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Species counts, depth and latitude from NOAA's annual groundfish trawl surveys (1999-2018) in the Northeast Pacific

Citation

Anderson, Marti; Walsh, Daniel; Sweatman, Winston; Punnett, Andrew (2022), Species counts, depth and latitude from NOAA's annual groundfish trawl surveys (1999-2018) in the Northeast Pacific, Dryad, Dataset, https://doi.org/10.5061/dryad.c59zw3rbp

Abstract

These data are provided as Supporting Information to the article appearing in Ecology Letters entitled: "Non-linear models of species’ responses to environmental and spatial gradients".

The article describes a parametric framework for modelling species-environment non-linear relationships, including an R package ('senlm'), available on Github: https://primer-e.github.io/senlm. The framework has two components: (i) a non-linear parametric mathematical function to model the mean species response along a gradient that allows asymmetry, flattening/peakedness or bimodality; and (ii) a statistical error distribution tailored for ecological data types, allowing intrinsic mean-variance relationships and zero-inflation. The article demonstrates the utility of this model framework, highlighting the flexibility of a range of possible mean functions and a broad range of potential error distributions, in analyses of fish species’ abundances along a depth gradient, and how they change over time and at different latitudes.

A vignette in R ('Vignette_S1.pdf') and associated R code ('Rcode_S1.txt') that utilise this dataset to demonstrate the senlm modeling framework are available as Supporting Information to the article.

Methods

These data are comprised of an excerpt from the West Coast Groundfish Bottom Trawl (Slope and Shelf Combination) Survey, conducted annually by the National Oceanic and Atmospheric Association (NOAA)’s Northwest Fisheries Science Center (NOAA Fisheries, NWFSC/FRAM, 2725 Montlake Blvd. East, Seattle, WA 98112) and available online (https://www.nwfsc.noaa.gov/data/map).

The data contain the following variables: trawl ID, area swept, latitude, depth, project name, and counts of abundances for each of 310 fish species for the years 1999-2018.

This excerpt was created by filtering the raw NOAA data as follows: (a) we removed trawls not marked as ‘satisfactory’; (b) we removed trawls whose swept area was either missing (recorded as ‘NA’), or was outside the interquartile range (1.57 – 2.01 ha) to ensure commensurability; (c) we removed trawls not belonging to one of the following projects: ‘Groundfish Slope Survey’, ‘Groundfish Shelf Survey’ or ‘Groundfish Shelf and Slope Combination Survey’; (d) we retained only the years 1999 – 2018; and (e) we retained only fish species that occurred in at least one trawl and that were identified to species level.

Note: In accordance with Dryad's policy regarding the provision of greographic coordinates, the column containing longitude in decimal degrees ("longitude_hi_prec_dd") has been omitted from this dataset to avoid unintended consequences for at-risk species - specifically those fish species listed by the IUCN as "Near Threatened", "Vulnerable", "Endangered" or "Critically Endangered".

Usage Notes

The data are provided in *.csv format. No special programs or software are required to open the data file. Data can be viewed in a text editor, or can easily be imported into any spreadsheet program, such as Excel.

Funding

Royal Society of New Zealand Marsden Grant, Award: 19-MAU-145