[Vegan-commits] r1762 - in pkg/vegan: inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 26 17:40:30 CEST 2011
Author: jarioksa
Date: 2011-08-26 17:40:29 +0200 (Fri, 26 Aug 2011)
New Revision: 1762
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/CCorA.Rd
pkg/vegan/man/MOStest.Rd
pkg/vegan/man/adipart.Rd
pkg/vegan/man/adonis.Rd
pkg/vegan/man/anosim.Rd
pkg/vegan/man/anova.cca.Rd
pkg/vegan/man/betadisper.Rd
pkg/vegan/man/bioenv.Rd
pkg/vegan/man/capscale.Rd
pkg/vegan/man/cca.Rd
pkg/vegan/man/decorana.Rd
pkg/vegan/man/eigenvals.Rd
pkg/vegan/man/envfit.Rd
pkg/vegan/man/fisherfit.Rd
pkg/vegan/man/humpfit.Rd
pkg/vegan/man/isomap.Rd
pkg/vegan/man/mantel.Rd
pkg/vegan/man/mantel.correlog.Rd
pkg/vegan/man/metaMDS.Rd
pkg/vegan/man/monoMDS.Rd
pkg/vegan/man/mrpp.Rd
pkg/vegan/man/mso.Rd
pkg/vegan/man/multipart.Rd
pkg/vegan/man/nestedtemp.Rd
pkg/vegan/man/oecosimu.Rd
pkg/vegan/man/permutest.betadisper.Rd
pkg/vegan/man/prc.Rd
pkg/vegan/man/procrustes.Rd
pkg/vegan/man/radfit.Rd
pkg/vegan/man/specpool.Rd
pkg/vegan/man/taxondive.Rd
pkg/vegan/man/tolerance.Rd
pkg/vegan/man/varpart.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
remove aliases to undocumened and non-exported print commands (but keep documented ones)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/inst/ChangeLog 2011-08-26 15:40:29 UTC (rev 1762)
@@ -24,7 +24,10 @@
levels. Checks that 'pool' length matches nrow of data.
* NAMESPACE: imports nobs from permute_0.5-3 in R 2.12.2 and older
- which do not yet have nobs() generic.
+ which do not yet have nobs() generic. Do not export orderingKM &
+ ordimedian. Remove aliases to non-exported and non-documented
+ print and print.summary methods in Rd files (but leave documented
+ ones).
* vegandocs: shows the permutation vignette of the 'permute'
package.
Modified: pkg/vegan/man/CCorA.Rd
===================================================================
--- pkg/vegan/man/CCorA.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/CCorA.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,5 @@
\name{CCorA}
\alias{CCorA}
-\alias{print.CCorA}
\alias{biplot.CCorA}
\concept{ordination}
Modified: pkg/vegan/man/MOStest.Rd
===================================================================
--- pkg/vegan/man/MOStest.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/MOStest.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,6 @@
\encoding{UTF-8}
\name{MOStest}
\alias{MOStest}
-\alias{print.MOStest}
\alias{plot.MOStest}
\alias{fieller.MOStest}
\alias{profile.MOStest}
Modified: pkg/vegan/man/adipart.Rd
===================================================================
--- pkg/vegan/man/adipart.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/adipart.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,6 @@
\encoding{UTF-8}
\name{adipart}
\alias{adipart}
-\alias{print.adipart}
\alias{hiersimu}
\alias{print.hiersimu}
\title{Additive Diversity Partitioning and Hierarchical Null Model Testing}
@@ -16,8 +15,6 @@
weights=c("unif", "prop"), relative = FALSE, nsimul=99, ...)
hiersimu(formula, data, FUN, location = c("mean", "median"),
relative = FALSE, drop.highest = FALSE, nsimul=99, ...)
-\method{print}{adipart}(x, ...)
-\method{print}{hiersimu}(x, ...)
