aor: Calculate Abundance-occupancy_relationship

In pctax: Professional Comprehensive Omics Data Analysis

Calculate Abundance-occupancy_relationship

Description

Calculate Abundance-occupancy_relationship

Plot a AOR

Usage

aor(otutab, ...)

## S3 method for class 'data.frame'
aor(
  otutab,
  top_r = 0.7,
  ocup_n = ceiling(0.8 * ncol(otutab)),
  special_n = ceiling(0.1 * ncol(otutab)),
  ...
)

## S3 method for class 'AOR'
plot(x, ...)

Arguments

otutab	otutab
...	add
top_r	percentage of top relative abundance
ocup_n	percentage of top occupied
special_n	how many occupancy define as specialists
x	AOR object

Value

AOR

ggplot

References

Barberán, A., Bates, S. T., Casamayor, E. & Fierer, N. (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities.

Examples

data(otutab, package = "pcutils")
aor(otutab) -> AOR
plot(AOR)

pctax documentation built on May 29, 2024, 10:03 a.m.