## compiled code
useDynLib(vegan)

## Export regular function names (no dots)

export(CCorA, MOStest, RsquareAdj, SSarrhenius, SSgitay, SSgleason,
SSlomolino, adipart, adonis, anosim, beals, betadisper, betadiver,
bgdispersal, bioenv, bioenvdist, bstick, cIndexKM, calibrate, capscale,
cascadeKM, cca, contribdiv, clamtest, commsim, dbrda, decorana,
decostand, designdist, coverscale, dispweight, dispindmorisita, distconnected,
diversity, downweight, drarefy, eigengrad, eigenvals, envfit,
estaccumR, estimateR, eventstar, factorfit, fisherfit, fitspecaccum,
gdispweight,goodness, hiersimu, humpfit, indpower, inertcomp, initMDS,
intersetcor, isomapdist, isomap, linestack, mantel, meandist,
metaMDSdist, metaMDSiter, metaMDSredist, MDSrotate, metaMDS, monoMDS,
mrpp, msoplot, mso, multipart, make.commsim, nestedbetajac, nestedbetasor, nestedchecker,
nesteddisc, nestedn0, nestednodf, nestedtemp, nullmodel, oecosimu, smbind,
ordiareatest, ordiR2step,
ordiarrows, ordiArrowMul, ordiArrowTextXY, ordibar, ordicloud,
ordicluster, ordiellipse, ordigrid,
ordihull, ordilabel, ordiplot, ordipointlabel, ordiresids,
ordisegments, ordispider, ordisplom, ordistep, ordisurf,
orditkplot, orditorp, ordixyplot, ordiYbar,
pcnm, permatfull, permatswap, permustats, permutest,
poolaccum, postMDS, prc, prestondistr, prestonfit, procrustes,
protest, radfit, radlattice, rankindex, rarefy, rarecurve, rareslope,
raupcrick, rda, renyiaccum, renyi, rrarefy, scores,
showvarparts, simper, spandepth, spantree, specaccum, specslope,
specnumber, specpool2vect, specpool, spenvcor,
stepacross, stressplot, swan, tabasco, taxa2dist, taxondive, tolerance,
treedist, treedive, treeheight, tsallisaccum, tsallis, varpart,
vectorfit, vegandocs, vegdist, vegemite, veiledspec, wascores,
wcmdscale, wisconsin)
## export pasteCall for 'permute'
export(pasteCall)
## export anova.cca for 'BiodiversityR': this should be fixed there
export(anova.cca)
export(as.mcmc.oecosimu, as.mcmc.permat)
## export oldCapscale for compatibility after new capscale design
export(oldCapscale)
## alternative implementation of adonis: may be eliminated later
export(adonis2)

## export regular functions with dot names

export(as.fisher, as.mlm, as.preston, as.rad, fieller.MOStest,
fisher.alpha, kendall.global, kendall.post, make.cepnames,
mantel.correlog, mantel.partial, no.shared, rad.lognormal, rad.null,
rad.preempt, rad.zipf, rad.zipfbrot, read.cep,
vif.cca)

## Export panel functions
export(panel.ordi, panel.ordiarrows, panel.ordi3d, prepanel.ordi3d)

## Export .Depracated functions (to be removed later)
export(commsimulator)
## Export .Defunct function names (on their way out)
S3method(density, adonis)
S3method(density, anosim)
S3method(density, mantel)
S3method(density, mrpp)
S3method(density, oecosimu)
S3method(density, permutest.cca)
S3method(density, protest)
S3method(densityplot, adonis)
S3method(densityplot, oecosimu)

## do NOT export the following internal functions

## export(ade2vegancca, orderingKM, ordiArgAbsorber, ordiArrowMul,
## ordiGetData, ordimedian, ordiNAexclude, ordiNApredict,
## ordiParseFormula, ordiTerminfo, pregraphKM, simpleRDA2, varpart2,
## varpart3, varpart4, veganCovEllipse, veganMahatrans)

