[Vegan-commits] r1696 - in pkg/vegan: . R inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 6 18:35:16 CEST 2011
Author: jarioksa
Date: 2011-08-06 18:35:16 +0200 (Sat, 06 Aug 2011)
New Revision: 1696
Modified:
pkg/vegan/NAMESPACE
pkg/vegan/R/anova.ccabyterm.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/deviance.cca.Rd
pkg/vegan/man/predict.cca.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
register S3 methods in NAMESPACE
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2011-08-06 14:58:16 UTC (rev 1695)
+++ pkg/vegan/NAMESPACE 2011-08-06 16:35:16 UTC (rev 1696)
@@ -2,3 +2,331 @@
useDynLib(vegan)
## Export
exportPattern(".")
+## Registration of S3 methods
+import(stats)
+import(graphics)
+importFrom(utils, head, tail)
+#importFrom(lattice, densityplot)
+# 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, 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, decorana)
+S3method(plot, envfit)
+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, 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, humpfit)
+S3method(predict, procrustes)
+S3method(predict, rda)
+# 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, summary.bioenv)
+S3method(print, summary.cca)
+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.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, 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, 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)
Modified: pkg/vegan/R/anova.ccabyterm.R
===================================================================
--- pkg/vegan/R/anova.ccabyterm.R 2011-08-06 14:58:16 UTC (rev 1695)
+++ pkg/vegan/R/anova.ccabyterm.R 2011-08-06 16:35:16 UTC (rev 1696)
@@ -26,7 +26,7 @@
df[ntrm:(ntrm + 1)] <- sim$df
chi[ntrm:(ntrm + 1)] <- sim$chi
if (!is.null(object$call$data))
- modelframe <- ordiGetData(object$call, NULL)
+ modelframe <- ordiGetData(object$call, globalenv())
else
modelframe <- NULL
for (.ITRM in ntrm:2) {
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-08-06 14:58:16 UTC (rev 1695)
+++ pkg/vegan/inst/ChangeLog 2011-08-06 16:35:16 UTC (rev 1696)
@@ -5,7 +5,13 @@
Version 1.91-0 (opened August 6, 2011)
* NAMESPACE: added namespace to vegan. At this stage exports
- everything and loads compiled code: changes nothing.
+ everything and loads compiled code (so that nothing changed in
+ from user's perspective). Some superfluous aliases were removed
+ with the registration of S3 methods, and scoping was changed a bit
+ in anova.ccabyterm. as.mcmc and densityplot are not yet registred:
+ these need changes in Imports field of DESCRIPTION (same with
+ vif.cca: vif is defined in car, but we could have our private vif
+ generic here?).
Version 1.90-2 (closed August 6, 2011)
Modified: pkg/vegan/man/deviance.cca.Rd
===================================================================
--- pkg/vegan/man/deviance.cca.Rd 2011-08-06 14:58:16 UTC (rev 1695)
+++ pkg/vegan/man/deviance.cca.Rd 2011-08-06 16:35:16 UTC (rev 1696)
@@ -2,7 +2,6 @@
\name{deviance.cca}
\alias{deviance.cca}
\alias{deviance.rda}
-\alias{deviance.capscale}
\alias{extractAIC.cca}
\title{ Statistics Resembling Deviance and AIC for Constrained Ordination}
\description{
Modified: pkg/vegan/man/predict.cca.Rd
===================================================================
--- pkg/vegan/man/predict.cca.Rd 2011-08-06 14:58:16 UTC (rev 1695)
+++ pkg/vegan/man/predict.cca.Rd 2011-08-06 16:35:16 UTC (rev 1696)
@@ -3,7 +3,6 @@
\alias{fitted.rda}
\alias{fitted.capscale}
\alias{residuals.cca}
-\alias{residuals.rda}
\alias{predict.cca}
\alias{predict.rda}
\alias{predict.decorana}
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-08-06 14:58:16 UTC (rev 1695)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-08-06 16:35:16 UTC (rev 1696)
@@ -23,6 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
+This is vegan 1.91-0
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -2032,7 +2033,7 @@
> ### Name: deviance.cca
> ### Title: Statistics Resembling Deviance and AIC for Constrained
> ### Ordination
-> ### Aliases: deviance.cca deviance.rda deviance.capscale extractAIC.cca
+> ### Aliases: deviance.cca deviance.rda extractAIC.cca
> ### Keywords: multivariate models
>
> ### ** Examples
@@ -4648,7 +4649,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x103d05870>
+<environment: 0x103a09710>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4664,7 +4665,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106050d10>
+<environment: 0x10601eb40>
Estimated degrees of freedom:
6.0761 total = 7.076141
@@ -4820,7 +4821,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10709b778>
+<environment: 0x1066de2a0>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4833,7 +4834,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10701f0e8>
+<environment: 0x105d7a0d0>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4846,7 +4847,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107031990>
+<environment: 0x106799940>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5452,8 +5453,8 @@
> ### Title: Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA,
> ### CA, PCA)
> ### Aliases: fitted.cca fitted.rda fitted.capscale residuals.cca
-> ### residuals.rda predict.cca predict.rda predict.decorana coef.cca
-> ### coef.rda calibrate.cca calibrate
+> ### predict.cca predict.rda predict.decorana coef.cca coef.rda
+> ### calibrate.cca calibrate
> ### Keywords: multivariate
>
> ### ** Examples
@@ -7038,7 +7039,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1084934a0>
+<environment: 0x1080ca318>
Estimated degrees of freedom:
2 total = 3
@@ -7503,7 +7504,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 103.782 1.214 106.025 0 0
+Time elapsed: 118.169 1.253 120.445 0 0
> grDevices::dev.off()
null device
1
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