low_abundance: Low Abundance Index
In microbiome: Microbiome Analytics
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
View source: R/low_abundance.R
Description
Calculates the concentration of low-abundance taxa below the
indicated detection threshold.
Usage
1
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
1
2
data(dietswap)
d <- low_abundance(dietswap, detection=0.2/100)
microbiome documentation built on Nov. 8, 2020, 5:08 p.m.
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.
Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/low_abundance.R
Description
Calculates the concentration of low-abundance taxa below the indicated detection threshold.
Usage
1 | 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
1 2 | 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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.