Explore dominant, codominant (and subdominant) patterns

Focusing in one structural layer and given the dominant/codominant taxon/taxa in each relevé, the user can obtain further information on dominance/codominance patterns and visualize the associated networks.

Usage

explore_dom_codom(
  l,
  plot.network = "no",
  m.percent = NULL,
  colourize.clusters = NULL,
  taxa.names = NULL,
  ...
)

Arguments

l

list A list of dominant/codominant (and subdominant) taxa, as produced by dom_codom_taxa function.

plot.network

character By default no plot is created (defults to "no"). "all" for plotting the entire network of dominance/codominance (and subdominant) taxa (can be messy). "simplified" for plotting a simplified network using a predefined algorithm. See Details.

m.percent

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

colourize.clusters

factor If plot.network is "all" or "simplified" this factor (giving an a priori relevé grouping) will be used to colour the plot. Order should be the same as in the l list. Defaults to NULL and no colour is added to the plot.

taxa.names

character A character vector with the names of taxa, i.e. corresponding to each row of m.percent. Only needed for plotting.

...

other arguments to be passed to plotweb function.

Value

A simplified list of dominant and/or codominant taxa in each relevé, dropping all subdominant taxa and, when sound, dropping taxa that are less frequent as dominant/codominant in the data set.

Details

The function accepts a list l of dominant/codominant (and subdominant) taxa as produced by dom_codom_taxa function and returns a simplified list presenting a single dominant or codomintant taxon in each relevé. This simplification is obtained using the following algorithm:

1. dominant/codominant taxa are sorted by its frequency (in the network);

2. starting with the most frequent taxon and looking at each relelvé, if that taxon is present as a dominant or codominant, thus it is ascribed to that relevé, otherwise the relevé remains empty;

3. the previous step is repeated with the next most frequent taxon for the remaining empty relevés, until all relevés have a taxon ascribed. Eventually, a list of the ascribed taxa (one per relevé) is returned.

If plot.network = "all" the function produces a plot of the full network of dominant/codominant (and subdominant) taxa using the bipartite package. Depending on input data, plotting the full network can be intricate. If plot.network = "simplified" a plot is similarly produced but using the referred simplified list (where only a single dominant or codominant taxon in considered for each relevé).

Author

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