Code and data: Temporal variability declines with increasing trophic levels and spatial scales in freshwater ecosystems

  • Tadeu Siqueira (Creator)
  • Charles P. Hawkins (Creator)
  • Julian Olden (Creator)
  • Jonathan Tonkin (Creator)
  • Lise Comte (Creator)
  • Victor S. Saito (Creator)
  • Thomas L. Anderson (Creator)
  • Gedimar P. Barbosa (Creator)
  • Núria Bonada (Creator)
  • Claudia C. Bonecker (Creator)
  • Miguel Cañedo-Argüelles (Creator)
  • Thibault Datry (Creator)
  • Michael B. Flinn (Creator)
  • Pau Fortuño (Creator)
  • Gretchen A. Gerrish (Creator)
  • Peter Haase (Creator)
  • Matthew J. Hill (Creator)
  • James M. Hood (Creator)
  • Kaisa-Leena Huttunen (Creator)
  • Michael J Jeffries (Creator)
  • Timo Muotka (Creator)
  • Daniel R. O'Donnell (Creator)
  • Riku Paavola (Creator)
  • Petr Paril (Creator)
  • Michael J. Paterson (Creator)
  • Christopher J. Patrick (Creator)
  • Gilmar Perbiche-Neves (Creator)
  • Luzia C. Rodrigues (Creator)
  • Susanne C. Schneider (Creator)
  • Michal Straka (Creator)
  • Albert Ruhi (Creator)

    Dataset

    Description

    Code and data to reproduce the results in Siqueira et al. (submitted) published as a Preprint (https://ecoevorxiv.org/mpf5x) The full set of results, including those made available as supplementary material, can be reproduced by running five scripts in the R_codes folder following this sequence: 00_Renv_help_reproduc.R 01_Dataprep_stability_metrics.R 02_SEM_analyses.R 03_Stab_figs.R 04_Stab_supp_m.R 05_Sensit_analysis.R and using the data available in the Input_data folder. The original raw data made available include the abundance (individual counts, biomass, coverage area) of a given taxon, at a given site, in a given year. See details here https://ecoevorxiv.org/mpf5x However, this is a collaborative effort and not all authors are allowed to share their raw data. One data set (LEPAS), out of 30, was not made available due to data sharing policies of The Ohio Division of Wildlife (ODOW). So, in code "01_Dataprep_stability_metrics.R" all data made available are imported, except the LEPAS data set. For this specific data set, code "01_Dataprep_stability_metrics.R" imports variability and synchrony components estimated using the methods described in Wang et al. (2019 Ecography; doi/10.1111/ecog.04290), diversity metrics (alpha and gamma diversity), and some variables describing the data set. A protocol for requesting access to the LEPAS data sets can be found here: https://ael.osu.edu/researchprojects/lake-erie-plankton-abundance-study-lepas Dataset owner: Ohio Department of Natural Resources – Division of Wildlife, managed by Jim Hood, Dept. of Evolution, Ecology, and Organismal Biology, The Ohio State University. Email: hood.211@osu.edu Reproducibility To improve reproducibility, I’m using the R package renv to register the versions of the R packages I use and to manage a local library that doesn’t affect the rest of my system. renv::init() is used to prepare a lockfile that records the exact versions of R packages I used in this project. Anyone who wants to reproduce the results described in the preprint can just download the whole R project (that includes code and data) and run codes from 00 to 05. I am making the whole R project folder (with everything needed to reproduce the results) available as a compressed file: Stab_R_project_full.zip
    Date made available2022
    PublisherZenodo

    Cite this