## Imports
import(stats)
import(graphics)
import(permute)
importFrom(utils, news, vignette, combn, flush.console, head, object.size,
           tail, str)
importFrom(tools, Rd2txt, startDynamicHelp)
import(grDevices) ## too many functions to be listed separately
import(lattice)
importFrom(parallel, mclapply, makeCluster, stopCluster, clusterEvalQ,
           parApply, parLapply, parSapply, parRapply, parCapply)
importFrom(MASS, isoMDS, sammon, Shepard, mvrnorm, lda)
importFrom(cluster, daisy, ellipsoidhull)
## 's' must be imported in mgcv < 1.8-0 (not needed later)
importFrom(mgcv, gam, s, te, predict.gam, summary.gam)
## Registration of S3 methods defined in vegan
# adipart: vegan
S3method(adipart, default)
S3method(adipart, formula)
# AIC: stats
S3method(AIC, fitspecaccum)
S3method(AIC, radfit)
S3method(AIC, radfit.frame)
# RsquareAdj: vegan
S3method(RsquareAdj, cca)
S3method(RsquareAdj, default)
S3method(RsquareAdj, glm)
S3method(RsquareAdj, lm)
S3method(RsquareAdj, rda)
# TukeyHSD: stats
S3method(TukeyHSD, betadisper)
# add1: stats
S3method(add1, cca)
# alias: stats
S3method(alias, cca)
# anova: stats
S3method(anova, betadisper)
S3method(anova, cca)
S3method(anova, prc)
# as.hclust: stats
S3method(as.hclust, spantree)
## Do not export as.mcmc now: would need import(coda)
# as.mcmc: coda <======= rare
#S3method(as.mcmc, oecosimu)
#S3method(as.mcmc, permat)
# as.mlm: vegan
S3method(as.mlm, cca)
S3method(as.mlm, rda)
# as.ts: stats
S3method(as.ts, oecosimu)
S3method(as.ts, permat)
# bioenv: vegan
S3method(bioenv, default)
S3method(bioenv, formula)
# biplot: stats
S3method(biplot, CCorA)
S3method(biplot, cca)
S3method(biplot, rda)
# boxplot: graphics
S3method(boxplot, betadisper)
S3method(boxplot, specaccum)
# bstick: vegan
S3method(bstick, cca)
S3method(bstick, decorana)
S3method(bstick, default)
S3method(bstick, prcomp)
S3method(bstick, princomp)
## c: base
S3method(c, permustats)
# calibrate: vegan
S3method(calibrate, cca)
S3method(calibrate, ordisurf)
# cca: vegan
S3method(cca, default)
S3method(cca, formula)
# coef: stats
S3method(coef, cca)
S3method(coef, radfit)
S3method(coef, radfit.frame)
S3method(coef, rda)
# confint: stats -- also uses MASS:::confint.glm & MASS:::profile.glm
# does this work with namespaces??
S3method(confint, MOStest)
# cophenetic: stats
S3method(cophenetic, spantree)
# density: stats
S3method(density, permustats)
# densityplot: lattice
S3method(densityplot, permustats)
# deviance: stats
S3method(deviance, cca)
S3method(deviance, rda)
S3method(deviance, radfit)
S3method(deviance, radfit.frame)
S3method(deviance, fitspecaccum)
# drop1: stats
S3method(drop1, cca)
# eigenvals: vegan
S3method(eigenvals, betadisper)
S3method(eigenvals, cca)
S3method(eigenvals, default)
S3method(eigenvals, dudi)
S3method(eigenvals, pca)
S3method(eigenvals, pcnm)
S3method(eigenvals, pco)
S3method(eigenvals, prcomp)
S3method(eigenvals, princomp)
S3method(eigenvals, wcmdscale)
# envfit: vegan
S3method(envfit, default)
S3method(envfit, formula)
# estimateR: vegan
S3method(estimateR, data.frame)
S3method(estimateR, default)
S3method(estimateR, matrix)
# extractAIC: stats
S3method(extractAIC, cca)
# fitted: stats
S3method(fitted, capscale)
S3method(fitted, cca)
S3method(fitted, dbrda)
S3method(fitted, procrustes)
S3method(fitted, radfit)
S3method(fitted, radfit.frame)
S3method(fitted, rda)
# goodness: vegan
S3method(goodness, cca)
S3method(goodness, metaMDS)
S3method(goodness, monoMDS)
# head: utils
S3method(head, summary.cca)
# hiersimu: vegan
S3method(hiersimu, default)
S3method(hiersimu, formula)
# methods for hclust object in base R: these would be better in R
S3method(reorder, hclust)
S3method(rev, hclust)
# identify: graphics
S3method(identify, ordiplot)
# labels: base
S3method(labels, envfit)
# lines: graphics
S3method(lines, fitspecaccum)
S3method(lines, humpfit)
S3method(lines, permat)
S3method(lines, preston)
S3method(lines, prestonfit)
S3method(lines, procrustes)
S3method(lines, radline)
S3method(lines, radfit)
S3method(lines, spantree)
S3method(lines, specaccum)
## logLik: stats
S3method(logLik, radfit)
S3method(logLik, radfit.frame)
# model.frame, model.matrix: stats
S3method(model.frame, cca)
S3method(model.matrix, cca)
# multipart: vegan
S3method(multipart, default)
S3method(multipart, formula)
# nobs: stats
S3method(nobs, CCorA)
S3method(nobs, adonis)
S3method(nobs, anova.cca)
S3method(nobs, betadisper)
S3method(nobs, cca)
S3method(nobs, decorana)
S3method(nobs, isomap)
S3method(nobs, metaMDS)
S3method(nobs, pcnm)
S3method(nobs, procrustes)
S3method(nobs, rad)
S3method(nobs, varpart)
S3method(nobs, wcmdscale)
# ordisurf: vegan
S3method(ordisurf, default)
S3method(ordisurf, formula)

