Legacy function to extract ERS information from detailed Norwegian fisheries logbooks from Excel files on the IMR server

Extracts ERS information from Excel files on the IMR server.

Usage

extractLogbook(
  path,
  species,
  method = "start",
  language = "norwegian",
  subspecies = FALSE,
  remove.sensitive = TRUE,
  print.filename = FALSE
)

Arguments

path

Character argument defining the path to the folder where data are located

species

Character argument defining the species. Species names can be given in Norwegian, English or Latin. Species names are sampled from FDIRcodes$speciesCodes.

method

Character argument specifying the method for position, time and depth extraction. Alternatives: "start" takes the reported start values, "end" extracts the reported end values and "average" takes an average of start and end values.

language

Character argument in lower case specifying the language of species names in the returned data table. Alternatives: "norwegian", "english", or "latin", The species names are acquired from FDIRcodes$speciesCodes.

subspecies

Logical. Should NS codes (i.e. species sub-categories) be used to translate species names? If FALSE, FAO codes are used leading to actual species names.

remove.sensitive

Logical indicating whether the function should remove sensitive data fields.

print.filename

Logical indicating whether the file name should be printed to console while processing. Useful for debugging.

Value

A data.table containing following columns:

• "year" year of the fishing event.

• "month" month of the fishing event.

• "lon" longitude coordinate for the fishing event in decimal degrees acquired based on the method argument.

• "lat" latitude coordinate for the fishing event in decimal degrees acquired based on the method argument.

• "gearId" reported gear ID (REDSKAP_NS) in the .psv files

• "gear" gear name translated from gearId based on FDIRcodes$gearCodes.

• "gearCat" gear category translated from gearId based on FDIRcodes$gearCodes.

• "fishTime" reported fishing time.

• "effort" reported fishing effort (number of hooks etc.)

• "dist" reported fishing distance in meters.

• "depth" reported fishing depth in meters acquired based on the method argument.

• "targetSpFAO" target species based on the FAO definition: the species with highest mass in catch.

• "targetSpRep" target species reported by the fishermen.

• "species" reported catch species based on the species, language and subspecies arguments. Translated from the species ID (FANGSTART_NS or FANGSTART_FAO) based on FDIRcodes$speciesCodes.

• "mass" reported catch of the species in kilograms.

Details

This function extracts information from the Norwegian fisheries logbooks provided in the .psv format on the IMR server. Note that these data are confidential and protected by the Norwegian Privacy Act (personvernloven). Keep the data on the server or in another safe place (not on the cloud). Do not send the input data around on email. The remove.sensitive argument can be used to disconnect the output from the confidential input data. This output can be distributed to people who have not signed the confidentiality statement (students, ICES colleagues, etc.) also using email. The data are property of the Norwegian Directorate of Fisheries and you should consult them if you plan to publish any parts of the dataset.

Note that the structure of logbook files is not confidential and therefore this function can be distributed freely. The data required by the function cannot (do not send those data on email).

There are many duplicate records in the logbook files on the server. This function removes these duplicates automatically, but the process takes time and is not very controlled. If you want to be sure about the data you include, copy the desired files to another folder (in a safe place) and run the function for that folder.

See also

Other ERS functions: downloadERS(), extractERS()

Author

Mikko Vihtakari (Institute of Marine Research)