global {microbiome} | R Documentation |
Global indicators of the ecoystem state, including richness, evenness, diversity, and other indicators
global(x, index = "all", rarity.detection = 0.2/100, rarity.prevalence = 20/100)
x |
A species abundance vector, or matrix (taxa/features x samples)
with the absolute count data (no relative abundances), or
|
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. |
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).
A data.frame of samples x global indicators
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation('microbiome')
global, dominance, rarity, phyloseq::estimate_richness
data(dietswap) d <- global(dietswap, index='gini') # d <- global(dietswap, index='all')