Alpha.Diversity: Alpha diversity

In hk1785/aMiAD: Adaptive Microbiome α-diversity-based Association Analysis (aMiAD)

Alpha diversity

Description

This function creates alpha-diversity metrics.

Usage

Alpha.Diversity(phylo, metrics = c("Observed", "Shannon", "Simpson", "PD", "PE" ,"PQE"), Normalize=TRUE)

Arguments

phylo	A microbiome data in 'phyloseq' format.
metrics	A vector of alpha-diversity metrics to be created. 'Observed', 'Shannon' (Shannon, 1948), 'Simpson' (Simpson, 1949), 'PD' (Faith, 1992), 'Chao1' (Chao, 1984), 'ACE' (Chao and Lee, 1992), 'PQE' (Rao, 1982; Warwick and Clarke, 1995) and 'PE' (Allen et al., 2009) are available alpha-diversity metrics. Default is c("Observed", "Shannon", "Simpson", "PD", "PE", "PQE").
Normalize	If TRUE (default), diversity is not affected by the height of the tree. If FALSE, it is proportional to the height of the tree.

Author(s)

Hyunwook Koh

References

Koh H. An adaptive microbiome alpha-diversity-based association analysis method. Sci Rep 2018; 8(18026)

Allen B, Kon M, Bar-Yam Y. A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. Am Nat 2009; 174(2): 236-43.

Chao A. Non-parametric estimation of the number of classes in a population. Scand J Stat 1984; 11: 265-70.

Chao A, Lee S. Estimating the number of classes via sample coverage. J Am Stat Assoc 1992; 87: 210-17.

Faith DP. Conservation evaluation and phylogenetic diversity. Biol Conserv 1992; 61: 1-10.

Rao CR. Diversity and dissimilarity coefficients: a unified approach. Theor Popul Biol 1982; 21(1): 24-43.

Shannon CE. A mathematical theory of communication. Bell Syst Tech J 1948; 27: 379-423 and 623-56.

Simpson EH. Measurement of diversity. Nature 1949; 163(688).

Warwick RM, Clarke KR. New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress. Mar Ecol Prog Ser 1995; 129(1): 301-5.

Examples

library(phyloseq)
library(picante)
library(entropart)
library(vegan)

# Import example microbiome data
data(sim.biom)

# Rarefy the microbiome data using the function, rarefy_even_depth, 
# in 'phyloseq' (https://joey711.github.io/phyloseq/) due to control varying 
# total reads per sample. This implementation is recommended.
set.seed(100)
rare.biom <- rarefy_even_depth(sim.biom, rngseed=TRUE)

# Create alpha-diversity metrics 
Alpha.Diversity(sim.biom)

hk1785/aMiAD documentation built on July 16, 2022, 4:39 p.m.