vitaliskim/msco: Multi-Species Co-Occurrence Analyses

Co-occurrence patterns are typically explored between species pairs. However, doing so inevitably ignore the possible higher-order interference and interactions among three or more species in a community. To address this, the multi-species co-occurrence (msco) index, which calculates the joint occupancy, was recently proposed (<DOI: to be added>). By reckoning with possible higher-order species interactions, the msco index can encapsulate nine possible archetypes of species co-occurrence patterns and avert the statistical type II error by examining patterns that would otherwise not be detected by any pairwise co-occurrence metrics. To dissect the effects of neutral encounter versus trait-based processes on multi-species co-occurrence and related higher-order interactions, generalised B-spline model has also been proposed (<DOI: to be added>). The R package ''msco'' implements the multi-species co-occurrence index and includes a list of functions for calculating this index for different orders, as well as testing and visualizing species co-occurrence archetypes. This package also implements the generalized B-spline model and related analyses.

install.packages("remotes")
remotes::install_github("vitaliskim/msco")