low_abundance: Low Abundance Index
In microbiome/microbiome: Microbiome Analytics
View source: R/low_abundance.R
low_abundance R Documentation
Low Abundance Index
Description
Calculates the concentration of low-abundance taxa below the
indicated detection threshold.
Usage
low_abundance(x, detection = 0.2/100)
Arguments
x
phyloseq-class object
detection
Detection threshold for absence/presence
(strictly greater by default).
Details
The low_abundance index gives the concentration of species at low
abundance, or the relative proportion of rare species in [0,1].
The species that are below the indicated detection threshold are
considered rare. Note that population prevalence is not considered.
If the detection argument is a vector, then a data.frame is returned,
one column for each detection threshold.
Value
A vector of indicators.
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
See Also
core_abundance, rarity, global
Examples
data(dietswap)
d <- low_abundance(dietswap, detection=0.2/100)
microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.
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View source: R/low_abundance.R
| low_abundance | R Documentation |
Low Abundance Index
Description
Calculates the concentration of low-abundance taxa below the indicated detection threshold.
Usage
low_abundance(x, detection = 0.2/100)
Arguments
x |
|
detection |
Detection threshold for absence/presence (strictly greater by default). |
Details
The low_abundance index gives the concentration of species at low abundance, or the relative proportion of rare species in [0,1]. The species that are below the indicated detection threshold are considered rare. Note that population prevalence is not considered. If the detection argument is a vector, then a data.frame is returned, one column for each detection threshold.
Value
A vector of indicators.
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
See Also
core_abundance, rarity, global
Examples
data(dietswap)
d <- low_abundance(dietswap, detection=0.2/100)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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