alphaDiversity: Calculate the alpha diversity indices

In otuSummary: Summarizing OTU Table Regarding the Composition, Abundance and Beta Diversity of Abundant and Rare Biospheres

Calculate the alpha diversity indices

Description

This function will calculate the alpha diversity indices for the total, abundant and rare biospheres.

Usage

alphaDiversity(otutab, siteInCol = FALSE, taxhead = NULL, threshold = 1,
    percent = FALSE, write = FALSE, ...)

Arguments

otutab	A OTU table of microbial community, which can contain a taxonomic column (if siteInCol) or row (if site in rows). The OTU table should be given in numeric (integer) counts.
siteInCol	Logical, if "TRUE", the OTU table contains samples in columns and taxa in rows. By default in this function, the siteInCol is FALSE, meaning the samples in rows.
taxhead	Character, specify the header of taxonomy if there is a taxonomic column in your data. By default this argument is NULL.
threshold	Numeric, the threshold of relative abundance upon which the rare biosphere will be subset.
percent	Logical, whether the input OTU table are given in relative abundance. FALSE means that the input OTU table is in numeric counts.
write	Logical, if TRUE, the result will be written out in a Tab separated data frame.
...	arguments to be passed to write.table().

Details

The rare biosphere is defined by the relative abundance cutoffs (which is the "threshold" argument in this function) (Lynch and Neufeld, 2015). This update (version 0.1.2) removed the dependencies on functions "specnumber", "diversity" and "estimateR" from the R package "vegan" (Oksanen et al, 2013), and removed the "gini" function from package 'reldist' (http://www.stat.ucla.edu/~handcock/RelDist).

Value

The function will return a list of length 3, including indices of observed, shannon, simpson, invsimpson, chao1, chao2, and evenness.

allBio	The alpha diversity indices for the whole community
abundBio	The alpha diversity indices for the abundant population
rareBio	The alpha diversity indices for the rare biosphere

Author(s)

Sizhong Yang <[e-mail]>

References

Lynch MDJ, Neufeld JD (2015). Ecology and exploration of the rare biosphere. Nature Reviews Microbiology 13: 217-229.

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB et al (2013). vegan: Community Ecology Package. R package version 2.0-7. http://CRAN.R-project.org/package=vegan.

Examples

data(otumothur)

test1 <- alphaDiversity(otutab = otumothur, siteInCol = TRUE,
    taxhead = "taxonomy", threshold = 1, percent = FALSE, write = FALSE)

test2 <- alphaDiversity(otutab = otumothur[,-ncol(otumothur)], siteInCol = TRUE,
    taxhead = NULL, threshold = 1, percent = FALSE, write = FALSE)

otuSummary documentation built on Sept. 8, 2023, 6:05 p.m.