## 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, bstick, cIndexKM, calibrate, capscale, cascadeKM,
cca, commsimulator, contribdiv, clamtest, decorana, decostand, designdist,
coverscale, dispindmorisita, distconnected, diversity, downweight,
drarefy, eigengrad, eigenvals, envfit, estaccumR, estimateR, eventstar,
factorfit, fisherfit, fitspecaccum, goodness, hiersimu, humpfit,
indpower, inertcomp, initMDS, intersetcor, isomapdist, isomap,
linestack, mantel, meandist, metaMDSdist, metaMDSiter, metaMDSredist,
MDSrotate, metaMDS, monoMDS, mrpp, msoplot, mso, multipart,
nestedbetajac, nestedbetasor, 
nestedchecker, nesteddisc, nestedn0, nestednodf, nestedtemp, oecosimu,
ordiR2step, ordiarrows, ordicloud, ordicluster,
ordiellipse, ordigrid, ordihull, ordilabel, ordiplot3d,
ordiplot, ordipointlabel, ordiresids, ordirgl, ordisegments,
ordispider, ordisplom, ordistep, ordisurf, orditkplot, orditorp,
ordixyplot, orglpoints, orglsegments, orglspider, orgltext, 
pcnm, permatfull, permatswap, permutest, poolaccum, postMDS, prc,
prestondistr, prestonfit, procrustes, protest, radfit, radlattice,
rankindex, rarecurve, rarefy, raupcrick, rda, renyiaccum, renyi,
rrarefy, scores, showvarparts, simper, spandepth, spantree, specaccum,
specnumber, specpool2vect, specpool, spenvcor, stepacross, stressplot,
swan, 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 for coda
export(as.mcmc.oecosimu, as.mcmc.permat)
## DEFUNCT: export names defined in vegan-defunct
export(permuted.index2, getNumObs)

## 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, rgl.isomap,
rgl.renyiaccum, vif.cca)

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

## Export .Depracated functions (to be removed later)
export(metaMDSrotate)

## do NOT export the following internal functions

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

## Registration of S3 methods
import(stats)
import(graphics)
importFrom(utils, head, tail)
importFrom(lattice, densityplot)
## nobs only exists in R 2.13.0 -- import from permute with older R
if (getRversion() < "2.13.0") {
    importFrom(permute, nobs)
}
# AIC: stats
S3method(AIC, radfit)
# 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)
## 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, 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)
# 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, rda)
# confint: stats -- also uses MASS:::confint.glm & MASS:::profile.glm
# does this work with namespaces??
S3method(confint, MOStest)
S3method(confint, fisherfit)
# cophenetic: stats
S3method(cophenetic, spantree)
# density: stats
S3method(density, oecosimu)
# densityplot: lattice
S3method(densityplot, oecosimu)
# deviance: stats
S3method(deviance, cca)
S3method(deviance, rda)
# drop1: stats
S3method(drop1, cca)
# eigenvals: vegan
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, procrustes)
S3method(fitted, radfit)
S3method(fitted, rda)
# goodness: vegan
S3method(goodness, cca)
S3method(goodness, metaMDS)
S3method(goodness, monoMDS)
S3method(goodness, rda)
# head: utils
S3method(head, summary.cca)
# identify: graphics
S3method(identify, ordiplot)
# lines: graphics
S3method(lines, humpfit)
S3method(lines, permat)
S3method(lines, preston)
S3method(lines, prestonfit)
S3method(lines, procrustes)
S3method(lines, radline)
S3method(lines, spantree)
# model.frame, model.matrix: stats
S3method(model.frame, cca)
S3method(model.matrix, cca)
# nobs: stats
S3method(nobs, CCorA)
S3method(nobs, adonis)
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)
# 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, nestedtemp)
S3method(plot, ordisurf)
S3method(plot, orditkplot)
S3method(plot, permat)
S3method(plot, poolaccum)
S3method(plot, prc)
S3method(plot, preston)
S3method(plot, prestonfit)
S3method(plot, procrustes)
S3method(plot, profile.fisherfit)
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)
# 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)
# predict: stats
S3method(predict, cca)
S3method(predict, decorana)
S3method(predict, fitspecaccum)
S3method(predict, humpfit)
S3method(predict, procrustes)
S3method(predict, rda)
S3method(predict, specaccum)
# print: base
S3method(print, CCorA)
S3method(print, MOStest)
S3method(print, adipart)
S3method(print, adonis)
S3method(print, anosim)
S3method(print, betadisper)
S3method(print, bioenv)
S3method(print, capscale)
S3method(print, cca)
S3method(print, decorana)
S3method(print, eigenvals)
S3method(print, envfit)
S3method(print, factorfit)
S3method(print, fisherfit)
S3method(print, hiersimu)
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, multipart)
S3method(print, nestedchecker)
S3method(print, nesteddisc)
S3method(print, nestedn0)
S3method(print, nestednodf)
S3method(print, nestedtemp)
S3method(print, oecosimu)
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, simper)
S3method(print, summary.bioenv)
S3method(print, summary.cca)
S3method(print, summary.clamtest)
S3method(print, summary.decorana)
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)
# profile: stats
# see note on 'confint'
S3method(profile, MOStest)
S3method(profile, fisherfit)
S3method(profile, humpfit)
# radfit: vegan
S3method(radfit, data.frame)
S3method(radfit, default)
# 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, lda)
S3method(scores, metaMDS)
S3method(scores, monoMDS)
S3method(scores, ordihull)
S3method(scores, ordiplot)
S3method(scores, orditkplot)
S3method(scores, pcnm)
S3method(scores, rda)
# screeplot: stats
S3method(screeplot, cca)
S3method(screeplot, decorana)
S3method(screeplot, prcomp)
S3method(screeplot, princomp)
# simulate: stats
S3method(simulate, capscale)
S3method(simulate, cca)
S3method(simulate, rda)
# stressplot: vegan
S3method(stressplot, default)
S3method(stressplot, monoMDS)
# summary: base
S3method(summary, anosim)
S3method(summary, bioenv)
S3method(summary, cca)
S3method(summary, clamtest)
S3method(summary, decorana)
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)
# 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)
