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

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.