vegan: Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

AuthorJari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Date of publication2016-04-04 07:26:57
MaintainerJari Oksanen <jari.oksanen@oulu.fi>
LicenseGPL-2
Version2.3-5
https://cran.r-project.org
https://github.com/vegandevs/vegan

View on R-Forge

Man pages

add1.cca: Add or Drop Single Terms to a Constrained Ordination Model

adipart: Additive Diversity Partitioning and Hierarchical Null Model...

adonis: Permutational Multivariate Analysis of Variance Using...

anosim: Analysis of Similarities

anova.cca: Permutation Test for Constrained Correspondence Analysis,...

as.mlm: Refit Constrained Ordination as a Multiple Response Linear...

BCI: Barro Colorado Island Tree Counts

beals: Beals Smoothing and Degree of Absence

betadisper: Multivariate homogeneity of groups dispersions (variances)

betadiver: Indices of beta Diversity

bgdispersal: Coefficients of Biogeographical Dispersal Direction

bioenv: Best Subset of Environmental Variables with Maximum (Rank)...

biplot.rda: PCA biplot

capscale: [Partial] Constrained Analysis of Principal Coordinates or...

cascadeKM: K-means partitioning using a range of values of K

cca: [Partial] [Constrained] Correspondence Analysis and...

cca.object: Result Object from Constrained Ordination with cca, rda or...

CCorA: Canonical Correlation Analysis

clamtest: Multinomial Species Classification Method (CLAM)

commsim: Create a Object for Null Model Algorithms

contribdiv: Contribution Diversity Approach

decorana: Detrended Correspondence Analysis and Basic Reciprocal...

decostand: Standardization Methods for Community Ecology

designdist: Design your own Dissimilarities

deviance.cca: Statistics Resembling Deviance and AIC for Constrained...

dispindmorisita: Morisita index of intraspecific aggregation

dispweight: Dispersion-based weighting of species counts

distconnected: Connectedness of Dissimilarities

diversity: Ecological Diversity Indices

dune: Vegetation and Environment in Dutch Dune Meadows.

dune.taxon: Taxonomic Classification and Phylogeny of Dune Meadow Species

eigenvals: Extract Eigenvalues from an Ordination Object

envfit: Fits an Environmental Vector or Factor onto an Ordination

eventstar: Scale Parameter at the Minimum of the Tsallis Evenness...

fisherfit: Fit Fisher's Logseries and Preston's Lognormal Model to...

goodness.cca: Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA,...

goodness.metaMDS: Goodness of Fit and Shepard Plot for Nonmetric...

humpfit: No-interaction Model for Hump-backed Species Richness vs....

indpower: Indicator Power of Species

isomap: Isometric Feature Mapping Ordination

kendall.global: Kendall coefficient of concordance

linestack: Plots One-dimensional Diagrams without Overwriting Labels

make.cepnames: Abbreviates a Botanical or Zoological Latin Name into an...

mantel: Mantel and Partial Mantel Tests for Dissimilarity Matrices

mantel.correlog: Mantel Correlogram

MDSrotate: Rotate First MDS Dimension Parallel to an External Variable

metaMDS: Nonmetric Multidimensional Scaling with Stable Solution from...

mite: Oribatid Mite Data with Explanatory Variables

model.matrix.cca: Reconstruct Model Frame and Model Matrices of Constrained...

monoMDS: Global and Local Non-metric Multidimensional Scaling and...

MOStest: Mitchell-Olds & Shaw Test for the Location of Quadratic...

mrpp: Multi Response Permutation Procedure and Mean Dissimilarity...

mso: Functions for performing and displaying a spatial...

multipart: Multiplicative Diversity Partitioning

nestedtemp: Nestedness Indices for Communities of Islands or Patches

nobs.adonis: Extract the Number of Observations from a vegan Fit.

nullmodel: Null Model and Simulation

oecosimu: Evaluate Statistics with Null Models of Biological...

ordiarrows: Add Arrows and Line Segments to Ordination Diagrams

ordiArrowTextXY: Support Functions for Drawing Vectors

ordihull: Display Groups or Factor Levels in Ordination Diagrams

ordilabel: Add Text on Non-transparent Label to an Ordination Plot.

ordiplot: Alternative plot and identify Functions for Ordination

ordipointlabel: Ordination Plots with Points and Optimized Locations for Text

ordiresids: Plots of Residuals and Fitted Values for Constrained...

ordistep: Choose a Model by Permutation Tests in Constrained Ordination

ordisurf: Fit and Plot Smooth Surfaces of Variables on Ordination.

