DOI: 10.5061/dryad.rbnzs7hds
title: Data and code for: Two dominant forms of multisite similarity decline – their origins and interpretation

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