564 lines
17 KiB
Plaintext
564 lines
17 KiB
Plaintext
## compiled code
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useDynLib(vegan, .registration = TRUE)
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## Export regular function names (no dots)
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export(CCorA, MOStest, RsquareAdj, SSarrhenius, SSgitay, SSgleason,
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SSlomolino, adipart, adonis2, anosim, beals, betadisper, betadiver,
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bgdispersal, bioenv, bioenvdist, bstick, cIndexKM, ca, calibrate, capscale,
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cascadeKM, cca, chaodist, contribdiv, clamtest, commsim, cutreeord,
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dbrda, decobackstand, decorana, decostand, designdist,
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coverscale, dispweight, dispindmorisita, distconnected,
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diversity, downweight, drarefy, eigengrad, eigenvals, envfit,
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estaccumR, estimateR, eventstar, factorfit, fisherfit, fitspecaccum,
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gdispweight,goodness, hiersimu, humpfit, indpower, inertcomp, initMDS,
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intersetcor, isomapdist, isomap, linestack, mantel, meandist,
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metaMDSdist, metaMDSiter, metaMDSredist, MDSrotate, metaMDS, monoMDS,
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mrpp, msoplot, mso, multipart, make.commsim, nestedbetajac, nestedbetasor, nestedchecker,
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nesteddisc, nestedn0, nestednodf, nestedtemp, nullmodel, oecosimu, smbind,
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ordiareatest, ordiR2step,
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ordiarrows, ordiArrowMul, ordiArrowTextXY, ordibar, ordicloud,
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ordicluster, ordiellipse, ordigrid,
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ordihull, ordilabel, ordiplot, ordipointlabel, ordiresids,
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ordisegments, ordispider, ordisplom, ordistep, ordisurf,
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orditkplot, orditorp, ordixyplot, ordiYbar,
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pca, pco, pcnm, permatfull, permatswap, permustats, permutest,
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poolaccum, postMDS, prc, prestondistr, prestonfit, procrustes,
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protest, radfit, radlattice, rankindex, rarefy, rarecurve, rareslope,
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raupcrick, rda, renyiaccum, renyi, rrarefy, scores,
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showvarparts, simper, simpson.unb, spandepth, spantree, specaccum, specslope,
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specnumber, specpool2vect, specpool, spenvcor, "sppscores<-", sppscores,
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stepacross, stressplot, swan, tabasco, taxa2dist, taxondive, tolerance,
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treedist, treedive, treeheight, tsallisaccum, tsallis, varpart,
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vectorfit, vegandocs, vegdist, avgdist, vegemite, veiledspec, wascores,
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wcmdscale, wisconsin)
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## export pasteCall for 'permute'
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export(pasteCall)
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## export anova.cca for 'BiodiversityR': this should be fixed there
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export(anova.cca)
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## export regular functions with dot names
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export(as.fisher, as.preston, as.rad, fieller.MOStest,
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fisher.alpha, kendall.global, kendall.post, make.cepnames,
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mantel.correlog, mantel.partial, no.shared, rad.lognormal, rad.null,
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rad.preempt, rad.zipf, rad.zipfbrot, read.cep,
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vif.cca)
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## Export panel functions
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export(panel.ordi, panel.ordiarrows, panel.ordi3d, prepanel.ordi3d)
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## Export .Defunct functions (to be removed later)
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export(commsimulator)
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export(as.mlm)
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S3method(as.mlm, cca)
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## Deprecated functions & methods
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export(as.mcmc.oecosimu)
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export(as.mcmc.permat)
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export(adonis)
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## do NOT export the following internal functions
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## export(orderingKM, ordiArgAbsorber, ordiArrowMul,
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## ordiGetData, ordimedian, ordiNAexclude, ordiNApredict,
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## ordiParseFormula, ordiTerminfo, pregraphKM, simpleRDA2, varpart2,
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## varpart3, varpart4, veganCovEllipse, veganMahatrans)
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## Imports
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## define S3 methods for these stats functions
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importFrom(stats, AIC, TukeyHSD, add1, alias, anova, as.hclust, as.ts,
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biplot, coef, confint, cooks.distance, cophenetic, density,
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deviance, df.residual, drop1, extractAIC, fitted,
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hatvalues, logLik, model.frame, model.matrix, nobs,
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predict, profile, qqnorm, reorder, residuals, rstandard,
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rstudent, screeplot, sigma, simulate, SSD, update, vcov,
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weights)
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## direct calls
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importFrom(stats, .getXlevels, add.scope, aggregate, aov, approx,
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as.dendrogram, as.dist, as.formula, cmdscale, coefficients,
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complete.cases, cor, cov, cov.wt, cutree, delete.response,
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dendrapply, dist, dnorm, drop.scope, estVar, factor.scope,
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family, formula, glm, glm.fit, hclust, heatmap, integrate,
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is.ts, kmeans, lm, median, na.action, na.fail, na.pass,
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napredict, naprint, nlm, nls, optim, optimize, p.adjust,
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p.adjust.methods, pchisq, pf, plogis, pnorm, poisson,
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ppoints, prcomp, printCoefmat, pt, qchisq, qf, qlogis,
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qnorm, quantile, quasipoisson, r2dtable, reformulate,
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rmultinom, rnorm, runif, sd, spline, summary.lm, terms, ts,
