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spurdog-psat-analysis

R analysis to process PSAT data, supplement to 'Seasonal habitat use and diel vertical migration in female spurdog (Squalus acanthias Linnaeus, 1758) in Nordic waters'

https://github.com/cakloecker/spurdog-psat-analysis

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (7.7%) to scientific vocabulary

Keywords

biologging dvm ecology fish-behavior movement-ecology psat r wavelet-analysis
Last synced: 6 months ago · JSON representation ·

Repository

R analysis to process PSAT data, supplement to 'Seasonal habitat use and diel vertical migration in female spurdog (Squalus acanthias Linnaeus, 1758) in Nordic waters'

Basic Info
  • Host: GitHub
  • Owner: cakloecker
  • License: agpl-3.0
  • Language: HTML
  • Default Branch: main
  • Homepage:
  • Size: 7.41 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
biologging dvm ecology fish-behavior movement-ecology psat r wavelet-analysis
Created almost 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Seasonal habitat use and diel vertical migration in female spurdogs

This repository contains R code used for analysing PSAT data and producing figures linked to the journal article entitled 'Seasonal habitat use and diel vertical migration in female spurdogs (Squalus acanthias Linnaeus, 1758) in Nordic waters' published in Movement Ecology. It processes archival PSAT data, incl. temperature, depth, light level and accelleration, of 19 female spurdogs tagged around the fjord system around Bergen, Norway for 82 - 366 days between 2019 and 2023. Amongst others it inspects the depth-temperature niche as well as periodicity in depth use across sub-daily to seasonal cycles using continous wavelet analysis.

Contained files

  • The 00_functions.R script defines functions, i.e. used in 04_analysis_paper-supp.Rmd, for calculating weights for niche plot, plotting time series, wavelet scalogramme etc.
  • The 5s resolution archival data is read in and summarised on a level of minutes, hours and days in 01_archive-preprocessing.R.
  • Data is inspected and cleaned in 02_data-cleaning.R to remove potential tagging or capture effects.
  • A wavelet analysis is performed in 03_wavelet-analysis.R for the hourly depth timeseries and adds a 'DVM' covariate indicating the presence of a significant 24h period in this timeseries.
  • The Rmd-file 04_analysis_paper-supp.Rmd is used to inspect and perform descriptive analysis on the data as well as to generate all figures contained in the main paper and the supplement. We also added the knitted 04_analysis_paper-supp.html to include respective output.
  • We also added the associated poster BLS8-Poster_4PI-21_20240221.pdf presented at the 8th International Bio-logging Science Symposium in Tokyo, Japan 2024.

Visual Abstract

VisualAbstract

Citation

Klöcker, C. A., Albert, O., Albert, O., Ferter, K. P., Bjelland, O., Lennox, R. J., Albretsen, J., Pohl, L., Dahlmo, L. S., Queiroz, N., & Junge, C. (2024). Seasonal habitat use and diel vertical migration in female spurdogs in Nordic waters.

Owner

  • Name: Antonia Klöcker
  • Login: cakloecker
  • Kind: user
  • Location: Tromsø
  • Company: Institute of Marine Research

Marine Ecologist | PhD Student | Movement Ecology of Sharks | Biogeographic Modelling | Stability Ecology | Ecosystem-based Management

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this code, please cite the related publication as below."
preferred-citation:
  authors:
  - family-names: "Klöcker"
    given-names: "C. Antonia"
    orcid: "https://orcid.org/0000-0001-7552-7892"
    email: antonia.kloecker@hi.no
    affiliation: Institute of Marine Research, Norway
  - family-names: "Albert"
    given-names: "Ole-Thomas"
  - family-names: "Albert"
    given-names: "Ole-Thomas"
  - family-names: "Ferter"
    given-names: "Keno P."
  - family-names: "Bjelland"
    given-names: "Otte"
  - family-names: "Lennox"
    given-names: "Robert J."
  - family-names: "Albretsen"
    given-names: "Jon"
  - family-names: "Pohl"
    given-names: "Lotte"
  - family-names: "Dahlmo"
    given-names: "Lotte Svengård"
  - family-names: "Queiroz"
    given-names: "Nuno"
  - family-names: "Junge"
    given-names: "Claudia"
    orcid: "https://orcid.org/0000-0001-7709-3856"
    email: claudia.junge@hi.no
    affiliation: Institute of Marine Research, Norway
  title: "Seasonal habitat use and diel vertical migration in female spurdogs in Nordic waters"
  type: generic
  year: 2024
  keywords: 
  - biologging
  - "archival tag"
  - PSAT
  - sharks
  - DVM
  - "wavelet analysis"
  - "fast starts"
  - niche
  - fishery
  - "North-East Atlantic"

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