}
\arguments{
\item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y}
@@ -44,7 +41,6 @@
\item{drop.highest}{Logical, to drop the highest level or not. When \code{FUN}
evaluates only arrays with at least 2 dimensions, highest level should be dropped,
or not selected at all.}
- \item{x}{An object to print.}
\item{\dots}{Other arguments passed to functions, e.g. base of logarithm for
Shannon diversity, or \code{method}, \code{thin} or \code{burnin} arguments for
\code{\link{oecosimu}}.}
Modified: pkg/vegan/man/adonis.Rd
===================================================================
--- pkg/vegan/man/adonis.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/adonis.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,6 @@
\encoding{UTF-8}
\name{adonis}
\alias{adonis}
-\alias{print.adonis}
\title{Permutational Multivariate Analysis of Variance Using Distance Matrices}
Modified: pkg/vegan/man/anosim.Rd
===================================================================
--- pkg/vegan/man/anosim.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/anosim.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,5 @@
\name{anosim}
\alias{anosim}
-\alias{print.anosim}
\alias{summary.anosim}
\alias{plot.anosim}
Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/anova.cca.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -8,7 +8,6 @@
\alias{permutest}
\alias{permutest.default}
\alias{permutest.cca}
-\alias{print.permutest.cca}
\title{Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates }
Modified: pkg/vegan/man/betadisper.Rd
===================================================================
--- pkg/vegan/man/betadisper.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/betadisper.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -4,7 +4,6 @@
\alias{anova.betadisper}
\alias{plot.betadisper}
\alias{boxplot.betadisper}
-\alias{print.betadisper}
\alias{TukeyHSD.betadisper}
\alias{ordimedian}
Modified: pkg/vegan/man/bioenv.Rd
===================================================================
--- pkg/vegan/man/bioenv.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/bioenv.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -2,9 +2,7 @@
\alias{bioenv}
\alias{bioenv.default}
\alias{bioenv.formula}
-\alias{print.bioenv}
\alias{summary.bioenv}
-\alias{print.summary.bioenv}
\title{Best Subset of Environmental Variables with
Maximum (Rank) Correlation with Community Dissimilarities }
Modified: pkg/vegan/man/capscale.Rd
===================================================================
--- pkg/vegan/man/capscale.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/capscale.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,5 @@
\name{capscale}
\alias{capscale}
-\alias{print.capscale}
\title{[Partial] Constrained Analysis of Principal Coordinates or
distance-based RDA }
Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/cca.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -2,11 +2,9 @@
\alias{cca}
\alias{cca.default}
\alias{cca.formula}
-\alias{print.cca}
\alias{rda}
\alias{rda.default}
\alias{rda.formula}
-\concept{ordination}
\title{ [Partial] [Constrained] Correspondence Analysis and Redundancy
Analysis }
Modified: pkg/vegan/man/decorana.Rd
===================================================================
--- pkg/vegan/man/decorana.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/decorana.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,5 @@
\name{decorana}
\alias{decorana}
-\alias{print.decorana}
\alias{summary.decorana}
\alias{print.summary.decorana}
\alias{plot.decorana}
@@ -8,7 +7,6 @@
\alias{scores.decorana}
\alias{points.decorana}
\alias{text.decorana}
-\concept{ordination}
\title{Detrended Correspondence Analysis and Basic Reciprocal Averaging }
\description{
Modified: pkg/vegan/man/eigenvals.Rd
===================================================================
--- pkg/vegan/man/eigenvals.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/eigenvals.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -10,7 +10,6 @@
\alias{eigenvals.dudi}
\alias{eigenvals.pca}
\alias{eigenvals.pco}
-\alias{print.eigenvals}
\alias{summary.eigenvals}
\title{
Modified: pkg/vegan/man/envfit.Rd
===================================================================
--- pkg/vegan/man/envfit.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/envfit.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -5,9 +5,6 @@
\alias{vectorfit}
\alias{factorfit}
\alias{plot.envfit}
-\alias{print.envfit}
-\alias{print.factorfit}