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uniroot, update.formula, var, weighted.mean)
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## S3methods for these
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importFrom(graphics, boxplot, identify, lines, pairs, persp, plot,
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points, text)
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## direct calls
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importFrom(graphics, abline, arrows, axis, barplot, box, contour,
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curve, grid, image, layout, legend, matlines, matplot,
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mtext, par, plot.new, plot.window, polygon, rect, rug,
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segments, strheight, strwidth, symbols, title)
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import(permute) ## vegan depends on permute: import everything
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importFrom(utils, news, vignette, combn, flush.console, head, object.size,
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read.fortran, read.fwf, tail, str)
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importFrom(tools, Rd2txt, startDynamicHelp)
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importFrom(grDevices, bmp, check.options, chull, col2rgb, dev.off,
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heat.colors, jpeg, palette, pdf, png, postscript, rainbow,
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rgb, svg, tiff, xfig, xy.coords)
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## import(grDevices) ## too many functions to be listed separately
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## import(lattice) # vegan depends on lattice: import all
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importFrom(lattice, densityplot, qqmath, bwplot, cloud, lpolygon, panel.abline,
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panel.arrows, panel.cloud, panel.densityplot, panel.lines,
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panel.number, panel.qqmath, panel.superpose, panel.text,
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panel.xyplot,prepanel.default.cloud, splom, xyplot,
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trellis.par.get)
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importFrom(parallel, mclapply, makeCluster, stopCluster, clusterEvalQ,
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parApply, parLapply, parSapply, parRapply, parCapply,
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splitIndices)
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importFrom(MASS, isoMDS, sammon, Shepard, mvrnorm, lda)
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importFrom(cluster, daisy, ellipsoidhull)
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## 's' must be imported in mgcv < 1.8-0 (not needed later)
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importFrom(mgcv, gam, s, te, predict.gam, summary.gam)
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## Registration of S3 methods defined in vegan
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# adipart: vegan
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S3method(adipart, default)
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S3method(adipart, formula)
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# AIC: stats
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S3method(AIC, fitspecaccum)
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S3method(AIC, radfit)
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S3method(AIC, radfit.frame)
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# RsquareAdj: vegan
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S3method(RsquareAdj, cca)
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S3method(RsquareAdj, default)
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S3method(RsquareAdj, glm)
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S3method(RsquareAdj, lm)
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S3method(RsquareAdj, rda)
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# TukeyHSD: stats
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S3method(TukeyHSD, betadisper)
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# add1: stats
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S3method(add1, cca)
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# alias: stats
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S3method(alias, cca)
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# anova: stats
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S3method(anova, betadisper)
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S3method(anova, cca)
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S3method(anova, prc)
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# as.hclust: stats
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S3method(as.hclust, spantree)
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## toCoda (used to be unexported & dysfunctional as.mcmc)
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export(toCoda)
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S3method(toCoda, oecosimu)
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S3method(toCoda, permat)
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# as.ts: stats
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S3method(as.ts, oecosimu)
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S3method(as.ts, permat)
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# bioenv: vegan
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S3method(bioenv, default)
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S3method(bioenv, formula)
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# biplot: stats
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S3method(biplot, CCorA)
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S3method(biplot, cca)
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S3method(biplot, rda)
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# boxplot: graphics
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S3method(boxplot, betadisper)
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S3method(boxplot, permustats)
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S3method(boxplot, specaccum)
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# bstick: vegan
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S3method(bstick, cca)
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S3method(bstick, decorana)
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S3method(bstick, default)
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S3method(bstick, prcomp)
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S3method(bstick, princomp)
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## c: base
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S3method(c, permustats)
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# calibrate: vegan
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S3method(calibrate, cca)
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S3method(calibrate, ordisurf)
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# cca: vegan
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S3method(cca, default)
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S3method(cca, formula)
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# coef: stats
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S3method(coef, cca)
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S3method(coef, radfit)
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S3method(coef, radfit.frame)
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S3method(coef, rda)
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# confint: stats -- also uses MASS:::confint.glm & MASS:::profile.glm
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# does this work with namespaces??
