merge_samples: Merge samples

In anttonalberdi/hilldiv: Integral Analysis of Diversity Based on Hill Numbers

Description

Combines samples into groups defined by the hierarchy table, with the possibility to convert abundances into incidence data.

Usage

merge_samples(countable,hierarchy,incidence)

Arguments

countable	A count table (matrix/data.frame) indicating the absolute or relative OTU/ASV abundances of multiple samples. Columns must refer to samples and rows to OTUs/ASVs.
hierarchy	A two-column matrix indicating the relation between samples (first column) and groups (second column).
relative	Whether to output relative values or not. Default=TRUE.
incidence	Whether to transform abundance into incidence data when merging. Default=FALSE.

Details

Merge samples

Value

A count table

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.

See Also

to.incidence

Examples

data(bat.diet.otutable)
data(bat.diet.hierarchy)
merge_samples(countable=bat.diet.otutable,hierarchy=bat.diet.hierarchy)
merge_samples(bat.diet.otutable,bat.diet.hierarchy)
merge_samples(countable=bat.diet.otutable,hierarchy=bat.diet.hierarchy, incidence=TRUE)

anttonalberdi/hilldiv documentation built on Feb. 14, 2021, 5:08 p.m.