vegclust-package {vegclust} | R Documentation |
Fuzzy Clustering of Vegetation Data Functions for fuzzy and hard clustering of vegetation data
Description
A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the basis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>. This package contains functions used to perform fuzzy and hard clustering of vegetation data under different models.
Details
The DESCRIPTION file:
Package: | vegclust |
Type: | Package |
Title: | Fuzzy Clustering of Vegetation Data |
Version: | 2.0.2 |
Date: | 2022-08-24 |
Authors@R: | c( person('Miquel', 'De Cáceres', role=c('aut','cre'), email='miquelcaceres@gmail.com')) |
Description: | A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the basis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>. |
Depends: | R (>= 3.4.0) |
Imports: | vegan |
License: | GPL (>= 2) |
URL: | https://emf-creaf.github.io/vegclust/ |
LazyLoad: | yes |
Encoding: | UTF-8 |
NeedsCompilation: | yes |
RoxygenNote: | 7.1.1 |
Suggests: | knitr, rmarkdown |
VignetteBuilder: | utils, knitr |
Author: | Miquel De Cáceres [aut, cre] |
Maintainer: | Miquel De Cáceres <miquelcaceres@gmail.com> |
Index of help topics:
CAP Cumulative abundance profile (CAP) CAS Cumulative abundance surface (CAS) as.memb Turns into membership matrix as.vegclust Turns into vegclust objects clustcentroid Cluster centers of a classification clustconst Constancy table of a classification clustvar Cluster variance concordance Concordance between two classifications conformveg Conform two community data tables crossmemb Cross-table of two fuzzy classifications defuzzify Defuzzifies a fuzzy partition hcr Heterogeneity-constrained random resampling (HCR) hier.vegclust Clustering with several number of clusters incr.vegclust Noise clustering with increasing number of clusters interclustdist Calculates the distance between pairs of cluster centroids medreg Regeneration of Mediterranean vegetation data set plot.CAP Draws cummulative abundance profiles plot.CAS Draws a cummulative abundance surface plot.mvegclust Plots clustering results relate.levels Relates two clustering level results. stratifyvegdata Reshapes community data from individual into stratified form treedata Synthetic vegetation data set with tree data vegclass Classifies vegetation communities vegclust Vegetation clustering methods vegclust-package Fuzzy Clustering of Vegetation Data Functions for fuzzy and hard clustering of vegetation data vegclust2kmeans Reshapes as kmeans object vegclustIndex Compute fuzzy evaluation statistics vegdiststruct Structural and compositional dissimilarity wetland Wetland vegetation data set
Author(s)
NA Maintainer: NA
References
De Caceres, M., Font, X, Oliva, F. (2010) The management of numerical vegetation classifications with fuzzy clustering methods. Journal of Vegetation Science 21 (6): 1138-1151.
De Cáceres, M., Legendre, P., & He, F. 2013. Dissimilarity measurements and the size structure of ecological communities (D. Faith, Ed.). Methods in Ecology and Evolution 4: 1167–1177.
Examples
## Loads data
data(wetland)
## This equals the chord transformation
wetland.chord = as.data.frame(sweep(as.matrix(wetland), 1,
sqrt(rowSums(as.matrix(wetland)^2)), "/"))
## Create noise clustering with 3 clusters. Perform 10 starts from random seeds
## and keep the best solution
wetland.nc = vegclust(wetland.chord, mobileCenters=3, m = 1.2, dnoise=0.75,
method="NC", nstart=10)