## permustats methods
S3method(permustats, adonis)
S3method(permustats, anosim)
S3method(permustats, mantel)
S3method(permustats, mrpp)
S3method(permustats, oecosimu)
S3method(permustats, ordiareatest)
S3method(permustats, permutest.betadisper)
S3method(permustats, permutest.cca)
S3method(permustats, protest)
S3method(permustats, anova.cca)
## these return an error: no permutation data
S3method(permustats, CCorA)
S3method(permustats, envfit)
S3method(permustats, factorfit)
S3method(permustats, vectorfit)
S3method(permustats, mso)

S3method(print, permustats)
S3method(summary, permustats)
S3method(print, summary.permustats)

# permutest: vegan
S3method(permutest, betadisper)
S3method(permutest, cca)
S3method(permutest, default)
# persp: graphics
S3method(persp, renyiaccum)
S3method(persp, tsallisaccum)
# plot: graphics
S3method(plot, MOStest)
S3method(plot, anosim)
S3method(plot, betadisper)
S3method(plot, betadiver)
S3method(plot, cascadeKM)
S3method(plot, cca)
S3method(plot, contribdiv)
S3method(plot, clamtest)
S3method(plot, decorana)
S3method(plot, envfit)
S3method(plot, fisher)
S3method(plot, fisherfit)
S3method(plot, fitspecaccum)
S3method(plot, humpfit)
S3method(plot, isomap)
S3method(plot, mantel.correlog)
S3method(plot, meandist)
S3method(plot, metaMDS)
S3method(plot, monoMDS)
S3method(plot, nestednodf)
S3method(plot, nestedtemp)
S3method(plot, ordisurf)
S3method(plot, ordipointlabel)
S3method(plot, orditkplot)
S3method(plot, permat)
S3method(plot, poolaccum)
S3method(plot, prc)
S3method(plot, preston)
S3method(plot, prestonfit)
S3method(plot, procrustes)
S3method(plot, rad)
S3method(plot, radfit)
S3method(plot, radfit.frame)
S3method(plot, radline)
S3method(plot, renyi)
S3method(plot, renyiaccum)
S3method(plot, spantree)
S3method(plot, specaccum)
S3method(plot, taxondive)
S3method(plot, varpart)
S3method(plot, varpart234)
S3method(plot, vegandensity) # <- .defunct in 2.4-0
S3method(plot, wcmdscale)
# points: graphics
S3method(points, cca)
S3method(points, decorana)
S3method(points, humpfit)
S3method(points, metaMDS)
S3method(points, ordiplot)
S3method(points, orditkplot)
S3method(points, procrustes)
S3method(points, radline)
S3method(points, radfit)
# predict: stats
S3method(predict, cca)
S3method(predict, decorana)
S3method(predict, fitspecaccum)
S3method(predict, humpfit)
S3method(predict, procrustes)
S3method(predict, radline)
S3method(predict, radfit)
S3method(predict, radfit.frame)
S3method(predict, rda)
S3method(predict, specaccum)
# print: base
S3method(print, CCorA)
S3method(print, MOStest)
S3method(print, adonis)
S3method(print, anosim)
S3method(print, betadisper)
S3method(print, bioenv)
S3method(print, cca)
S3method(print, commsim)
S3method(print, decorana)
S3method(print, eigenvals)
S3method(print, envfit)
S3method(print, factorfit)
S3method(print, fisherfit)
S3method(print, humpfit)
S3method(print, isomap)
S3method(print, mantel)
S3method(print, mantel.correlog)
S3method(print, metaMDS)
S3method(print, monoMDS)
S3method(print, mrpp)
S3method(print, mso)
S3method(print, nestedchecker)
S3method(print, nesteddisc)
S3method(print, nestedn0)
S3method(print, nestednodf)
S3method(print, nestedtemp)
S3method(print, nullmodel)
S3method(print, oecosimu)
S3method(print, ordiareatest)
S3method(print, permat)
S3method(print, permutest.betadisper)
S3method(print, permutest.cca)
S3method(print, poolaccum)
S3method(print, prestonfit)
S3method(print, procrustes)
S3method(print, protest)
