GetFunctionalHillNumber — GetFunctionalHillNumber • ecomet

This function calculates the functional Hill number for a given mmo object, normalization method, and distance metric. See https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18685 for details of the functional Hill number calculation.

Usage

GetFunctionalHillNumber(
  feature,
  metadata,
  distance_matrix,
  q = 1,
  threshold = 0,
  scale_dissim = TRUE
)

Arguments

feature: Feature table with columns: id, feature, then sample columns
metadata: Metadata table with sample and group columns
distance_matrix: Feature distance matrix
q: The order of the Hill number to calculate (default: 1). Larger q values give more weight to evenness portion of the hill number over richness.
threshold: Numeric; detection threshold for presence (default: 0)
scale_dissim: Boolean; whether to scale the distance matrix to be between 0 and 1 (default: TRUE)

Value

A data frame containing the functional Hill number for each group in the metadata, with columns for group and hill number.