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Dominant, codominant (and subdominant) taxa

Source: R/dom_codom_taxa.R
dom_codom_taxa.Rd

Identifies the dominant/codominant (and subdominant) taxa in the relevés of a phytosociological table, within the respective structural layer.

Usage

dom_codom_taxa(
  m,
  taxa.names,
  layer,
  struct,
  selected.layer,
  threshold.dom = 3,
  threshold.codom = 2
)

Arguments

m

matrix A phytosociological table, where rows correspond to taxa and columns correspond to relevés.

taxa.names

character A character vector with the names of taxa, i.e. corresponding to each row of m.

layer

factor A vector giving the layer for each row of m.

struct

factor A vector with the structural layer in each relevé, as the result of the structural_layer function.

selected.layer

character A vector with the name of the structural layer that will be processed.

threshold.dom

numeric The minimum Braun-Blanquet index of a taxon, transformed to ordinal values, to be considered dominant. Defaults to 3.

threshold.codom

numeric The minimum Braun-Blanquet index of a taxon, transformed to ordinal values, to be considered codominant. Defaults to 2.

Value

A list of dominant and/or codominant taxa in each relevé, for each of the structural layers present in struct.

Details

The function accepts a phytosociological table, with Braun-Blanquet indices transformed to ordinal values, and returns the dominant taxon or the codomintant taxa in each relevé.

This function allows the user to explore the vegetation structure within relevés of a phytosociological table. It can also be used as a tool to assist the verification of appropriateness of data for the subsequent analyses or (a sort of) a posteriori entitation. A taxon is dominant if: (i) it belongs to the structural layer and it is the single taxon presenting the highest cover value in that layer. A taxon is codominant if: (ii) it belongs to the structural layer and it presents the highest cover value ex aequo (tied taxa) OR (iii) it belongs to the structural layer and it presents a BB index value immediately below the dominant taxon (which can also be called subdominant taxa).

Author

Tiago Monteiro-Henriques. E-mail: tmh.dev@icloud.com.