Structural layer

Identifies the structural layer for each relevé in a phytosociological table.

Usage

structural_layer(
  m.percent,
  layer,
  hierarchy,
  threshold = 20,
  type.of.sum = "simple"
)

Arguments

m.percent

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

layer

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

hierarchy

character A character vector giving the structural order/hierarchy of the layers (the ordering from the highest/more complex to the smallest/less complex layer).

threshold

numeric A single number or a vector, giving the minimum summed percentage value of a layer so it can be considered the structural layer. Defaults to 20 (the value is recycled for all layers). A vector of the same length of hierarchy can be given with different thresholds for each layer (the order should be the same as in hierarchy).

type.of.sum

character If "simple" (the default), the function simply sums the percentage cover within each layer. If "independent" the function returns the sum under the independence assumption (independent overlap of covers).

Value

A factor with the dominating layer in each relevé. NA is introduced if the summed cover do not reach the given threshold in any layer.

Details

The type.of.sum defaults to "simple", which might be more appropriate when aggregating different taxa within the same layer (Tichy´ et al. 2011).

References

Tichy´ L., Holt J. and Nejezchlebová M. 2011. JUICE: program for management, analysis and classification of ecological data. 1st part. 2nd Edition of the Program Manual. Czech Republic.

Author

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