Description Usage Arguments Details Value Author(s) References See Also Examples
Transform a count (OTU/ASV) table from abundance to incidence.
1 | to.incidence(otutable, hierarchy, relative)
|
otutable |
A matrix/data.frame indicating the (relative) 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 transform the incidence vector or matrix to relative (0-1) values. Default: relative=FALSE. |
To incidence
A vector of incidence data of a single system if no hierarchy table is specified and a matrix of incidence data of multiple systems if a hierarchy table is specified.
Antton Alberdi, anttonalberdi@gmail.com
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.
1 2 3 4 5 6 | data(bat.diet.otutable)
data(bat.diet.hierarchy)
to.incidence(bat.diet.otutable)
to.incidence(bat.diet.otutable,bat.diet.hierarchy)
to.incidence(bat.diet.otutable,bat.diet.hierarchy,relative=TRUE)
to.incidence(otutable=bat.diet.otutable,hierarchy=bat.diet.hierarchy,relative=TRUE)
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