Package: labdsv 2.1-0

labdsv: Ordination and Multivariate Analysis for Ecology

A variety of ordination and community analyses useful in analysis of data sets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses.

Authors:David W. Roberts <[email protected]>

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labdsv.pdf |labdsv.html✨
labdsv/json (API)

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

Peer review:

Datasets:
  • brycesite - Site Data for Bryce Canyon National Park
  • bryceveg - Bryce Canyon Vegetation Data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

6.18 score 3 stars 13 packages 434 scripts 3.0k downloads 161 mentions 65 exports 8 dependencies

Last updated 2 years agofrom:8a8565f635. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-win-x86_64NOTENov 22 2024
R-4.5-linux-x86_64NOTENov 22 2024
R-4.4-win-x86_64NOTENov 22 2024
R-4.4-mac-x86_64NOTENov 22 2024
R-4.4-mac-aarch64NOTENov 22 2024
R-4.3-win-x86_64NOTENov 22 2024
R-4.3-mac-x86_64NOTENov 22 2024
R-4.3-mac-aarch64NOTENov 22 2024

Exports:abundtransabuoccas.dsvordas.euclideanas.metricbestnmdsbesttsnecalibrateccmchullordcompspecconcovconstconvexdefactorizedematrifydensitydgadisanadroppltdropspcdsvdisdsvlsellipenvrtesteuclidifyfactorizegsrhellingerhilighthomoteneityimportanceindvalis.metricisamicloadingsmatrifymetrifyneighborsnmdsordcommordcomporddistordneighborsordpartordtestpcapcoplotidpredictraretaxareconcilerndcommrnddistsamptotscoresspcdiscspcmaxspecidstepdistsurfthulltsnevarplotvegtab

Dependencies:clusterlatticeMASSMatrixmgcvnlmeRcppRtsne

Readme and manuals

Help Manual

Help pageTopics
Species Abundance Data Transformationabundtrans
Abundance/Occurrence Graphical Analysisabuocc
Convert existing and external ordinations to dsv formatas.dsvord
Site Data for Bryce Canyon National Parkbrycesite
Bryce Canyon Vegetation Databryceveg
Calculate fitted environmental attributes in an ordinationcalibrate calibrate.dsvord
Community Composition Modelingccm
Compositional Specificity Analysiscompspec indspc plot.compspec
Constancy-Coverage Table for Ecological Community Dataconcov
Constancy Tableconst
Convex Data Transformationconvex
Change Factors in Data.frames to Character Vectorsdefactorize
Create Three Column Database Form Data Frame from Sparse Data Framesdematrify
Direct Gradient Analysisdga
Dissimilarity Analysisdisana
Dropping Plots with Missing Values From Taxon and Site Data Framesdropplt
Dropping Species with Few Occurrencesdropspc
Dissimilarity Indices and Distance Measuresdsvdis
LabDSV Object ls() Commanddsvls
Environmental Distribution Testenvrtest
Nearest Euclidean Space Representation of a Dissimilarity Objectas.euclidean euclidify
Change Character Vectors in Data.frames to Factorsfactorize
Global Search and Replace for Data.framesgsr
Hellinger Data Transformationhellinger
Homoteneity Analysis of Classified Ecological Communitieshomoteneity
Importance Tableimportance importance.default
Dufrene-Legendre Indicator Species Analysisduleg indval indval.default indval.stride summary.indval
Indicator Species Analysis Minimizing Intermediate Occurrencesduarm isamic
Create Taxon Data.frames From Three Column Database Formmatrify
Nearest Metric Space Representation of a Dissimilarity Objectas.metric is.metric metrify
Neighborsneighbors
Nonmetric Multidimensional Scalingbestnmds nmds
Re-Order the Rows and Columns of a Taxon Data Frameordcomm
Ordination to Dissimilarity Comparisonordcomp
Ordination Point Pair-Wise Distance Calculationorddist
Nearest Neighbors Plotted in Ordination Spaceordneighbors
Ordination Partitioningordpart ordpart.dsvord ordpart.nmds ordpart.pca ordpart.pco
Ordination Distribution Testordtest
Principal Components Analysisloadings loadings.pca pca scores scores.pca summary summary.pca varplot varplot.pca
Principal Coordinates Analysispco
Plotting Routines For LabDSV Ordinationschullord.dsvord density.dsvord ellip ellip.dsvord hilight.dsvord plot.dsvord plotid.dsvord points.dsvord surf.dsvord thull.dsvord
Plotting a Tensioned Hullplot.thull thull
Predict species abundances in an ordinationpredict predict.dsvord
Identify Rare Taxa in a Data Setraretaxa
Reconcile Community and Site Data.Framesreconcile
Randomize a Community Data.Framerndcomm rndtaxa
Random Distancernddist
Sample total standardizationsamptot
Species Discrimination Analysisspcdisc
Species Maximum Standardizationspcmax
Step-Across Distancestepdist
t-Distributed Stochastic Neighbor Embeddingbesttsne tsne
Vegetation Tablevegtab