orditkplot: Ordination Plot with Movable Labels

orditorp: Add Text or Points to Ordination Plots

ordixyplot: Trellis (Lattice) Plots for Ordination

pcnm: Principal Coordinates of Neighbourhood Matrix

permatfull: Matrix Permutation Algorithms for Presence-Absence and Count...

permustats: Extract, Analyse and Display Permutation Results

permutations: Permutation tests in Vegan

permutest.betadisper: Permutation test of multivariate homogeneity of groups...

plot.cca: Plot or Extract Results of Constrained Correspondence...

prc: Principal Response Curves for Treatments with Repeated...

predict.cca: Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA,...

procrustes: Procrustes Rotation of Two Configurations and PROTEST

pyrifos: Response of Aquatic Invertebrates to Insecticide Treatment

radfit: Rank - Abundance or Dominance / Diversity Models

rankindex: Compares Dissimilarity Indices for Gradient Detection

rarefy: Rarefaction Species Richness

raupcrick: Raup-Crick Dissimilarity with Unequal Sampling Densities of...

read.cep: Reads a CEP (Canoco) data file

renyi: Renyi and Hill Diversities and Corresponding Accumulation...

reorder.hclust: Reorder a Hierarchical Clustering Tree

RsquareAdj: Adjusted R-square

scores: Get Species or Site Scores from an Ordination

screeplot.cca: Screeplots for Ordination Results and Broken Stick...

simper: Similarity Percentages

simulate.rda: Simulate Responses with Gaussian Error or Permuted Residuals...

sipoo: Birds in the Archipelago of Sipoo (Sibbo)

spantree: Minimum Spanning Tree

specaccum: Species Accumulation Curves

specpool: Extrapolated Species Richness in a Species Pool

SSarrhenius: Self-Starting nls Species-Area Models

stepacross: Stepacross as Flexible Shortest Paths or Extended...

stressplot.wcmdscale: Display Ordination Distances Against Observed Distances in...

taxondive: Indices of Taxonomic Diversity and Distinctness

tolerance: Species tolerances and sample heterogeneities

treedive: Functional Diversity and Community Distances from Species...

tsallis: Tsallis Diversity and Corresponding Accumulation Curves

varechem: Vegetation and environment in lichen pastures

varpart: Partition the Variation of Community Matrix by 2, 3, or 4...

vegan-defunct: Defunct Functions in Package 'vegan'

vegan-deprecated: Deprecated Functions in vegan package

vegandocs: Display vegan Documentation

vegan-internal: Internal vegan functions

vegan-package: Community Ecology Package: Ordination, Diversity and...