-\alias{print.vectorfit}
\alias{scores.envfit}
\title{Fits an Environmental Vector or Factor onto an Ordination }
Modified: pkg/vegan/man/fisherfit.Rd
===================================================================
--- pkg/vegan/man/fisherfit.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/fisherfit.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -2,7 +2,6 @@
\alias{fisherfit}
\alias{as.fisher}
\alias{plot.fisherfit}
-\alias{print.fisherfit}
\alias{profile.fisherfit}
\alias{confint.fisherfit}
\alias{plot.profile.fisherfit}
@@ -11,7 +10,6 @@
\alias{as.preston}
\alias{plot.prestonfit}
\alias{lines.prestonfit}
-\alias{print.prestonfit}
\alias{veiledspec}
\title{Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data}
Modified: pkg/vegan/man/humpfit.Rd
===================================================================
--- pkg/vegan/man/humpfit.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/humpfit.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,8 +1,6 @@
\name{humpfit}
\alias{humpfit}
-\alias{print.humpfit}
\alias{summary.humpfit}
-\alias{print.summary.humpfit}
\alias{lines.humpfit}
\alias{plot.humpfit}
\alias{points.humpfit}
Modified: pkg/vegan/man/isomap.Rd
===================================================================
--- pkg/vegan/man/isomap.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/isomap.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -3,8 +3,6 @@
\alias{isomapdist}
\alias{plot.isomap}
\alias{summary.isomap}
-\alias{print.summary.isomap}
-\alias{print.isomap}
\alias{rgl.isomap}
\title{ Isometric Feature Mapping Ordination }
Modified: pkg/vegan/man/mantel.Rd
===================================================================
--- pkg/vegan/man/mantel.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/mantel.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,6 @@
\name{mantel}
\alias{mantel}
\alias{mantel.partial}
-\alias{print.mantel}
\title{Mantel and Partial Mantel Tests for Dissimilarity Matrices }
\description{
Modified: pkg/vegan/man/mantel.correlog.Rd
===================================================================
--- pkg/vegan/man/mantel.correlog.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/mantel.correlog.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,6 @@
\encoding{UTF-8}
\name{mantel.correlog}
\alias{mantel.correlog}
-\alias{print.mantel.correlog}
\alias{plot.mantel.correlog}
\title{ Mantel Correlogram }
Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/metaMDS.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -6,7 +6,6 @@
\alias{metaMDSredist}
\alias{initMDS}
\alias{postMDS}
-\alias{print.metaMDS}
\alias{plot.metaMDS}
\alias{points.metaMDS}
\alias{text.metaMDS}
Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/monoMDS.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,5 @@
\name{monoMDS}
\alias{monoMDS}
-\alias{print.monoMDS}
\alias{scores.monoMDS}
\alias{plot.monoMDS}
Modified: pkg/vegan/man/mrpp.Rd
===================================================================
--- pkg/vegan/man/mrpp.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/mrpp.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,9 +1,7 @@
\name{mrpp}
\alias{mrpp}
-\alias{print.mrpp}
\alias{meandist}
\alias{summary.meandist}
-\alias{print.summary.meandist}
\alias{plot.meandist}
\title{Multi Response Permutation Procedure and Mean Dissimilarity Matrix}
Modified: pkg/vegan/man/mso.Rd
===================================================================
--- pkg/vegan/man/mso.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/mso.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,5 @@
\name{mso}
\alias{mso}
-\alias{print.mso}
\alias{msoplot}
\title{ Functions for performing and displaying a spatial partitioning
Modified: pkg/vegan/man/multipart.Rd
===================================================================
--- pkg/vegan/man/multipart.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/multipart.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,8 +1,8 @@
\encoding{UTF-8}
\name{multipart}
\alias{multipart}
-\alias{print.multipart}
\title{Multiplicative Diversity Partitioning}
+
\description{
In multiplicative diversity partitioning, mean values of alpha diversity at lower levels of a sampling
hierarchy are compared to the total diversity in the entire data set or the pooled samples (gamma diversity).
@@ -10,7 +10,6 @@
\usage{
multipart(formula, data, index=c("renyi", "tsallis"), scales = 1,
global = FALSE, relative = FALSE, nsimul=99, ...)
