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Data and code for: Two dominant forms of multisite similarity decline – their origins and interpretation

Cite this dataset

Deane, David (2022). Data and code for: Two dominant forms of multisite similarity decline – their origins and interpretation [Dataset]. Dryad. https://doi.org/10.5061/dryad.rbnzs7hds

Abstract

Contains data and code for peer review of the draft manuscript 'Two dominant forms of multisite similarity decline – their origins and interpretation' in review at Ecology and Evolution (Manuscript ID: ECE-2022-10-01523).

The data are a subset of the metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES" database reported in A global database for metacommunity ecology, integrating species, traits, environment and space by A. Jeliazkov, D. Mijatovic, S. Chantepie, N. Andrew, R. Arlettaz, L. Barbaro, et al. Scientific Data 2020 Vol. 7 Issue 1 Pages e6. Data were downloaded from the Figshare repository: https://doi.org/10.6084/m9.figshare.c.4459637 on 9 Nov 2021.

Methods

The 80 datasets in the original database were first filtered to select only abundance (or similar quantitative) estimate of species in each site. This yielded 69 datasets. Several of these were experimental treatments (e.g., logged vs unlogged) or were time series re-surveys of the same sites. Because our interest was in structures within a single habitat type and point in time, these datasets were subdivided into discrete units. In total, this (coincidentally) resulted in 80 datasets for analysis. These data are in the cestesAbSplit.RData object, with matching metadata in mdat_cestesSplit.csv.

cestesAbSplit.RData - a list containing the sites x species matrices for the 80 datasets used for analysis. 

mdat_cestesSplit.csv - matching metadata for the 80 datasets (name and source of the data, taxonomic grouping, kingdom, realm, extent in km2, total sites, total species. *This file is only included to run the R analysis*. Data are repeated, with full description in Appendix S5 (see Readme tab). 

Appendix S5 Metadata.xlsx - metadata and values of standardized effect sizes from empirical analyses with ReadMe file explaining each field. The effect sizes were calculated using the scripts in Rcode_form_of_zeta.R (requires R_function.R) and can be reproduced by running the scripts (some very small numerical differences might occur in simulated values based on randomisation). 

Usage notes

To rerun the analysis in R, simply load all files into the working directory and run R scripts "Rcode_form_of_zeta.R" and 'R_function.R'. The code calls each of the data sources when needed and assumes they are in the working directory.

  • cestesAbSplit.RData - RData object containing the 80 datasets used for analysis 
  • mdat_cestesSplit.csv - metadata used in empirical analyses (called from Rcode script)
  • Appendix S5 Metadata.xlsx - metadata and values of standardized effect sizes from empirical analyses
  • R_function.R - set of custom functions used in simulations and in analysis (source this file before running Rcode_form_of_zeta.R)
  • Rcode_form_of_zeta.R - R code used to analyse the data
  • sad.lst.RData - list of simulated species abundance distributions called in analysis

Funding

Australian Research Council, Award: DP200101680

National Research Foundation of South Africa, Award: 89967