vegdist: Dissimilarity Indices for Community Ecologists

vegemite: Display Compact Ordered Community Tables

wascores: Weighted Averages Scores for Species

wcmdscale: Weighted Classical (Metric) Multidimensional Scaling

Functions

add1.cca Man page
ade2vegancca Man page
adipart Man page
adipart.default Man page
adipart.formula Man page
adonis Man page
AIC.fitspecaccum Man page
AIC.radfit Man page
AIC.radfit.frame Man page
alias.cca Man page
anosim Man page
anova.betadisper Man page
anova.cca Man page
anova.ccabyaxis Man page
anova.ccabymargin Man page
anova.ccabyterm Man page
anova.ccanull Man page
anova.prc Man page
as.fisher Man page
as.hclust.spantree Man page
as.mcmc.oecosimu Man page
as.mcmc.permat Man page
as.mlm Man page
as.mlm.cca Man page
as.mlm.rda Man page
as.preston Man page
as.rad Man page
as.ts.oecosimu Man page
as.ts.permat Man page
BCI Man page
BCI.env Man page
beals Man page
betadisper Man page
betadiver Man page
bgdispersal Man page
bioenv Man page
bioenv.default Man page
bioenvdist Man page
bioenv.formula Man page
biplot.CCorA Man page
biplot.rda Man page
boxplot.betadisper Man page
boxplot.specaccum Man page
bstick Man page
bstick.cca Man page
bstick.decorana Man page
bstick.default Man page
bstick.prcomp Man page
bstick.princomp Man page
calibrate Man page
calibrate.cca Man page
calibrate.ordisurf Man page
capscale Man page
cascadeKM Man page
cca Man page
cca.default Man page
cca.formula Man page
cca.object Man page
CCorA Man page
centroids.cca Man page
cIndexKM Man page
clamtest Man page
coef.cca Man page
coef.radfit Man page
coef.radfit.frame Man page
coef.rda Man page
commsim Man page
commsimulator Man page
confint.MOStest Man page
contribdiv Man page
cophenetic.spantree Man page
coverscale Man page
decorana Man page
decostand Man page
density.adonis Man page
density.anosim Man page
density.mantel Man page
density.mrpp Man page
density.oecosimu Man page
density.permustats Man page
density.permutest.cca Man page
densityplot.adonis Man page
densityplot.oecosimu Man page
densityplot.permustats Man page
density.protest Man page
designdist Man page
deviance.cca Man page
deviance.fitspecaccum Man page
deviance.radfit Man page
deviance.radfit.frame Man page
deviance.rda Man page
dispindmorisita Man page
dispweight Man page
distconnected Man page
diversity Man page
downweight Man page
drarefy Man page
drop1.cca Man page
dune Man page
dune.env Man page
dune.phylodis Man page
dune.taxon Man page
eigengrad Man page
eigenvals Man page
eigenvals.betadisper Man page
eigenvals.cca Man page
eigenvals.default Man page
eigenvals.dudi Man page
eigenvals.pca Man page
eigenvals.pcnm Man page
eigenvals.pco Man page
eigenvals.prcomp Man page
eigenvals.princomp Man page
eigenvals.wcmdscale Man page
envfit Man page
envfit.default Man page
envfit.formula Man page
estaccumR Man page
estimateR Man page
estimateR.data.frame Man page
estimateR.default Man page
estimateR.matrix Man page
eventstar Man page
extractAIC.cca Man page
factorfit Man page
fieller.MOStest Man page
fisher.alpha Man page
fisherfit Man page
fitspecaccum Man page
fitted.capscale Man page
fitted.cca Man page
fitted.procrustes Man page
fitted.radfit Man page
fitted.radfit.frame Man page
fitted.rda Man page
.} for EACH ! (+ one \usage{} & \arguments{ Man page
gdispweight Man page
getPermuteMatrix Man page
goodness Man page
goodness.cca Man page
goodness.metaMDS Man page
goodness.monoMDS Man page
head.summary.cca Man page
hierParseFormula Man page
hiersimu Man page
hiersimu.default Man page
hiersimu.formula Man page
howHead Man page
humpfit Man page
identify.ordiplot Man page
indpower Man page
inertcomp Man page
initMDS Man page
intersetcor Man page
isomap Man page
isomapdist Man page
kendall.global Man page
kendall.post Man page
labels.envfit Man page
lines.fitspecaccum Man page
lines.humpfit Man page
lines.permat Man page
lines.preston Man page
lines.prestonfit Man page
lines.procrustes Man page