-\method{print}{multipart}(x, ...)
}
\arguments{
\item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y}
@@ -30,7 +29,6 @@
\item{nsimul}{Number of permutation to use if \code{matr} is not of class 'permat'.
If \code{nsimul = 0}, only the \code{FUN} argument is evaluated. It is thus possible
to reuse the statistic values without using a null model.}
- \item{x}{An object to print.}
\item{\dots}{Other arguments passed to \code{\link{oecosimu}}, i.e.
\code{method}, \code{thin} or \code{burnin}.}
}
Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/nestedtemp.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -5,11 +5,6 @@
\alias{nestedn0}
\alias{nesteddisc}
\alias{nestednodf}
-\alias{print.nestedchecker}
-\alias{print.nestedn0}
-\alias{print.nesteddisc}
-\alias{print.nestedtemp}
-\alias{print.nestednodf}
\alias{plot.nestedtemp}
\title{ Nestedness Indices for Communities of Islands or Patches }
Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/oecosimu.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -2,7 +2,6 @@
\name{oecosimu}
\alias{oecosimu}
\alias{commsimulator}
-\alias{print.oecosimu}
\alias{as.ts.oecosimu}
\alias{as.mcmc.oecosimu}
\alias{density.oecosimu}
Modified: pkg/vegan/man/permutest.betadisper.Rd
===================================================================
--- pkg/vegan/man/permutest.betadisper.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/permutest.betadisper.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,6 +1,6 @@
\name{permutest.betadisper}
\alias{permutest.betadisper}
-\alias{print.permutest.betadisper}
+
\title{Permutation test of multivariate homogeneity of groups dispersions
(variances)}
\description{
Modified: pkg/vegan/man/prc.Rd
===================================================================
--- pkg/vegan/man/prc.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/prc.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,6 @@
\name{prc}
\alias{prc}
\alias{summary.prc}
-\alias{print.summary.prc}
\alias{plot.prc}
\title{Principal Response Curves for Treatments with Repeated Observations }
Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/procrustes.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,8 +1,6 @@
\name{procrustes}
\alias{procrustes}
-\alias{print.procrustes}
\alias{summary.procrustes}
-\alias{print.summary.procrustes}
\alias{plot.procrustes}
\alias{points.procrustes}
\alias{text.procrustes}
Modified: pkg/vegan/man/radfit.Rd
===================================================================
--- pkg/vegan/man/radfit.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/radfit.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -13,9 +13,6 @@
\alias{plot.rad}
\alias{radlattice}
\alias{points.radline}
-\alias{print.radfit.frame}
-\alias{print.radfit}
-\alias{print.radline}
\alias{summary.radfit.frame}
\alias{rad.preempt}
\alias{rad.lognormal}
Modified: pkg/vegan/man/specpool.Rd
===================================================================
--- pkg/vegan/man/specpool.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/specpool.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -2,7 +2,6 @@
\alias{specpool}
\alias{specpool2vect}
\alias{poolaccum}
-\alias{print.poolaccum}
\alias{summary.poolaccum}
\alias{plot.poolaccum}
\alias{estimateR}
Modified: pkg/vegan/man/taxondive.Rd
===================================================================
--- pkg/vegan/man/taxondive.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/taxondive.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,8 +1,6 @@
\name{taxondive}
