Package: vegclust 2.0.3

Miquel De Cáceres

vegclust: Fuzzy Clustering of Vegetation Data

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>.

Authors:Miquel De Cáceres [aut, cre]

vegclust_2.0.3.tar.gz
vegclust_2.0.3.zip(r-4.7)vegclust_2.0.3.zip(r-4.6)vegclust_2.0.3.zip(r-4.5)
vegclust_2.0.3.tgz(r-4.6-any)vegclust_2.0.3.tgz(r-4.5-any)
vegclust_2.0.3.tar.gz(r-4.7-any)vegclust_2.0.3.tar.gz(r-4.6-any)
vegclust_2.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
vegclust/json (API)

# Install 'vegclust' in R:
install.packages('vegclust', repos = c('https://emf-creaf.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emf-creaf/vegclust/issues

Pkgdown/docs site:https://emf-creaf.github.io

Datasets:
  • medreg - Regeneration of Mediterranean vegetation data set
  • treedata - Synthetic vegetation data set with tree data
  • wetland - Wetland vegetation data set Vegetation of the Adelaide river alluvial plain (Australia). This data set was published by Bowman & Wilson (1987) and used in Dale (1988) to compare fuzzy classification approaches.

On CRAN:

Conda:

6.61 score 2 stars 7 packages 76 scripts 1.3k downloads 1 mentions 35 exports 8 dependencies

Last updated from:59a4b4d59c. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK162
source / vignettesOK166
linux-release-x86_64OK140
macos-release-arm64OK88
macos-oldrel-arm64OK108
windows-develOK94
windows-releaseOK130
windows-oldrelOK90
wasm-releaseOK103

Exports:as.membas.stratifiedvegdataas.vegclustCAPCAP2matrixCAPcentersCAPquantileCASCAS2matrixCAScentersCASmarginCASquantileclustcentroidclustconstclustmedoidclustvarconcordanceconformvegcrossmembdefuzzifyhcrhier.vegclusthier.vegclustdistincr.vegclustinterclustdistrandom.vegclustrandom.vegclustdistrelate.levelsstratifyvegdatavegclassvegclustvegclust2kmeansvegclustdistvegclustIndexvegdiststruct

Dependencies:clusterlatticeMASSMatrixmgcvnlmepermutevegan

How to use the vegclust package
Introduction | What is this tutorial about? | Example vegetation data | Clustering methods in vegclust | Resemblance space | Prototype-based clustering | Clustering models | Hard (crisp) or fuzzy memberships | Centroids or medoids | Partitive clustering | Noise clustering | Possibilistic clustering | Dissimilarity-based duals | Medoid-based clustering and dissimilarity matrices | Centroid-based clustering and dissimilarity matrices | Managing vegetation classifications | Creating classifications: vegclust and vegclustdist() | The K-means model | The Fuzzy C-means model | The Noise clustering model | Medoid-based clustering | Supervised classification: as.vegclust() and vegclass() | Extending vegetation classifications | Conforming vegetation data sets | Re-calculating the centroids of the initial classification | Calling vegclust with fixed prototypes | Extending or refining classifications? | Using vegclustdist() with fixed prototypes | Cluster characterization | Cluster prototypes: clustcentroid() and clustmedoid() | Cluster internal variability: clustvar() | Distance between clusters: interclustdist() | Constancy classes: clustconst() | Bibliography

Last update: 2021-06-08
Started: 2021-06-04

Describing vegetation in terms of structure and composition
Introduction | Post-fire vegetation regeneration data | Cumulative abundance profiles | Cumulative abundance surfaces | Dissimilarities in structure and composition | Classification of vegetation stands | References

Last update: 2020-06-10
Started: 2018-05-03

Readme and manuals

Help Manual

Help pageTopics
Turns into membership matrixas.memb
Turns into vegclust objectsas.vegclust
Cumulative abundance profile (CAP)CAP CAP2matrix CAPcenters CAPquantile
Cumulative abundance surface (CAS)CAS CAS2matrix CAScenters CASmargin CASquantile
Cluster centers of a classificationclustcentroid clustmedoid
Constancy table of a classificationclustconst summary.clustconst
Cluster varianceclustvar
Concordance between two classificationsconcordance
Conform two community data tablesconformveg
Cross-table of two fuzzy classificationscrossmemb
Defuzzifies a fuzzy partitiondefuzzify
Heterogeneity-constrained random resampling (HCR)hcr
Clustering with several number of clustershier.vegclust hier.vegclustdist random.vegclust random.vegclustdist
Noise clustering with increasing number of clustersincr.vegclust
Distance between pairs of cluster centroidsinterclustdist
Regeneration of Mediterranean vegetation data setmedreg
Draws cummulative abundance profilesplot.CAP plot.stratifiedvegdata
Draws a cummulative abundance surfaceplot.CAS
Plots clustering resultsplot.mvegclust
Relates two clustering level resultsrelate.levels
Reshapes community data from individual into stratified formas.stratifiedvegdata stratifyvegdata
Synthetic vegetation data set with tree datatreedata
Classifies vegetation communitiesvegclass
Vegetation clustering methodsvegclust vegclustdist
Reshapes as kmeans objectvegclust2kmeans
Fuzzy evaluation statisticsvegclustIndex
Structural and compositional dissimilarityvegdiststruct
Wetland vegetation data set Vegetation of the Adelaide river alluvial plain (Australia). This data set was published by Bowman & Wilson (1987) and used in Dale (1988) to compare fuzzy classification approaches.wetland