rare_members: Rare Taxa
In microbiome: Microbiome Analytics

Description Usage Arguments Details Value Author(s) References See Also Examples

Determine members of the rare microbiota with given abundance and prevalence threshold.

1	rare_members(x, detection = 1/100, prevalence = 50/100, include.lowest = FALSE)

`x`	`phyloseq-class` object
`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 less prevalent than the given prevalence threshold. Optionally, never exceeds the given abundance threshold (by default, all abundanecs accepted). For matrix, lists columns that satisfy these criteria.

Vector of rare taxa

Leo Lahti microbiome-admin@googlegroups.com

To cite the microbiome R package, see citation('microbiome')

core_members

data(dietswap)
# Detection threshold: the taxa never exceed the given detection threshold
# Prevalence threshold 20 percent (strictly greater by default)
a <- rare_members(dietswap, detection=100/100, prevalence=20/100)