\alias{taxondive}
-\alias{print.taxondive}
\alias{summary.taxondive}
-\alias{print.summary.taxondive}
\alias{plot.taxondive}
\alias{taxa2dist}
Modified: pkg/vegan/man/tolerance.Rd
===================================================================
--- pkg/vegan/man/tolerance.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/tolerance.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -1,7 +1,7 @@
\name{tolerance}
\alias{tolerance}
\alias{tolerance.cca}
-\alias{print.tolerance.cca}
+
\title{Species tolerances and sample heterogeneities}
\usage{
tolerance(x, \dots)
Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/man/varpart.Rd 2011-08-26 15:40:29 UTC (rev 1762)
@@ -4,8 +4,6 @@
\alias{varpart3}
\alias{varpart4}
\alias{showvarparts}
-\alias{print.varpart}
-\alias{print.varpart234}
\alias{plot.varpart}
\alias{plot.varpart234}
\alias{simpleRDA2}
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-08-26 15:39:03 UTC (rev 1761)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-08-26 15:40:29 UTC (rev 1762)
@@ -54,7 +54,7 @@
>
> ### Name: CCorA
> ### Title: Canonical Correlation Analysis
-> ### Aliases: CCorA print.CCorA biplot.CCorA
+> ### Aliases: CCorA biplot.CCorA
> ### Keywords: multivariate
>
> ### ** Examples
@@ -140,8 +140,8 @@
>
> ### Name: MOStest
> ### Title: Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
-> ### Aliases: MOStest print.MOStest plot.MOStest fieller.MOStest
-> ### profile.MOStest confint.MOStest
+> ### Aliases: MOStest plot.MOStest fieller.MOStest profile.MOStest
+> ### confint.MOStest
> ### Keywords: models regression
>
> ### ** Examples
@@ -510,7 +510,7 @@
> ### Name: adipart
> ### Title: Additive Diversity Partitioning and Hierarchical Null Model
> ### Testing
-> ### Aliases: adipart print.adipart hiersimu print.hiersimu
+> ### Aliases: adipart hiersimu print.hiersimu
> ### Keywords: multivariate
>
> ### ** Examples
@@ -590,7 +590,7 @@
> ### Name: adonis
> ### Title: Permutational Multivariate Analysis of Variance Using Distance
> ### Matrices
-> ### Aliases: adonis print.adonis
+> ### Aliases: adonis
> ### Keywords: multivariate nonparametric
>
> ### ** Examples
@@ -690,7 +690,7 @@
>
> ### Name: anosim
> ### Title: Analysis of Similarities
-> ### Aliases: anosim print.anosim summary.anosim plot.anosim
+> ### Aliases: anosim summary.anosim plot.anosim
> ### Keywords: multivariate nonparametric htest
>
> ### ** Examples
@@ -743,7 +743,6 @@
> ### Redundancy Analysis and Constrained Analysis of Principal Coordinates
> ### Aliases: anova.cca anova.ccanull anova.ccabyaxis anova.ccabyterm
> ### anova.ccabymargin anova.prc permutest permutest.default permutest.cca
-> ### print.permutest.cca
> ### Keywords: multivariate htest
>
> ### ** Examples
@@ -1056,7 +1055,7 @@
> ### Name: betadisper
> ### Title: Multivariate homogeneity of groups dispersions (variances)
> ### Aliases: betadisper scores.betadisper anova.betadisper plot.betadisper
-> ### boxplot.betadisper print.betadisper TukeyHSD.betadisper ordimedian
+> ### boxplot.betadisper TukeyHSD.betadisper ordimedian
> ### Keywords: methods multivariate hplot
>
> ### ** Examples
@@ -1384,8 +1383,7 @@
> ### Name: bioenv
> ### Title: Best Subset of Environmental Variables with Maximum (Rank)
> ### Correlation with Community Dissimilarities
-> ### Aliases: bioenv bioenv.default bioenv.formula print.bioenv
-> ### summary.bioenv print.summary.bioenv
+> ### Aliases: bioenv bioenv.default bioenv.formula summary.bioenv
> ### Keywords: multivariate
>
> ### ** Examples
@@ -1451,7 +1449,7 @@
> ### Name: capscale
