groupDist: Single time slice compositional partitioning based on...

In adamkocsis/obigeo: Occurrence-based biogeography

Single time slice compositional partitioning based on distance-based cluster analysis

Description

This function calculates a distance matrix from the data and runs cluster analysis on it. The dendrogram is then cut to form higher level units.

Usage

groupDist(
  contingency,
  binary = TRUE,
  dist = "jaccard",
  method = "ward.D2",
  counts = FALSE,
  kgs = FALSE,
  plot = FALSE,
  feedback = FALSE,
  ...
)

Arguments

contingency	(matrix) Numeric matrix, species in rows, localities in columns.
binary	(logical) If set to TRUE, the contingency table will be reduced to a binary matrix before the distances are calculated.
dist	(character) The distance calculation method, the method argument of the vegdist function in vegan.
method	(character) The type of clustering used, the method argument of hclust function.
counts	(logical) If binary is FALSE, should proportions be used, or counts?
kgs	(logical) Should the kgs (TRUE) or the cutree (FALSE) function be used for cutting the trees?
plot	(logical) Should the dendrogram be plotted?
...	functions passed to the cutree or the kgs functions.

adamkocsis/obigeo documentation built on Oct. 14, 2024, 8:46 a.m.