global {microbiome} | R Documentation

## Global Ecosystem State Variables

### Description

Global indicators of the ecoystem state, including richness, evenness, diversity, and other indicators

### Usage

    global(x, index = "all", rarity.detection = 0.2/100,
      rarity.prevalence = 20/100)

### Arguments

`x` | A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or `phyloseq-class` object
`index` | Default is ‘NULL’, meaning that all available global indices will be included. For specific options, see details.
`rarity.detection` | Detection threshold for determining rare taxa.
`rarity.prevalence` | Prevalence threshold for determining rare taxa.

### Details

This function returns global indices of the ecosystem state using default choices for detection, prevalence and other parameters for simplicity and standardization. See the individual functions for more options. All indicators from the richness, diversities, evenness, dominance, and rarity functions are available. Some additional measures, such as Chao1 and ACE are available via `estimate_richness` function in the phyloseq package but not included here. The index names are given the prefix richness_, evenness_, diversities_, dominance_, or rarity_ in the output table to avoid confusion between similarly named but different indices (e.g. Simpson diversity and Simpson dominance).

### Value

A data.frame of samples x global indicators

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

See citation('microbiome')

### See Also

global, dominance, rarity, phyloseq::estimate_richness

### Examples

    data(dietswap)
    d <- global(dietswap, index='gini')
    # d <- global(dietswap, index='all')

[Package microbiome version 1.0.2 Index]