S3method(print, radfit)
S3method(print, radfit.frame)
S3method(print, radline)
S3method(print, specaccum)
S3method(print, simmat)
S3method(print, simper)
S3method(print, summary.bioenv)
S3method(print, summary.cca)
S3method(print, summary.clamtest)
S3method(print, summary.decorana)
S3method(print, summary.dispweight)
S3method(print, summary.eigenvals)
S3method(print, summary.humpfit)
S3method(print, summary.isomap)
S3method(print, summary.meandist)
S3method(print, summary.permat)
S3method(print, summary.prc)
S3method(print, summary.procrustes)
S3method(print, summary.simper)
S3method(print, summary.taxondive)
S3method(print, taxondive)
S3method(print, tolerance.cca)
S3method(print, varpart)
S3method(print, varpart234)
S3method(print, vectorfit)
S3method(print, wcmdscale)
# profile: stats
# see note on 'confint'
S3method(profile, MOStest)
S3method(profile, humpfit)
## qqmath: lattice
S3method(qqmath, permustats)
## qqnorm: stats
S3method(qqnorm, permustats)
# radfit: vegan
S3method(radfit, data.frame)
S3method(radfit, default)
S3method(radfit, matrix)
# rda: vegan
S3method(rda, default)
S3method(rda, formula)
# residuals: stats
S3method(residuals, cca)
S3method(residuals, procrustes)
# scores: vegan
S3method(scores, betadisper)
S3method(scores, betadiver)
S3method(scores, cca)
S3method(scores, decorana)
S3method(scores, default)
S3method(scores, envfit)
S3method(scores, hclust)
S3method(scores, lda)
S3method(scores, metaMDS)
S3method(scores, monoMDS)
S3method(scores, ordihull)
S3method(scores, ordiplot)
S3method(scores, orditkplot)
S3method(scores, pcnm)
S3method(scores, rda)
S3method(scores, wcmdscale)
# screeplot: stats
S3method(screeplot, cca)
S3method(screeplot, decorana)
S3method(screeplot, prcomp)
S3method(screeplot, princomp)
# simulate: stats
S3method(simulate, capscale)
S3method(simulate, cca)
S3method(simulate, dbrda)
S3method(simulate, rda)
S3method(simulate, nullmodel)
# specslope: vegan
S3method(specslope, specaccum)
S3method(specslope, fitspecaccum)
# str: utils
S3method(str, nullmodel)
# stressplot: vegan
S3method(stressplot, default)
S3method(stressplot, monoMDS)
S3method(stressplot, wcmdscale)
S3method(stressplot, capscale)
S3method(stressplot, dbrda)
S3method(stressplot, cca)
S3method(stressplot, rda)
S3method(stressplot, prcomp)
S3method(stressplot, princomp)
# summary: base
S3method(summary, anosim)
S3method(summary, bioenv)
S3method(summary, cca)
S3method(summary, clamtest)
S3method(summary, decorana)
S3method(summary, dispweight)
S3method(summary, eigenvals)
S3method(summary, humpfit)
S3method(summary, isomap)
S3method(summary, meandist)
S3method(summary, ordiellipse)
S3method(summary, ordihull)
S3method(summary, permat)
S3method(summary, poolaccum)
S3method(summary, prc)
S3method(summary, procrustes)
S3method(summary, radfit.frame)
S3method(summary, simper)
S3method(summary, specaccum)
S3method(summary, taxondive)
# tail: utils
S3method(tail, summary.cca)
# text: graphics
S3method(text, cca)
S3method(text, decorana)
S3method(text, metaMDS)
S3method(text, ordiplot)
S3method(text, orditkplot)
S3method(text, procrustes)
# tolerance: vegan -- or analogue?? Gav?
S3method(tolerance, cca)
# update: stats
S3method(update, nullmodel)
# vif: car -- but not used as a S3method within vegan
# because of car definition: could be defined as exported 'vif' generic
# in vegan with namespace
#S3method(vif, cca)
# weights: stats
S3method(weights, cca)
S3method(weights, decorana)
S3method(weights, rda)
