AMAP, sediment, water 2023 onwards), Ireland, Norway, Portugal, Spain (2005 onwards), Sweden, The Netherlands (2007 onwards), United Kingdom. All other stations are matched by coordinates.

  • area: a vector of strings containing one or more of "OSPAR", "HELCOM" and "AMAP"; this restricts the stations to those in the corresponding convention area(s); NULL matches to all stations in the station dictionary

  • datatype: a logical specifying whether the stations should be restricted to those with an appropriate datatype. If TRUE, a contaminant measurement in biota (for example) will only be matched to stations with station_datatype containing the string "CF". Similarly, a biological effect measurement in biota will only be matched to stations with station_datatype containing the string "EF"

  • temporal: a logical with TRUE indicating that stations should be restricted to those with station_purpm containing the string "T"

  • governance_type: a string: "none", "data", "stations" or "both" which controls how data and station governance are used in station matching. Data governance information is found in data$is_amap_monitoring, data$is_helcom_monitoring and data$is_ospar_monitoring which are based on the monitoring programme (MPROG) information provided in submissions to the ICES data base. Station governance information is found in stations$station_programgovernance which is provided by data submitters to the ICES station dictionary. governance_type is used in conjunction with governance_id (see below) as follows:

    • "none" means that data and station governance are both ignored

    • "data" means that matching will be restricted by data governance but not station governance. For example, if governance_id == "HELCOM", then data will only be matched to a station if is_helcom_monitoring == TRUE (with all stations considered regardless of station governance). If governance_id takes multiple values, e.g. c("OSPAR", "AMAP"), then data will only be matched to a station if e.g. either is_ospar_monitoring == TRUE or is_amap_monitoring == TRUE.

    • "stations" means that matching will be restricted by station governance but not by data governance. For example, if governance_id == "HELCOM", then the stations will be restricted to those where station_programgovernance contains "HELCOM" (with all data considered regardless of data governance). If governance_id takes mulitple values, e.g. c("OSPAR", "AMAP"), then the stations will be restricted to those where station_programgovernance contains e.g. either "OSPAR" or "AMAP".

    • "both" uses both data and station governance. For example, if governance_id == "HELCOM" then data will only be matched if is_helcom_monitoring == TRUE and the candidate stations will be restricted to those where station_programmegovernance contains "HELCOM". If governance_id contains multiple values, e.g. c("OSPAR", "AMAP"), then data with is_ospar_monitoring == TRUE and is_amap_monitoring == FALSE are matched to stations where station_programgovernance contains "OSPAR"; data with is_ospar_monitoring == FALSE and is_amap_monitoring == TRUE are matched with stations where station_programgovernance contains "AMAP"; but measurements where is_ospar_monitoring == TRUE and is_amap_monitoring == TRUE are matched to stations where station_programgovernance contains either "OSPAR" or "AMAP".

  • governance_id: used in conjunction with governance_type. If governance_type == "none", then governance_id should be set to NULL. Otherwise, governance_id must be a vector of strings containing one or more of "AMAP", "HELCOM" and "OSPAR".

  • grouping: a logical with TRUE indicating that stations will be grouped into meta-stations as specified by stations$station_asmtmimeparent which is provided by data submitters to the ICES station dictionary. Defaults to FALSE apart from when info$purpose == "OSPAR".

  • check_coordinates: a logical with TRUE indicating that, when stations are matched by name, the sample coordinates must also be within the station geometry. Not implemented yet, so defaults to FALSE.

The default values of info$add_stations depend on info$purpose as follows:

  • "AMAP": list(method = "both", area = "AMAP", datatype = FALSE, temporal = FALSE, governance_type = "none", governance_id = NULL, group = FALSE, check_coordinates = FALSE)

  • "HELCOM": list(method = "both", area = "HELCOM", datatype = FALSE, temporal = FALSE, governance_type = "none", governance_id = NULL, group = FALSE, check_coordinates = FALSE)

  • "OSPAR": list(method = "both", area = "OSPAR", datatype = TRUE, temporal = TRUE, governance_type = "both", governance_id = c("OSPAR", "AMAP"), group = TRUE, check_coordinates = FALSE)

  • "custom": list(method = "name", area = NULL, datatype = FALSE, temporal = FALSE, governance_type = "none", governance_id = NULL, group = FALSE, check_coordinates = FALSE)