core_members {microbiome} | R Documentation |
Determine members of the core microbiota with given abundance and prevalences
core_members(x, detection = 1/100, prevalence = 50/100, include.lowest = FALSE)
x |
|
detection |
Detection threshold for absence/presence (strictly greater by default). |
prevalence |
Prevalence threshold (in [0, 1]). The required prevalence is strictly greater by default. To include the limit, set include.lowest to TRUE. |
include.lowest |
Include the lower boundary of the detection and prevalence cutoffs. FALSE by default. |
For phyloseq object, lists taxa that are more prevalent with the given detection threshold. For matrix, lists columns that satisfy these criteria.
Vector of core members
Contact: Leo Lahti microbiome-admin@googlegroups.com
A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')
data(dietswap) # Detection threshold 1 (strictly greater by default); # Note that the data (dietswap) is here in absolute counts # (and not compositional, relative abundances) # Prevalence threshold 50 percent (strictly greater by default) a <- core_members(dietswap, 1, 50/100)