MayaGans/CoreMicro: Testing Widely Used Core Microbiome Assignment Methods

Companion package to manuscript: The hypothesis of a ‘core’ community receives poor support when confronted with simulated and empirical data. Package allows for the comparison of commonly utilized methods for assignment of taxa into core or non-core groups. Package includes tools for calculation of summary statistics for taxon abundance data and visualization of subsequent core and non-core assignments. Each of the four core assignment methods included can be customized to alter thresholds required for core inclusion. This allows researchers to alter cutoffs and determine if core assignment methods agree at certain cutoffs, facilitating comparison of multiple core assignment methods. As per the companion manuscript, core assignments should only be used for biological interpretation when assignment is robust to methodology, e.g. multiple methods agree on core assignment.

install.packages("remotes")
remotes::install_github("MayaGans/CoreMicro")