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S3method(confint, MOStest)
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# cooks.distance: stats
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S3method(cooks.distance, cca)
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# cophenetic: stats
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S3method(cophenetic, spantree)
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# density: stats
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S3method(density, permustats)
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# densityplot: lattice
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S3method(densityplot, permustats)
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# deviance: stats
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S3method(deviance, cca)
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S3method(deviance, rda)
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S3method(deviance, radfit)
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S3method(deviance, radfit.frame)
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S3method(deviance, fitspecaccum)
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# df.residual: stats
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S3method(df.residual, cca)
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# drop1: stats
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S3method(drop1, cca)
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# eigenvals: vegan
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S3method(eigenvals, betadisper)
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S3method(eigenvals, cca)
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S3method(eigenvals, decorana)
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S3method(eigenvals, default)
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S3method(eigenvals, dudi)
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S3method(eigenvals, pca)
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S3method(eigenvals, pcnm)
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S3method(eigenvals, pco)
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S3method(eigenvals, prcomp)
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S3method(eigenvals, princomp)
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S3method(eigenvals, wcmdscale)
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# envfit: vegan
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S3method(envfit, default)
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S3method(envfit, formula)
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# estimateR: vegan
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S3method(estimateR, data.frame)
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S3method(estimateR, default)
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S3method(estimateR, matrix)
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# extractAIC: stats
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S3method(extractAIC, cca)
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# fitted: stats
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S3method(fitted, capscale)
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S3method(fitted, cca)
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S3method(fitted, dbrda)
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S3method(fitted, procrustes)
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S3method(fitted, radfit)
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S3method(fitted, radfit.frame)
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S3method(fitted, rda)
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# goodness: vegan
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S3method(goodness, cca)
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S3method(goodness, metaMDS)
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S3method(goodness, monoMDS)
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# hatvalues: stats
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S3method(hatvalues, cca)
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S3method(hatvalues, rda)
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# hiersimu: vegan
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S3method(hiersimu, default)
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S3method(hiersimu, formula)
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# methods for hclust object in base R: these would be better in R
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S3method(reorder, hclust)
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S3method(rev, hclust)
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# identify: graphics
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S3method(identify, ordiplot)
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# labels: base
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S3method(labels, cca)
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S3method(labels, envfit)
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# lines: graphics
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S3method(lines, fitspecaccum)
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S3method(lines, permat)
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S3method(lines, preston)
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S3method(lines, prestonfit)
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S3method(lines, procrustes)
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S3method(lines, radline)
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S3method(lines, radfit)
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S3method(lines, spantree)
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S3method(lines, specaccum)
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## logLik: stats
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S3method(logLik, fitspecaccum)
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S3method(logLik, radfit)
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S3method(logLik, radfit.frame)
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# model.frame, model.matrix: stats
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S3method(model.frame, cca)
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S3method(model.matrix, cca)
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S3method(model.matrix, rda)
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# multipart: vegan
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S3method(multipart, default)
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S3method(multipart, formula)
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# nobs: stats
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S3method(nobs, CCorA)
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S3method(nobs, anova.cca)
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S3method(nobs, betadisper)
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S3method(nobs, cca)
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S3method(nobs, decorana)
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S3method(nobs, fitspecaccum)
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S3method(nobs, isomap)
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S3method(nobs, metaMDS)
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S3method(nobs, pcnm)
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S3method(nobs, procrustes)
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S3method(nobs, rad)
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S3method(nobs, varpart)
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S3method(nobs, wcmdscale)
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# ordisurf: vegan
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S3method(ordisurf, default)
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S3method(ordisurf, formula)
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# pairs: graphics
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S3method(pairs, permustats)
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## permustats methods
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S3method(permustats, anosim)
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S3method(permustats, mantel)
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S3method(permustats, mrpp)
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S3method(permustats, oecosimu)
