potential_analysis {microbiome}R Documentation

Bootstrapped Potential Analysis

Description

Analysis of multimodality based on bootstrapped potential analysis of Livina et al. (2010) as described in Lahti et al. (2014).

Usage

potential_analysis(x, peak.threshold = 0, bw.adjust = 1, bs.iter = 100,
  min.density = 1)

Arguments

x

Input data vector

peak.threshold

Mode detection threshold

bw.adjust

Bandwidth adjustment

bs.iter

Bootstrap iterations

min.density

minimum accepted density for a maximum; as a multiple of kernel height

Value

List with following elements:

References

See Also

plot_potential

Examples

# Example data; see help(peerj32) for details
data(peerj32)

# Log10 abundance of Dialister
x <- log10(abundances(peerj32$phyloseq)['Dialister',])

# Bootstrapped potential analysis
# In practice, use more bootstrap iterations
res <- potential_analysis(x, peak.threshold=0, bw.adjust=1,
    bs.iter=9, min.density=1)


[Package microbiome version 1.2.1 Index]