DOI: 10.5061/dryad.7h44j0zw6
title: comspat: an R package to analyze within-community spatial organization using species combinations

description: The diversity of species combinations observable in sampling units
 reflects a species’ uneven distribution and preference for specific
 abiotic and biotic conditions – a phenomenon most commonly expressed in
 terms of ecological assembly rules of plant communities and other sessile
 organisms (e.g., subtidal algae, invertebrates and coral reefs). We
 present comspat, a new R package that uses grid or transect data sets to
 measure the number of realized (observed) species combinations (NRC) and
 the Shannon diversity of realized species combinations (compositional
 diversity; CD) as a function of spatial scale. NRC and CD represent two
 measures from a model family developed by Pál Juhász-Nagy based on
 Information Theory. Classical Shannon diversity measures biodiversity
 based on the number and relative abundance of species, whereas the
 specific version of Shannon diversity presented here characterizes
 biodiversity and provides information on species coexistence
 relationships; both measures operate at fine-scale within the sampling
 unit or within the community. comspat offers two commonly applied null
 models, complete spatial randomness and random shift, to disentangle the
 textural, intraspecific, and interspecific effects on the observed spatial
 patterns. Combined, these models assist users in detecting and
 interpreting spatial associations and inferring assembly mechanisms. Our
 open-sourced package provides a vignette that describes the method and
 reproduces the figures from this paper to help users contextualize and
 apply functions to their data.
description: We
 introduce comspat, which calculates the number of realized
 species combinations (NRC) and diversity of species combinations (called
 compositional diversity; CD) as a function of the sampling
 scale. comspat provides two main functions: one to calculate
 results (‘comspat’) and one to assist in their interpretation
 (‘comspat_plot’). The package includes five data sets to
 demonstrate its operation; we used three in-text (see Tsakalos et al.
 2022) and present the remaining in the vignette.
 <em>Data included in the
 manuscript</em> The
 manuscript used three grid data sets (64 × 64 sampling units), including:
 one simulation (grid_patchy_associated) and two simulation derivatives
 (grid_random and grid_patchy_no_isc) produced by randomization. We used a spatially
 explicit individual-based simulation model (PATPRO) to create the
 grid_patchy_associated data set; this simulation represents a
 realistic grid community pattern featuring interspecific species
 associations and environmental responses (Bartha et al. 1998, Czaran,
 1993). RS and CSR randomizations of the original simulation
 (grid_patchy_associated) produced
 the grid_n_isc and grid_random data sets. The grid_n_isc data set maintains species-level patterns;
 however, the interspecific relationships are randomized.
 The grid_random data set shows random species distribution, no
 intraspecific autocorrelations and no interspecific spatial associations.
 For additional details, please see the package
 vignette. <em>Data not included in the
 manuscript, </em><em>but included in the package at the time
 of submission</em> The package
 contains two transects with real data sampled in open sand grassland in
 Hungary (Bartha et al. 2008). These real transect data sets were from
 Bartha et al.'s (2008) long-term study on the effect of climate
 change on the interannual variability of grassland communities. The
 transect data sets represent: (1) the spatial pattern data of frequent
 species (species with more than 25 presences along the transect) selected
 as a threshold from standard textbooks; tran_grass_s), and (2) the spatial pattern data of plant
 functional types (PFT; in this case data of species which belong to the
 same functional groups were merged; tran_grass_t). These data represent the same transect and
 same community; however, when merging species, all rare species were also
 considered within the PFT. For simplicity, we have only selected a 25 m
 example with a very typical pattern; this extent (transect length) is
 already representative of the community pattern.
 <strong>References</strong>
 Tsakalos, J. L. et al. 2022.
 comspat: an R package to analyze within-community spatial
 organization using species combinations. – Ecography, doi:
 10.1111/ecog.06216 Bartha, S.
 et al. 2008. Will interannual variability in sand grassland communities
 increase with climate change?. –Community Ecol., 9: 13–21.
description: The most recent version of the comspat
 package can be accessed from github's public repository
 (https://github.com/jamestsakalos/comspat). The authors also plan to
 submit the package to The Comprehensive R Archive Network.