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S3method(permustats, ordiareatest)
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S3method(permustats, permutest.betadisper)
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S3method(permustats, permutest.cca)
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S3method(permustats, protest)
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S3method(permustats, anova.cca)
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## these return an error: no permutation data
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S3method(permustats, CCorA)
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S3method(permustats, envfit)
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S3method(permustats, factorfit)
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S3method(permustats, vectorfit)
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S3method(permustats, mso)
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S3method(print, permustats)
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S3method(summary, permustats)
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S3method(print, summary.permustats)
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# permutest: vegan
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S3method(permutest, betadisper)
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S3method(permutest, cca)
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S3method(permutest, default)
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# persp: graphics
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S3method(persp, renyiaccum)
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S3method(persp, tsallisaccum)
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# plot: graphics
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S3method(plot, MOStest)
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S3method(plot, anosim)
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S3method(plot, betadisper)
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S3method(plot, betadiver)
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S3method(plot, cascadeKM)
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S3method(plot, cca)
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S3method(plot, contribdiv)
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S3method(plot, clamtest)
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S3method(plot, decorana)
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S3method(plot, envfit)
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S3method(plot, fisher)
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S3method(plot, fisherfit)
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S3method(plot, fitspecaccum)
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S3method(plot, isomap)
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S3method(plot, mantel.correlog)
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S3method(plot, meandist)
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S3method(plot, metaMDS)
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S3method(plot, monoMDS)
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S3method(plot, nestednodf)
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S3method(plot, nestedtemp)
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S3method(plot, ordisurf)
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S3method(plot, ordipointlabel)
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S3method(plot, orditkplot)
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S3method(plot, permat)
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S3method(plot, poolaccum)
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S3method(plot, prc)
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S3method(plot, preston)
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S3method(plot, prestonfit)
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S3method(plot, procrustes)
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S3method(plot, rad)
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S3method(plot, radfit)
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S3method(plot, radfit.frame)
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S3method(plot, radline)
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S3method(plot, rda)
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S3method(plot, renyi)
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S3method(plot, renyiaccum)
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S3method(plot, spantree)
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S3method(plot, specaccum)
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S3method(plot, taxondive)
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S3method(plot, varpart)
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S3method(plot, varpart234)
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S3method(plot, wcmdscale)
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# points: graphics
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S3method(points, cca)
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S3method(points, decorana)
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S3method(points, metaMDS)
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S3method(points, monoMDS)
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S3method(points, ordiplot)
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S3method(points, orditkplot)
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S3method(points, procrustes)
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S3method(points, radline)
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S3method(points, radfit)
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# predict: stats
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S3method(predict, cca)
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S3method(predict, decorana)
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S3method(predict, dbrda)
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S3method(predict, fitspecaccum)
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S3method(predict, procrustes)
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S3method(predict, radline)
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S3method(predict, radfit)
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S3method(predict, radfit.frame)
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S3method(predict, rda)
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S3method(predict, specaccum)
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# print: base
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S3method(print, CCorA)
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S3method(print, MOStest)
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S3method(print, anosim)
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S3method(print, rad)
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S3method(print, betadisper)
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S3method(print, bioenv)
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S3method(print, cca)
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S3method(print, commsim)
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S3method(print, decorana)
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S3method(print, eigenvals)
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S3method(print, envfit)
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S3method(print, factorfit)
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S3method(print, fisherfit)
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S3method(print, isomap)
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S3method(print, mantel)
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S3method(print, mantel.correlog)
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S3method(print, metaMDS)
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S3method(print, monoMDS)
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S3method(print, mrpp)
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S3method(print, mso)
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S3method(print, nestedchecker)
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S3method(print, nesteddisc)
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S3method(print, nestedn0)
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S3method(print, nestednodf)
