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| ## 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, chaodist, contribdiv, clamtest, commsim, cutreeord, | |
| 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, avgdist, 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) | |
| ## alternative implementation of adonis: may be eliminated later | |
| export(adonis2) | |
| ## export regular functions with dot names | |
| export(as.fisher, 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 .Defunct functions (to be removed later) | |
| export(commsimulator) | |
| ## Deprecated functions & methods | |
| export(as.mlm) | |
| S3method(as.mlm, cca) | |
| S3method(as.mlm, rda) | |
| ## 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.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) | |
| # cooks.distance: stats | |
| S3method(cooks.distance, cca) | |
| # 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) | |
| # df.residual: stats | |
| S3method(df.residual, cca) | |
| # 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) | |
| # hatvalues: stats | |
| S3method(hatvalues, cca) | |
| S3method(hatvalues, rda) | |
| # 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) | |
| S3method(model.matrix, rda) | |
| # 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, wcmdscale) | |
| # points: graphics | |
| S3method(points, cca) | |
| S3method(points, decorana) | |
| S3method(points, humpfit) | |
| S3method(points, metaMDS) | |
| S3method(points, monoMDS) | |
| 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) | |
| ## qr: base | |
| S3method(qr, cca) | |
| # 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) | |
| # rstandard, rstudent: stats | |
| S3method(rstandard, cca) | |
| S3method(rstudent, cca) | |
| # 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) | |
| # sigma: stats | |
| S3method(sigma, cca) | |
| # 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) | |
| # SSD: stats | |
| S3method(SSD, cca) | |
| # 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, monoMDS) | |
| 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) | |
| # vcov: stats | |
| S3method(vcov, cca) | |
| # weights: stats | |
| S3method(weights, cca) | |
| S3method(weights, decorana) | |
| S3method(weights, rda) |