noncore_abundance {microbiome} | R Documentation |
Calculates the noncore_abundance community index.
noncore_abundance(x, detection = 0.1/100, prevalence = 50/100)
x |
|
detection |
Detection threshold for absence/presence (strictly greater by default). |
prevalence |
Prevalence threshold (in [0, 1]; strictly greater by default) |
The noncore_abundance index gives the relative proportion of rare species (ie. those that are not part of the core microbiota) in the interval [0,1]. This is the complement (1-x) of the core abundance. The rarity function provides the abundance of the least abundant taxa within each sample, regardless of the population prevalence.
A vector of indices
Contact: Leo Lahti microbiome-admin@googlegroups.com
core_abundance, rarity, diversity
data(dietswap) d <- noncore_abundance(dietswap, detection=0.1/100, prevalence=50/100)