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(
  mmo,
  normalization = "None",
  q = 1,
  distance = "dreams",
  filter_feature = FALSE,
  feature_list = NULL
)

Arguments

mmo: The mmo object containing feature data and metadata
normalization: The normalization method to use for feature data. Options are 'None', 'Log', 'Meancentered', or 'Z' (default: 'None')
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.
distance: The distance metric to use for calculating dissimilarity. Options are 'dreams', 'm2ds', or 'cosine' (default: 'dreams')
filter_feature: A boolean indicating whether to filter the feature data by a specific list (default: FALSE)
feature_list: A list of feature names to filter the feature data by, if filter_feature is TRUE (default: NULL)

Value

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

Examples

if (FALSE) {
hill_number <- GetFunctionalHillNumber(mmo, normalization = 'Z', q = 1, distance = 'dreams', filter_feature = FALSE)
hill_number <- GetFunctionalHillNumber(mmo, normalization = 'Z', q = 3, distance = 'dreams', filter_feature = TRUE, feature_list = Glucosinolates)
}