> ### Title: [Partial] Constrained Analysis of Principal Coordinates or
> ### distance-based RDA
-> ### Aliases: capscale print.capscale
+> ### Aliases: capscale
> ### Keywords: multivariate
>
> ### ** Examples
@@ -1603,8 +1601,7 @@
> ### Name: cca
> ### Title: [Partial] [Constrained] Correspondence Analysis and Redundancy
> ### Analysis
-> ### Aliases: cca cca.default cca.formula print.cca rda rda.default
-> ### rda.formula
+> ### Aliases: cca cca.default cca.formula rda rda.default rda.formula
> ### Keywords: multivariate
>
> ### ** Examples
@@ -1819,9 +1816,8 @@
>
> ### Name: decorana
> ### Title: Detrended Correspondence Analysis and Basic Reciprocal Averaging
-> ### Aliases: decorana print.decorana summary.decorana
-> ### print.summary.decorana plot.decorana downweight scores.decorana
-> ### points.decorana text.decorana
+> ### Aliases: decorana summary.decorana print.summary.decorana plot.decorana
+> ### downweight scores.decorana points.decorana text.decorana
> ### Keywords: multivariate
>
> ### ** Examples
@@ -2377,8 +2373,7 @@
> ### Title: Extract Eigenvalues from an Ordination Object
> ### Aliases: eigenvals eigenvals.default eigenvals.prcomp
> ### eigenvals.princomp eigenvals.cca eigenvals.wcmdscale eigenvals.pcnm
-> ### eigenvals.dudi eigenvals.pca eigenvals.pco print.eigenvals
-> ### summary.eigenvals
+> ### eigenvals.dudi eigenvals.pca eigenvals.pco summary.eigenvals
> ### Keywords: multivariate
>
> ### ** Examples
@@ -2424,8 +2419,7 @@
> ### Name: envfit
> ### Title: Fits an Environmental Vector or Factor onto an Ordination
> ### Aliases: envfit envfit.default envfit.formula vectorfit factorfit
-> ### plot.envfit print.envfit print.factorfit print.vectorfit
-> ### scores.envfit
+> ### plot.envfit scores.envfit
> ### Keywords: multivariate aplot htest
>
> ### ** Examples
@@ -2534,10 +2528,9 @@
> ### Name: fisherfit
> ### Title: Fit Fisher's Logseries and Preston's Lognormal Model to
> ### Abundance Data
-> ### Aliases: fisherfit as.fisher plot.fisherfit print.fisherfit
-> ### profile.fisherfit confint.fisherfit plot.profile.fisherfit prestonfit
-> ### prestondistr as.preston plot.prestonfit lines.prestonfit
-> ### print.prestonfit veiledspec
+> ### Aliases: fisherfit as.fisher plot.fisherfit profile.fisherfit
+> ### confint.fisherfit plot.profile.fisherfit prestonfit prestondistr
+> ### as.preston plot.prestonfit lines.prestonfit veiledspec
> ### Keywords: univar distribution
>
> ### ** Examples
@@ -2904,9 +2897,8 @@
> ### Name: humpfit
> ### Title: No-interaction Model for Hump-backed Species Richness vs.
> ### Biomass
-> ### Aliases: humpfit print.humpfit summary.humpfit print.summary.humpfit
-> ### lines.humpfit plot.humpfit points.humpfit predict.humpfit
-> ### profile.humpfit
+> ### Aliases: humpfit summary.humpfit lines.humpfit plot.humpfit
+> ### points.humpfit predict.humpfit profile.humpfit
> ### Keywords: models regression nonlinear
>
> ### ** Examples
@@ -3013,8 +3005,7 @@
>
> ### Name: isomap
> ### Title: Isometric Feature Mapping Ordination
-> ### Aliases: isomap isomapdist plot.isomap summary.isomap
-> ### print.summary.isomap print.isomap rgl.isomap
+> ### Aliases: isomap isomapdist plot.isomap summary.isomap rgl.isomap
> ### Keywords: multivariate
>
> ### ** Examples
@@ -3217,7 +3208,7 @@
>
> ### Name: mantel
> ### Title: Mantel and Partial Mantel Tests for Dissimilarity Matrices
-> ### Aliases: mantel mantel.partial print.mantel
+> ### Aliases: mantel mantel.partial
> ### Keywords: multivariate htest
>
> ### ** Examples
@@ -3270,7 +3261,7 @@
>
> ### Name: mantel.correlog