lines.radfit Man page
lines.radline Man page
lines.spantree Man page
lines.specaccum Man page
linestack Man page
logLik, radfit Man page
logLik, radfit.frame Man page
make.cepnames Man page
make.commsim Man page
mantel Man page
mantel.correlog Man page
mantel.partial Man page
MDSrotate Man page
meandist Man page
metaMDS Man page
metaMDSdist Man page
metaMDSiter Man page
metaMDSredist Man page
metaMDSrotate Man page
mite Man page
mite.env Man page
mite.pcnm Man page
mite.xy Man page
model.frame.cca Man page
model.matrix.cca Man page
monoMDS Man page
MOStest Man page
mrpp Man page
mso Man page
msoplot Man page
multipart Man page
multipart.default Man page
multipart.formula Man page
nestedbetajac Man page
nestedbetasor Man page
nestedchecker Man page
nesteddisc Man page
nestedn0 Man page
nestednodf Man page
nestedtemp Man page
nobs.adonis Man page
nobs.betadisper Man page
nobs.cca Man page
nobs.CCorA Man page
nobs.decorana Man page
nobs.isomap Man page
nobs.metaMDS Man page
nobs.pcnm Man page
nobs.procrustes Man page
nobs.rad Man page
nobs.varpart Man page
nobs.wcmdscale Man page
no.shared Man page
nullmodel Man page
oecosimu Man page
orderingKM Man page
ordiareatest Man page
ordiArgAbsorber Man page
ordiArrowMul Man page
ordiarrows Man page
ordiArrowTextXY Man page
ordicloud Man page
ordicluster Man page
ordiellipse Man page
ordiGetData Man page
ordigrid Man page
ordihull Man page
ordilabel Man page
ordilattice.getEnvfit Man page
ordimedian Man page
ordiNAexclude Man page
ordiNApredict Man page
ordiParseFormula Man page
ordiplot Man page
ordipointlabel Man page
ordiR2step Man page
ordiresids Man page
ordisegments Man page
ordispider Man page
ordisplom Man page
ordistep Man page
ordisurf Man page
ordisurf.default Man page
ordisurf.formula Man page
ordiTerminfo Man page
orditkplot Man page
orditorp Man page
ordixyplot Man page
panel.ordi Man page
panel.ordi3d Man page
panel.ordiarrows Man page
pasteCall Man page
pcnm Man page
permatfull Man page
permatswap Man page
permustats Man page
permustats.adonis Man page
permustats.anosim Man page
permustats.anova.cca Man page
permustats.CCorA Man page
permustats.envfit Man page
permustats.factorfit Man page
permustats.mantel Man page
permustats.mrpp Man page
permustats.mso Man page
permustats.oecosimu Man page
permustats.ordiareatest Man page
permustats.permutest.betadisper Man page
permustats.permutest.cca Man page
permustats.protest Man page
permustats.vectorfit Man page
permutations Man page
permutest Man page
permutest.betadisper Man page
permutest.cca Man page
permutest.default Man page
persp.renyiaccum Man page
persp.tsallisaccum Man page
plot.anosim Man page
plot.betadisper Man page
plot.betadiver Man page
plot.cascadeKM Man page
plot.cca Man page
plot.clamtest Man page
plot.contribdiv Man page
plot.decorana Man page
plot.envfit Man page
plot.fisher Man page
plot.fisherfit Man page
plot.fitspecaccum Man page
plot.humpfit Man page
plot.isomap Man page
plot.mantel.correlog Man page
plot.meandist Man page
plot.metaMDS Man page
plot.monoMDS Man page
plot.MOStest Man page
plot.nestednodf Man page
plot.nestedtemp Man page
plot.ordipointlabel Man page
plot.ordisurf Man page
plot.orditkplot Man page
plot.permat Man page
plot.poolaccum Man page
plot.prc Man page
plot.preston Man page
plot.prestonfit Man page
plot.procrustes Man page
plot.rad Man page
plot.radfit Man page
plot.radfit.frame Man page
plot.radline Man page
plot.renyi Man page
plot.renyiaccum Man page
plot.spantree Man page
plot.specaccum Man page
plot.taxondive Man page
plot.varpart Man page
plot.varpart234 Man page
plot.vegandensity Man page
plot.wcmdscale Man page
points.cca Man page
points.decorana Man page
points.humpfit Man page
points.metaMDS Man page
points.ordiplot Man page
points.orditkplot Man page
points.procrustes Man page
points.radfit Man page
points.radline Man page
poolaccum Man page
postMDS Man page
prc Man page
predict.cca Man page
predict.decorana Man page
