divent_hill_matrix_pq: Compute Hill diversity numbers for all samples in an OTU...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Compute Hill diversity numbers for all samples in an OTU table

Description

Iterates over all samples in an OTU table and computes Hill diversity numbers using divent::div_hill().

Usage

divent_hill_matrix_pq(comm, q, ...)

Arguments

comm	(data.frame or matrix) OTU table with samples as rows and taxa as columns.
q	(numeric vector) Hill diversity orders to compute. Hill numbers are more appropriate in DNA metabarcoding studies when q > 0 (Alberdi & Gilbert, 2019; Calderón-Sanou et al., 2019).
...	Additional arguments passed to divent::div_hill() (e.g. estimator = "naive" to reproduce vegan-equivalent results).

Value

A data.frame with one row per sample and one column per value in q. Column names are the string representation of the q values. Row names match the input row names.

References

Alberdi, A., & Gilbert, M. T. P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/1755-0998.13014")}

Calderón-Sanou, I., Münkemüller, T., Boyer, F., Zinger, L., & Thuiller, W. (2019). From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? Journal of Biogeography, 47. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/jbi.13681")}

See Also

divent::div_hill(), hill_pq(), hill_tuckey_pq()

Examples

data("data_fungi_mini", package = "MiscMetabar")
data_f <- prune_samples(
  sample_names(data_fungi_mini)[1:5],
  data_fungi_mini
)
otu <- as.data.frame(phyloseq::otu_table(
  taxa_as_columns(data_f)
))
divent_hill_matrix_pq(otu, q = c(0, 1, 2))

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.