> ### Title: Mantel Correlogram
-> ### Aliases: mantel.correlog print.mantel.correlog plot.mantel.correlog
+> ### Aliases: mantel.correlog plot.mantel.correlog
> ### Keywords: multivariate
>
> ### ** Examples
@@ -3403,8 +3394,7 @@
> ### Title: Nonmetric Multidimensional Scaling with Stable Solution from
> ### Random Starts, Axis Scaling and Species Scores
> ### Aliases: metaMDS metaMDSdist metaMDSiter metaMDSredist initMDS postMDS
-> ### print.metaMDS plot.metaMDS points.metaMDS text.metaMDS scores.metaMDS
-> ### metaMDSrotate
+> ### plot.metaMDS points.metaMDS text.metaMDS scores.metaMDS metaMDSrotate
> ### Keywords: multivariate
>
> ### ** Examples
@@ -3613,7 +3603,7 @@
> ### Name: monoMDS
> ### Title: Global and Local Non-metric Multidimensional Scaling and Linear
> ### and Hybrid Scaling
-> ### Aliases: monoMDS print.monoMDS scores.monoMDS plot.monoMDS
+> ### Aliases: monoMDS scores.monoMDS plot.monoMDS
> ### Keywords: multivariate
>
> ### ** Examples
@@ -3644,8 +3634,7 @@
> ### Name: mrpp
> ### Title: Multi Response Permutation Procedure and Mean Dissimilarity
> ### Matrix
-> ### Aliases: mrpp print.mrpp meandist summary.meandist
-> ### print.summary.meandist plot.meandist
+> ### Aliases: mrpp meandist summary.meandist plot.meandist
> ### Keywords: multivariate nonparametric htest
>
> ### ** Examples
@@ -3738,7 +3727,7 @@
> ### Name: mso
> ### Title: Functions for performing and displaying a spatial partitioning
> ### of cca or rda results
-> ### Aliases: mso print.mso msoplot
+> ### Aliases: mso msoplot
> ### Keywords: spatial multivariate
>
> ### ** Examples
@@ -3842,7 +3831,7 @@
>
> ### Name: multipart
> ### Title: Multiplicative Diversity Partitioning
-> ### Aliases: multipart print.multipart
+> ### Aliases: multipart
> ### Keywords: multivariate
>
> ### ** Examples
@@ -3920,8 +3909,7 @@
> ### Name: nestedtemp
> ### Title: Nestedness Indices for Communities of Islands or Patches
> ### Aliases: nestedtemp nestedchecker nestedn0 nesteddisc nestednodf
-> ### print.nestedchecker print.nestedn0 print.nesteddisc print.nestedtemp
-> ### print.nestednodf plot.nestedtemp
+> ### plot.nestedtemp
> ### Keywords: univar
>
> ### ** Examples
@@ -3972,8 +3960,8 @@
>
> ### Name: oecosimu
> ### Title: Null Models for Biological Communities
-> ### Aliases: oecosimu commsimulator print.oecosimu as.ts.oecosimu
-> ### as.mcmc.oecosimu density.oecosimu densityplot.oecosimu
+> ### Aliases: oecosimu commsimulator as.ts.oecosimu as.mcmc.oecosimu
+> ### density.oecosimu densityplot.oecosimu
> ### Keywords: multivariate datagen
>
> ### ** Examples
@@ -4699,7 +4687,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x103b0b1c8>
+<environment: 0x1039d4b48>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4715,7 +4703,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106462988>
+<environment: 0x1045cae68>
Estimated degrees of freedom:
6.0761 total = 7.076141
@@ -4871,7 +4859,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106a3ced8>
+<environment: 0x105f2d9f0>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4884,7 +4872,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106d97520>
+<environment: 0x1065a98e0>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4897,7 +4885,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1066c0430>
+<environment: 0x106bbb980>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5143,7 +5131,7 @@
> ### Name: permutest.betadisper
> ### Title: Permutation test of multivariate homogeneity of groups
> ### dispersions (variances)
