hill_div: Hill numbers computation

In hilldiv: Integral Analysis of Diversity Based on Hill Numbers

Description

Compute neutral or phylogenetic Hill numbers from a single sample (vector) or count table (matrix). Hill numbers or numbers equivalents of diversity indices are diversity measures that compute diversity in effective number of OTUs, i.e. the number of equally abundant OTUs that would be needed to give the same value of diversity.

Usage

hill_div(count, qvalue, tree, dist)

Arguments

count	A vector or a matrix/data.frame indicating the (relative) counts of one or multiple samples, respectively. If a matrix/data.frame is provided, columns must refer to samples and rows to OTUs.
qvalue	A positive integer or decimal number (>=0), usually between 0 and 3.
tree	An ultrametic tree of class 'phylo'. The tip labels must match the names of the vector values (if one sample) or matrix rows (if multiple samples). Use the function match_data() if the OTU names do not match.
dist	A dist object indicating the pairwise distances between samples. NOT implemented yet

Details

Hill numbers computation

Author(s)

Antton Alberdi, [e-mail]

References

Alberdi, A., Gilbert, M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources, 19, 804-817.

Jost, L. (2006). Entropy and diversity. Oikos, 113, 363-375.

Hill, M. O. (1973). Diversity and evenness: a unifying notation and its consequences. Ecology, 54, 427-432.

See Also

index_div, div_part

Examples

data(bat.diet.otutable)
data(bat.diet.tree)
data(bat.diet.hierarchy)
#One sample
bat.diet.sample <- bat.diet.otutable[,1]
hill_div(bat.diet.sample,0)
hill_div(bat.diet.sample,qvalue=1)
#One sample (phylogenetic)
names(bat.diet.sample) <- rownames(bat.diet.otutable)
hill_div(bat.diet.sample,1,bat.diet.tree)
#Multiple samples
hill_div(bat.diet.otutable,0)
#Incidence-based
bat.diet.otutable.incidence <- to.incidence(bat.diet.otutable,bat.diet.hierarchy)
hill_div(bat.diet.otutable.incidence,qvalue=1)
hill_div(to.incidence(bat.diet.otutable,bat.diet.hierarchy),1)

hilldiv documentation built on Oct. 1, 2019, 5:04 p.m.