predict.fitspecaccum Man page
predict.humpfit Man page
predict.procrustes Man page
predict.radfit Man page
predict.radfit.frame Man page
predict.radline Man page
predict.rda Man page
predict.specaccum Man page
pregraphKM Man page
prepanel.ordi3d Man page
prestondistr Man page
prestonfit Man page
print.commsim Man page
print.nullmodel Man page
print.permat Man page
print.simmat Man page
print.specaccum Man page
print.summary.cca Man page
print.summary.decorana Man page
print.summary.permat Man page
procrustes Man page
profile.humpfit Man page
profile.MOStest Man page
protest Man page
pyrifos Man page
qqmath.permustats Man page
qqnorm.permustats Man page
radfit Man page
radfit.data.frame Man page
radfit.default Man page
radlattice Man page
rad.lognormal Man page
rad.null Man page
rad.preempt Man page
rad.zipf Man page
rad.zipfbrot Man page
rankindex Man page
rarecurve Man page
rarefy Man page
rareslope Man page
raupcrick Man page
rda Man page
rda.default Man page
rda.formula Man page
read.cep Man page
renyi Man page
renyiaccum Man page
reorder.hclust Man page
residuals.cca Man page
residuals.procrustes Man page
rev.hclust Man page
rrarefy Man page
RsquareAdj Man page
RsquareAdj.cca Man page
RsquareAdj.default Man page
RsquareAdj.glm Man page
RsquareAdj.lm Man page
RsquareAdj.rda Man page
scores Man page
scores.betadisper Man page
scores.betadiver Man page
scores.cca Man page
scores.decorana Man page
scores.default Man page
scores.envfit Man page
scores.hclust Man page
scores.lda Man page
scores.metaMDS Man page
scores.monoMDS Man page
scores.ordihull Man page
scores.ordiplot Man page
scores.orditkplot Man page
scores.pcnm Man page
scores.rda Man page
scores.wcmdscale Man page
screeplot.cca Man page
screeplot.decorana Man page
screeplot.prcomp Man page
screeplot.princomp Man page
showvarparts Man page
simper Man page
simpleRDA2 Man page
simulate.capscale Man page
simulate.cca Man page
simulate.nullmodel Man page
simulate.rda Man page
sipoo Man page
spandepth Man page
spantree Man page
specaccum Man page
specnumber Man page
specpool Man page
specpool2vect Man page
specslope Man page
spenvcor Man page
SSarrhenius Man page
SSgitay Man page
SSgleason Man page
SSlomolino Man page
stepacross Man page
stressplot Man page
stressplot.capscale Man page
stressplot.cca Man page
stressplot.default Man page
stressplot.monoMDS Man page
stressplot.prcomp Man page
stressplot.princomp Man page
stressplot.rda Man page
stressplot.wcmdscale Man page
str.nullmodel Man page
summary.anosim Man page
summary.bioenv Man page
summary.cca Man page
summary.clamtest Man page
summary.decorana Man page
summary.dispweight Man page
summary.eigenvals Man page
summary.humpfit Man page
summary.isomap Man page
summary.meandist Man page
summary.ordiellipse Man page
summary.ordihull Man page
summary.permat Man page
summary.permustats Man page
summary.poolaccum Man page
summary.prc Man page
summary.procrustes Man page
summary.radfit.frame Man page
summary.simper Man page
summary.specaccum Man page
summary.taxondive Man page
swan Man page
tabasco Man page
tail.summary.cca Man page
taxa2dist Man page
taxondive Man page
text.cca Man page
text.decorana Man page
text.metaMDS Man page
text.ordiplot Man page
text.orditkplot Man page
text.procrustes Man page
tolerance Man page
tolerance.cca Man page
treedist Man page
treedive Man page
treeheight Man page
tsallis Man page
tsallisaccum Man page
TukeyHSD.betadisper Man page
update.nullmodel Man page
varechem Man page
varespec Man page
varpart Man page
varpart2 Man page
varpart3 Man page
varpart4 Man page
vectorfit Man page
vegan Man page
veganCovEllipse Man page
vegan-defunct Man page
vegan-deprecated Man page
vegandocs Man page
veganMahatrans Man page
vegan-package Man page
vegdist Man page
vegemite Man page
veiledspec Man page
vif.cca Man page
wascores Man page
wcmdscale Man page
weights.cca Man page
weights.decorana Man page
weights.rda Man page
wisconsin Man page

