core_abundance {microbiome} | R Documentation |
Calculates the community core abundance index.
core_abundance( x, detection = 0.1/100, 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. |
The core abundance index gives the relative proportion of the core species (in [0,1]). The core taxa are defined as those that exceed the given population prevalence threshold at the given detection level.
A vector of core abundance indices
Contact: Leo Lahti microbiome-admin@googlegroups.com
rarity
data(dietswap) d <- core_abundance(dietswap, detection=0.1/100, prevalence=50/100)