-> ### Aliases: permutest.betadisper print.permutest.betadisper
+> ### Aliases: permutest.betadisper
> ### Keywords: methods multivariate
>
> ### ** Examples
@@ -5373,7 +5361,7 @@
> ### Name: prc
> ### Title: Principal Response Curves for Treatments with Repeated
> ### Observations
-> ### Aliases: prc summary.prc print.summary.prc plot.prc
+> ### Aliases: prc summary.prc plot.prc
> ### Keywords: multivariate
>
> ### ** Examples
@@ -5618,10 +5606,10 @@
>
> ### Name: procrustes
> ### Title: Procrustes Rotation of Two Configurations and PROTEST
-> ### Aliases: procrustes print.procrustes summary.procrustes
-> ### print.summary.procrustes plot.procrustes points.procrustes
-> ### text.procrustes lines.procrustes residuals.procrustes
-> ### fitted.procrustes predict.procrustes protest print.protest
+> ### Aliases: procrustes summary.procrustes plot.procrustes
+> ### points.procrustes text.procrustes lines.procrustes
+> ### residuals.procrustes fitted.procrustes predict.procrustes protest
+> ### print.protest
> ### Keywords: multivariate htest
>
> ### ** Examples
@@ -5710,9 +5698,8 @@
> ### Title: Rank - Abundance or Dominance / Diversity Models
> ### Aliases: radfit radfit.default radfit.data.frame AIC.radfit as.rad
> ### coef.radfit fitted.radfit lines.radline plot.radfit.frame plot.radfit
-> ### plot.radline plot.rad radlattice points.radline print.radfit.frame
-> ### print.radfit print.radline summary.radfit.frame rad.preempt
-> ### rad.lognormal rad.zipf rad.zipfbrot rad.null
+> ### plot.radline plot.rad radlattice points.radline summary.radfit.frame
+> ### rad.preempt rad.lognormal rad.zipf rad.zipfbrot rad.null
> ### Keywords: univar distribution
>
> ### ** Examples
@@ -6209,9 +6196,9 @@
>
> ### Name: specpool
> ### Title: Extrapolated Species Richness in a Species Pool
-> ### Aliases: specpool specpool2vect poolaccum print.poolaccum
-> ### summary.poolaccum plot.poolaccum estimateR estimateR.default
-> ### estimateR.matrix estimateR.data.frame estaccumR
+> ### Aliases: specpool specpool2vect poolaccum summary.poolaccum
+> ### plot.poolaccum estimateR estimateR.default estimateR.matrix
+> ### estimateR.data.frame estaccumR
> ### Keywords: univar
>
> ### ** Examples
@@ -6349,8 +6336,7 @@
>
> ### Name: taxondive
> ### Title: Indices of Taxonomic Diversity and Distinctness
-> ### Aliases: taxondive print.taxondive summary.taxondive
-> ### print.summary.taxondive plot.taxondive taxa2dist
+> ### Aliases: taxondive summary.taxondive plot.taxondive taxa2dist
> ### Keywords: univar
>
> ### ** Examples
@@ -6423,7 +6409,7 @@
>
> ### Name: tolerance
> ### Title: Species tolerances and sample heterogeneities
-> ### Aliases: tolerance tolerance.cca print.tolerance.cca
+> ### Aliases: tolerance tolerance.cca
>
> ### ** Examples
>
@@ -6680,8 +6666,8 @@
> ### Name: varpart
> ### Title: Partition the Variation of Community Matrix by 2, 3, or 4
> ### Explanatory Matrices
-> ### Aliases: varpart varpart2 varpart3 varpart4 showvarparts print.varpart
-> ### print.varpart234 plot.varpart plot.varpart234 simpleRDA2
+> ### Aliases: varpart varpart2 varpart3 varpart4 showvarparts plot.varpart
+> ### plot.varpart234 simpleRDA2
> ### Keywords: multivariate
>
> ### ** Examples
@@ -7122,7 +7108,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1083443f8>
+<environment: 0x107af8040>
Estimated degrees of freedom:
2 total = 3
@@ -7587,7 +7573,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 104.154 1.15 107.798 0 0
+Time elapsed: 122.3 1.391 125.699 0 0
> grDevices::dev.off()
null device
1
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