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S3method(print, nestedtemp)
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S3method(print, nullmodel)
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S3method(print, oecosimu)
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S3method(print, ordiareatest)
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S3method(print, permat)
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S3method(print, permutest.betadisper)
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S3method(print, permutest.cca)
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S3method(print, poolaccum)
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S3method(print, prestonfit)
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S3method(print, procrustes)
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S3method(print, protest)
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S3method(print, radfit)
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S3method(print, radfit.frame)
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S3method(print, radline)
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S3method(print, rda)
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S3method(print, specaccum)
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S3method(print, simmat)
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S3method(print, simper)
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S3method(print, summary.bioenv)
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S3method(print, summary.cca)
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S3method(print, summary.clamtest)
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S3method(print, summary.decorana)
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S3method(print, summary.dispweight)
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S3method(print, summary.eigenvals)
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S3method(print, summary.isomap)
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S3method(print, summary.meandist)
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S3method(print, summary.permat)
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S3method(print, summary.prc)
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S3method(print, summary.procrustes)
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S3method(print, summary.simper)
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S3method(print, summary.taxondive)
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S3method(print, summary.varpart)
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S3method(print, taxondive)
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S3method(print, tolerance.cca)
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S3method(print, varpart)
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S3method(print, varpart234)
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S3method(print, vectorfit)
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S3method(print, wcmdscale)
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# profile: stats
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# see note on 'confint'
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S3method(profile, MOStest)
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## qqmath: lattice
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S3method(qqmath, permustats)
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## qqnorm: stats
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S3method(qqnorm, permustats)
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## qr: base
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S3method(qr, cca)
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# radfit: vegan
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S3method(radfit, data.frame)
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S3method(radfit, default)
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S3method(radfit, matrix)
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# rda: vegan
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S3method(rda, default)
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S3method(rda, formula)
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# residuals: stats
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S3method(residuals, cca)
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S3method(residuals, procrustes)
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# rstandard, rstudent: stats
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S3method(rstandard, cca)
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S3method(rstudent, cca)
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# scores: vegan
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S3method(scores, betadisper)
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S3method(scores, betadiver)
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S3method(scores, cca)
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S3method(scores, decorana)
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S3method(scores, default)
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S3method(scores, envfit)
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S3method(scores, hclust)
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S3method(scores, lda)
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S3method(scores, metaMDS)
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S3method(scores, monoMDS)
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S3method(scores, ordihull)
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S3method(scores, ordiplot)
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S3method(scores, orditkplot)
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S3method(scores, pcnm)
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S3method(scores, rda)
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S3method(scores, wcmdscale)
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# screeplot: stats
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S3method(screeplot, cca)
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S3method(screeplot, decorana)
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S3method(screeplot, prcomp)
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S3method(screeplot, princomp)
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# sigma: stats
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S3method(sigma, cca)
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# simulate: stats
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S3method(simulate, capscale)
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S3method(simulate, cca)
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S3method(simulate, dbrda)
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S3method(simulate, rda)
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S3method(simulate, nullmodel)
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|
# specslope: vegan
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S3method(specslope, specaccum)
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|
S3method(specslope, fitspecaccum)
|
|
## sppscores<-: vegan
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S3method("sppscores<-", capscale)
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S3method("sppscores<-", dbrda)
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S3method("sppscores<-", metaMDS)
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|
# SSD: stats
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|
S3method(SSD, cca)
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|
# str: utils
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|
S3method(str, nullmodel)
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|
# stressplot: vegan
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|
S3method(stressplot, default)
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|
S3method(stressplot, monoMDS)
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|
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, 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)
|
|
S3method(summary, varpart)
|
|
# text: graphics
|
|
S3method(text, cca)
|
|
S3method(text, decorana)
|
|
S3method(text, metaMDS)
|
|
S3method(text, monoMDS)
|
|
S3method(text, ordiplot)
|
|
S3method(text, orditkplot)
|
|
S3method(text, procrustes)
|
|
# tolerance
|
|
S3method(tolerance, cca)
|
|
S3method(tolerance, decorana)
|
|
# 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)
|