Taxonomic Dominance

taxa_dom(
  .dataframe,
  .key_col,
  .counts_col,
  .group_col,
  .dom_level,
  .filter = NULL,
  .unnest_col = NULL
)

Arguments

.dataframe	A data frame where each row should represent the number of individuals enumerated for a single taxon collected during a single sampling event.
.key_col	One unquoted column name that represents a key (i.e., unique ID) for a sampling event for which to group (i.e., aggregate) the data.
.counts_col	One unquoted column name that represents taxonomic counts.
.group_col	One unquoted column name that represents a taxomic rank or group of interest.
.dom_level	A numeric value, typically 1-5, the number of dominant used during the calculation.
.filter	A logical statement to subset the data frame prior to calculating the metric of interest.
.unnest_col	One unqouted column name that represents nested data. If this column is NULL (default), then the data will not be unnested.

Value

A numeric vector. Percent of individuals that represent the most abundant taxon or taxa. .dom_level can be used to specify 1st-5th most abundant taxa by specifying the corresponding numeric value (1-5). Values >1 include all of the previous dominance levels. For example, .dom_level = 3 is the percentage of the most dominant taxon, the second most dominant taxon, and the third most dominant taxon. During calculation the taxa are ranked in descending order. If there are two taxa with the same count at the specified .dom_level, only one taxon is used. Consider the following vector as an example of taxonomic counts: c(10, 10, 5, 2, 2, 1). If .dom_level == 1, only the first "10" is selected. If .dom_level == 2, the first two "10"s are selected.

This measure is related to taxa evenness. Typically degradation is associated with elevated levels of the most dominant taxon (taxa); therefore, this metric typically increases with degradation.