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Clean a datras_raw object following the FishGlob workflow

Source: R/fishglob.R
clean_fishglob.Rd

Apply the main cleaning steps used in the FishGlob data workflow to a datras_raw / DATRASraw object.

Usage

clean_fishglob(x)

Arguments

x

A datras_raw object.

Value

A cleaned datras_raw object following the FishGlob workflow.

Details

This function follows the ICES DATRAS cleaning workflow used to construct the FishGlob data set, including filtering of valid hauls and species records, selected survey renaming, removal of hauls affected by incomplete bycatch recording, and species harmonization.

The cleaning steps are adapted from the FishGlob data-processing workflow described in Maureaud et al. (2021) and the associated code repository.

The function currently performs the following operations:

  • retains only valid hauls (HaulVal == "V"),

  • removes records with missing Valid_Aphia,

  • keeps only selected SpecVal codes,

  • keeps only selected DataType codes,

  • renames selected surveys to match FishGlob conventions,

  • removes hauls affected by incomplete bycatch recording for selected surveys,

  • harmonizes species names and taxonomic identifiers using correct_species().

Survey renaming currently includes:

  • "SCOWCGFS" to "SWC-IBTS"

  • "SCOROC" to "ROCKALL"

The treatment of bycatch-recording codes follows the FishGlob workflow for the NS-IBTS and BITS surveys.

References

Maureaud, A., Frelat, R., Pécuchet, L., Shackell, N., Mérigot, B., Pinsky, M. L., Amador, K., Anderson, S. C., Arkhipkin, A., Auber, A., Barri, I., et al. (2021). Are we ready to track climate-driven shifts in marine species across international boundaries? A global survey of scientific bottom trawl data. Global Change Biology, 27(2), 220–236.

FishGlob workflow code: https://github.com/fishglob/FishGlob_data/tree/main/cleaning_codes

See also

clean_datras(), correct_species()

Examples

if (FALSE) { # \dontrun{
x_clean <- clean_fishglob(x)
} # }