Files

DESCRIPTION
NAMESPACE
R
R/AIC.radfit.R R/CCorA.R R/MDSrotate.R R/MOStest.R R/RsquareAdj.R R/SSarrhenius.R R/SSgitay.R R/SSgleason.R R/SSlomolino.R R/TukeyHSD.betadisper.R R/add1.cca.R R/ade2vegancca.R R/adipart.R R/adipart.default.R R/adipart.formula.R R/adonis.R R/alias.cca.R R/anosim.R R/anova.betadisper.R R/anova.cca.R R/anova.ccabyterm.R R/anova.ccalist.R R/anova.ccanull.R R/anova.prc.R R/as.fisher.R R/as.hclust.spantree.R R/as.mcmc.oecosimu.R R/as.mcmc.permat.R R/as.mlm.R R/as.mlm.cca.R R/as.mlm.rda.R R/as.preston.R R/as.rad.R R/as.ts.oecosimu.R R/as.ts.permat.R R/beals.R R/betadisper.R R/betadiver.R R/bgdispersal.R R/bioenv.R R/bioenv.default.R R/bioenv.formula.R R/biplot.CCorA.R R/biplot.rda.R R/boxplot.betadisper.R R/boxplot.specaccum.R R/bstick.R R/bstick.cca.R R/bstick.decorana.R R/bstick.default.R R/bstick.prcomp.R R/bstick.princomp.R R/cIndexKM.R R/calibrate.R R/calibrate.cca.R R/calibrate.ordisurf.R R/capscale.R R/cascadeKM.R R/cca.R R/cca.default.R R/cca.formula.R R/centroids.cca.R R/checkSelect.R R/clamtest.R R/coef.cca.R R/coef.radfit.R R/coef.rda.R R/commsim.R R/confint.MOStest.R R/contribdiv.R R/cophenetic.spantree.R R/coverscale.R R/decorana.R R/decostand.R R/designdist.R R/deviance.cca.R R/deviance.rda.R R/dispindmorisita.R R/dispweight.R R/distconnected.R R/diversity.R R/downweight.R R/drop1.cca.R R/eigengrad.R R/eigenvals.R R/envfit.R R/envfit.default.R R/envfit.formula.R R/estaccumR.R R/estimateR.R R/estimateR.data.frame.R R/estimateR.default.R R/estimateR.matrix.R R/eventstar.R R/extractAIC.cca.R R/factorfit.R R/fieller.MOStest.R R/fisher.alpha.R R/fisherfit.R R/fitspecaccum.R R/fitted.capscale.R R/fitted.cca.R R/fitted.procrustes.R R/fitted.radfit.R R/fitted.rda.R R/gdispweight.R R/getPermuteMatrix.R R/goodness.R R/goodness.cca.R R/goodness.metaMDS.R R/head.summary.cca.R R/hierParseFormula.R R/hiersimu.R R/hiersimu.default.R R/hiersimu.formula.R R/howHead.R R/humpfit.R R/identify.ordiplot.R R/indpower.R R/inertcomp.R R/initMDS.R R/intersetcor.R R/isomap.R R/isomapdist.R R/kendall.global.R R/kendall.post.R R/labels.envfit.R R/lines.humpfit.R R/lines.permat.R R/lines.prestonfit.R R/lines.procrustes.R R/lines.radline.R R/lines.spantree.R R/linestack.R R/make.cepnames.R R/make.commsim.R R/mantel.R R/mantel.correlog.R R/mantel.partial.R R/meandist.R R/metaMDS.R R/metaMDSdist.R R/metaMDSiter.R R/metaMDSredist.R R/model.frame.cca.R R/model.matrix.cca.R R/monoMDS.R R/mrpp.R R/mso.R R/msoplot.R R/multipart.R R/multipart.default.R R/multipart.formula.R R/nestedbetasor.R R/nestedchecker.R R/nesteddisc.R R/nestedn0.R R/nestednodf.R R/nestedtemp.R R/no.shared.R R/nobs.R R/nullmodel.R R/oecosimu.R R/orderingKM.R R/ordiArgAbsorber.R R/ordiArrowMul.R R/ordiArrowTextXY.R R/ordiGetData.R R/ordiNAexclude.R R/ordiParseFormula.R R/ordiR2step.R R/ordiTerminfo.R R/ordiareatest.R R/ordiarrows.R R/ordicloud.R R/ordicluster.R R/ordiellipse.R R/ordigrid.R R/ordihull.R R/ordilabel.R R/ordilattice.getEnvfit.R R/ordimedian.R R/ordiplot.R R/ordipointlabel.R R/ordiresids.R R/ordisegments.R R/ordispider.R R/ordisplom.R R/ordistep.R R/ordisurf.R R/orditkplot.R R/orditorp.R R/ordixyplot.R R/panel.ordi.R R/panel.ordi3d.R R/pasteCall.R R/pcnm.R R/permatfull.R R/permatswap.R R/permustats.R R/permuted.index.R R/permutest.betadisper.R R/permutest.cca.R R/persp.renyiaccum.R R/persp.tsallisaccum.R R/plot.MOStest.R R/plot.anosim.R R/plot.betadisper.R R/plot.betadiver.R R/plot.cascadeKM.R R/plot.cca.R R/plot.clamtest.R R/plot.contribdiv.R R/plot.decorana.R R/plot.envfit.R R/plot.fisherfit.R