Calculate within-site diversity metrics — hib_calc_div

This function calculates multiple, user specified measures of site-level (taxonomic) diversity for sites in the associated HibDatabase.

Usage

hib_calc_div_within(obj, metrics)

Arguments

obj: A HibDatabase object.
metrics: Character vector, any/all of; "Total_abundance", "Species_richness", "Chao1_diversity", "Simpson_diversity", "Rarefied_species_richness", "Mean_abundance", "Geometric_mean_abundance", "Shannon_diversity", "HillShannon_diversity", "HillSimpson_diversity", "PIE", "Equalness". Metrics can be provided in upper or lower case and as unambiguous abbreviations (internal processing is done using lower-case).

Value

HibDatabase with updated '$diversity_within' tibble

Details

As is standard for R6 Classes, the HibDatabase is modified in-place. If effort correction (hib_effort_correction()) has previously been conducted, diversity metrics will be estimated using effort corrected measurements.

Examples

if (FALSE) { # \dontrun{
  hib_db <- hib_calc_div_within(hib_db, c("Total_abundance", "Species_richness"))
} # }