Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/rare_abundance.R
Calculates the rare abundance community index.
1 2 3 4 5 6 | rare_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. |
This 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
1 2 | data(dietswap)
d <- rare_abundance(dietswap, detection=0.1/100, prevalence=50/100)
|
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