R/plot.humpfit.R R/plot.isomap.R R/plot.mantel.correlog.R R/plot.meandist.R R/plot.metaMDS.R R/plot.nestedtemp.R R/plot.ordipointlabel.R R/plot.ordisurf.R R/plot.orditkplot.R R/plot.permat.R R/plot.poolaccum.R R/plot.prc.R R/plot.preston.R R/plot.prestonfit.R R/plot.procrustes.R R/plot.rad.R R/plot.radfit.R R/plot.radfit.frame.R R/plot.radline.R R/plot.renyi.R R/plot.renyiaccum.R R/plot.spantree.R R/plot.specaccum.R R/plot.taxondive.R R/plot.varpart.R R/plot.varpart234.R R/points.cca.R R/points.decorana.R R/points.humpfit.R R/points.metaMDS.R R/points.ordiplot.R R/points.orditkplot.R R/points.procrustes.R R/points.radline.R R/poolaccum.R R/postMDS.R R/prc.R R/predict.cca.R R/predict.decorana.R R/predict.fitspecaccum.R R/predict.humpfit.R R/predict.radline.R R/predict.rda.R R/predict.specaccum.R R/pregraphKM.R R/prepanel.ordi3d.R R/prestondistr.R R/prestonfit.R R/print.CCorA.R R/print.MOStest.R R/print.adonis.R R/print.anosim.R R/print.betadisper.R R/print.bioenv.R R/print.capscale.R R/print.cca.R R/print.commsim.R R/print.decorana.R R/print.envfit.R R/print.factorfit.R R/print.fisherfit.R R/print.humpfit.R R/print.isomap.R R/print.mantel.R R/print.mantel.correlog.R R/print.metaMDS.R R/print.monoMDS.R R/print.mrpp.R R/print.mso.R R/print.nestedchecker.R R/print.nesteddisc.R R/print.nestedn0.R R/print.nestednodf.R R/print.nestedtemp.R R/print.nullmodel.R R/print.oecosimu.R R/print.permat.R R/print.permutest.betadisper.R R/print.permutest.cca.R R/print.poolaccum.R R/print.prestonfit.R R/print.procrustes.R R/print.protest.R R/print.radfit.R R/print.radfit.frame.R R/print.radline.R R/print.simmat.R R/print.specaccum.R R/print.summary.bioenv.R R/print.summary.cca.R R/print.summary.clamtest.R R/print.summary.decorana.R R/print.summary.humpfit.R R/print.summary.isomap.R R/print.summary.meandist.R R/print.summary.permat.R R/print.summary.prc.R R/print.summary.procrustes.R R/print.summary.taxondive.R R/print.taxondive.R R/print.varpart.R R/print.varpart234.R R/print.vectorfit.R R/print.wcmdscale.R R/procrustes.R R/profile.MOStest.R R/profile.humpfit.R R/protest.R R/rad.lognormal.R R/rad.null.R R/rad.preempt.R R/rad.zipf.R R/rad.zipfbrot.R R/radfit.R R/radfit.data.frame.R R/radfit.default.R R/radlattice.R R/rankindex.R R/rarecurve.R R/rarefy.R R/rareslope.R R/raupcrick.R R/rda.R R/rda.default.R R/rda.formula.R R/read.cep.R R/renyi.R R/renyiaccum.R R/residuals.cca.R R/residuals.procrustes.R R/rrarefy.R R/scalingUtils.R R/scores.R R/scores.betadisper.R R/scores.betadiver.R R/scores.cca.R R/scores.decorana.R R/scores.default.R R/scores.envfit.R R/scores.lda.R R/scores.metaMDS.R R/scores.ordihull.R R/scores.ordiplot.R R/scores.orditkplot.R R/scores.pcnm.R R/scores.rda.R R/screeplot.cca.R R/screeplot.decorana.R R/screeplot.prcomp.R R/screeplot.princomp.R R/showvarparts.R R/simper.R R/simpleRDA2.R R/simulate.nullmodel.R R/simulate.rda.R R/spandepth.R R/spantree.R R/specaccum.R R/specnumber.R R/specpool.R R/specpool2vect.R R/specslope.R R/spenvcor.R R/stepacross.R R/str.nullmodel.R R/stressplot.R R/stressplot.wcmdscale.R R/summary.anosim.R R/summary.bioenv.R R/summary.cca.R R/summary.clamtest.R R/summary.decorana.R R/summary.dispweight.R R/summary.humpfit.R R/summary.isomap.R R/summary.meandist.R R/summary.ordiellipse.R R/summary.ordihull.R R/summary.permat.R R/summary.poolaccum.R R/summary.prc.R R/summary.procrustes.R R/summary.radfit.frame.R R/summary.specaccum.R R/summary.taxondive.R R/swan.R R/tabasco.R R/taxa2dist.R R/taxondive.R R/text.cca.R R/text.decorana.R R/text.metaMDS.R R/text.ordiplot.R R/text.orditkplot.R R/tolerance.R R/tolerance.cca.R R/treedist.R R/treedive.R R/treeheight.R R/tsallis.R R/tsallisaccum.R R/update.nullmodel.R R/varpart.R R/varpart2.R R/varpart3.R R/varpart4.R R/vectorfit.R R/vegan-defunct.R R/vegan-deprecated.R R/veganCovEllipse.R R/veganMahatrans.R R/vegandocs.R R/vegdist.R R/vegemite.R R/veiledspec.R R/vif.cca.R R/wascores.R R/wcmdscale.R R/weights.cca.R R/weights.decorana.R R/weights.rda.R R/wisconsin.R R/zzz.R
