comspat: an R package to analyze within‐community spatial organization using species combinations

Abstract

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.

High-Resolution Transect Sampling and Multiple Scale Diversity Analyses for Evaluating Grassland Resilience to Climatic Extremes

“…We used information theory models [42,43] for calculating temporal association (coincidence) between drought events and minima of species richness (for details of the methodology and calculations, see Supplementary S5 [42][43][44][45]). The significance of the observed multiple associations was tested by null models randomizing observed peaks among dates (999 complete randomizations over time).…”

Spatial phylogenetic and phenotypic patterns reveal ontogenetic shifts in ecological processes of plant community assembly

“…We conducted multivariate spatial point pattern analyses to test if the locations of a focal species are independent of the landscape of phylogenetic (or phenotypic) neighbourhood dissimilarity (Shen et al 2013, Wiegand et al 2017). To test for spatial independence, we simulated 999 realizations of a toroidal shift null model that is sometimes called random shift null model (Lotwick and Silverman 1982, Wiegand and Moloney 2014, Tsakalos et al 2022). It involves random shifts of the whole of the pattern of the focal species relative to the patterns of the heterospecifics that are left unchanged.…”