build
build/vignette.rds
data
data/BCI.env.rda
data/BCI.rda
data/dune.env.rda
data/dune.phylodis.rda
data/dune.rda
data/dune.taxon.rda
data/mite.env.rda
data/mite.pcnm.rda
data/mite.rda
data/mite.xy.rda
data/pyrifos.rda
data/sipoo.rda
data/varechem.rda
data/varespec.rda
inst
inst/ChangeLog
inst/NEWS.Rd
inst/ONEWS
inst/doc
inst/doc/FAQ-vegan.Rmd
inst/doc/FAQ-vegan.html
inst/doc/decision-vegan.R
inst/doc/decision-vegan.Rnw
inst/doc/decision-vegan.pdf
inst/doc/diversity-vegan.R
inst/doc/diversity-vegan.Rnw
inst/doc/diversity-vegan.pdf
inst/doc/intro-vegan.R
inst/doc/intro-vegan.Rnw
inst/doc/intro-vegan.pdf
inst/doc/partitioning.R
inst/doc/partitioning.Rnw
inst/doc/partitioning.pdf
man
man/BCI.Rd man/CCorA.Rd man/MDSrotate.Rd man/MOStest.Rd man/RsquareAdj.Rd man/SSarrhenius.Rd man/add1.cca.Rd man/adipart.Rd man/adonis.Rd man/anosim.Rd man/anova.cca.Rd man/as.mlm.Rd man/beals.Rd man/betadisper.Rd man/betadiver.Rd man/bgdispersal.Rd man/bioenv.Rd man/biplot.rda.Rd man/capscale.Rd man/cascadeKM.Rd man/cca.Rd man/cca.object.Rd man/clamtest.Rd man/commsim.Rd man/contribdiv.Rd man/decorana.Rd man/decostand.Rd man/designdist.Rd man/deviance.cca.Rd man/dispindmorisita.Rd man/dispweight.Rd man/distconnected.Rd man/diversity.Rd man/dune.Rd man/dune.taxon.Rd man/eigenvals.Rd man/envfit.Rd man/eventstar.Rd man/fisherfit.Rd man/goodness.cca.Rd man/goodness.metaMDS.Rd man/humpfit.Rd man/indpower.Rd man/isomap.Rd man/kendall.global.Rd man/linestack.Rd man/make.cepnames.Rd man/mantel.Rd man/mantel.correlog.Rd man/metaMDS.Rd man/mite.Rd man/model.matrix.cca.Rd man/monoMDS.Rd man/mrpp.Rd man/mso.Rd man/multipart.Rd man/nestedtemp.Rd man/nobs.adonis.Rd man/nullmodel.Rd man/oecosimu.Rd man/ordiArrowTextXY.Rd man/ordiarrows.Rd man/ordihull.Rd man/ordilabel.Rd man/ordiplot.Rd man/ordipointlabel.Rd man/ordiresids.Rd man/ordistep.Rd man/ordisurf.Rd man/orditkplot.Rd man/orditorp.Rd man/ordixyplot.Rd man/pcnm.Rd man/permatfull.Rd man/permustats.Rd man/permutations.Rd man/permutest.betadisper.Rd man/plot.cca.Rd man/prc.Rd man/predict.cca.Rd man/procrustes.Rd man/pyrifos.Rd man/radfit.Rd man/rankindex.Rd man/rarefy.Rd man/raupcrick.Rd man/read.cep.Rd man/renyi.Rd man/reorder.hclust.Rd man/scores.Rd man/screeplot.cca.Rd man/simper.Rd man/simulate.rda.Rd man/sipoo.Rd man/spantree.Rd man/specaccum.Rd man/specpool.Rd man/stepacross.Rd man/stressplot.wcmdscale.Rd man/taxondive.Rd man/tolerance.Rd man/treedive.Rd man/tsallis.Rd man/varechem.Rd man/varpart.Rd man/vegan-defunct.Rd man/vegan-deprecated.Rd man/vegan-internal.Rd man/vegan-package.Rd man/vegandocs.Rd man/vegdist.Rd man/vegemite.Rd man/wascores.Rd man/wcmdscale.Rd
src
src/cepin.f
src/data2hill.c
src/decorana.f
src/goffactor.c
src/monoMDS.f
src/nestedness.c
src/ordering.f
src/pnpoly.c
src/stepacross.c
src/vegdist.c
vignettes
vignettes/FAQ-vegan.Rmd
vignettes/decision-vegan.Rnw
vignettes/diversity-vegan.Rnw
vignettes/intro-vegan.Rnw
vignettes/partitioning.Rnw
vignettes/varpart23.pdf
vignettes/varpart4.pdf
vignettes/vegan.bib
vignettes/vegan.sty

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