[Vegan-commits] r2994 - in pkg/vegan: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 26 12:04:06 CET 2016
Author: jarioksa
Date: 2016-02-26 12:04:05 +0100 (Fri, 26 Feb 2016)
New Revision: 2994
Modified:
pkg/vegan/inst/NEWS.Rd
pkg/vegan/man/cca.Rd
pkg/vegan/man/diversity.Rd
pkg/vegan/man/nestedtemp.Rd
pkg/vegan/man/oecosimu.Rd
pkg/vegan/man/plot.cca.Rd
pkg/vegan/man/simper.Rd
pkg/vegan/man/specpool.Rd
pkg/vegan/man/varpart.Rd
pkg/vegan/man/vegan-package.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local
Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/inst/NEWS.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -21,7 +21,8 @@
\itemize{
\item \code{vegandocs} is deprecated. Current \R{} provides better
- tools for seeing extra documentation.
+ tools for seeing extra documentation (\code{news()} and
+ \code{browseVignettes()}).
} %itemize
} %deprecated
@@ -30,9 +31,9 @@
\itemize{
\item All vignettes are built with standard \R{} tools and can be
- browsed with \code{browseVignettes}. Earlier \code{FAQ-vegan} and
+ browsed with \code{browseVignettes}. \code{FAQ-vegan} and
\code{partitioning} were only accessible with \code{vegandocs}
- function.
+ function.
} %itemize
} %vignettes
@@ -44,7 +45,9 @@
removed. Version 6.1 of \code{texi2dvi} was incompatible with \R{}
and prevented building \pkg{vegan}. The \code{FAQ-vegan} that was
earlier built with \code{texi2dvi} uses now \pkg{knitr}. Because
- of this, \pkg{vegan} is now dependent on \R-3.0.0.
+ of this, \pkg{vegan} is now dependent on \R-3.0.0. Fixes issue
+ \href{https://github.com/vegandevs/vegan/issues/158}{#158} in
+ Github.
} %itemize
} % building
Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/cca.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -271,10 +271,6 @@
data(dune.env)
dune.Manure <- rda(dune ~ Manure, dune.env)
plot(dune.Manure)
-## For further documentation:
-\dontrun{
-vegandocs("decision")
}
-}
\keyword{ multivariate }
Modified: pkg/vegan/man/diversity.Rd
===================================================================
--- pkg/vegan/man/diversity.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/diversity.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -79,12 +79,12 @@
\seealso{These functions calculate only some basic indices, but many
others can be derived with them (see Examples). Facilities related to
diversity are discussed in a \pkg{vegan} vignette that can be read
- with command \code{vegandocs("diversity")}. Functions
- \code{\link{renyi}} and \code{\link{tsallis}} estimate a series of
- generalized diversity indices. Function \code{\link{rarefy}} finds
- estimated number of species for given sample size. Beta diversity can
- be estimated with \code{\link{betadiver}}. Diversities can be
- partitioned with \code{\link{adipart}} and \code{\link{multipart}}. }
+ with \code{browseVignettes("vegan")}. Functions \code{\link{renyi}}
+ and \code{\link{tsallis}} estimate a series of generalized diversity
+ indices. Function \code{\link{rarefy}} finds estimated number of
+ species for given sample size. Beta diversity can be estimated with
+ \code{\link{betadiver}}. Diversities can be partitioned with
+ \code{\link{adipart}} and \code{\link{multipart}}. }
\author{ Jari Oksanen and Bob O'Hara (\code{fisher.alpha}).}
Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/nestedtemp.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -93,7 +93,7 @@
cautious in interpreting the results. The details of calculations are
explained in the \code{\link{vignette}} \emph{Design decisions and
implementation} that you can read using functions
- \code{\link{vignette}} or \code{\link{vegandocs}}. Function
+ \code{\link{browseVignettes}}. Function
\code{\link[bipartite]{nestedness}} in the \pkg{bipartite} package is
a direct port of the BINMATNEST programme of
\enc{Rodríguez-Gironés}{Rodriguez-Girones} & Santamaria (2006).
Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/oecosimu.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -80,8 +80,7 @@
processing. The parallel processing is done with \pkg{parallel}
package. If you define a \code{nestfun} in Windows that needs other
\R packages than \pkg{vegan} or \pkg{permute}, you must set up a
- socket cluster before the call. See \code{\link{vegandocs}}
- \code{decision-vegan} for details. }
+ socket cluster before the call. }
\item{x}{An \code{oecosimu} result object.}
\item{\dots}{Other arguments to functions.}
Modified: pkg/vegan/man/plot.cca.Rd
===================================================================
--- pkg/vegan/man/plot.cca.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/plot.cca.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -88,9 +88,10 @@
\item{const}{General scaling constant to \code{rda} scores. The
default is to use a constant that gives biplot scores, that is,
scores that approximate original data (see \code{\link{vignette}}
- \samp{decision-vegan.pdf} with \code{\link{vegandocs}} for details
- and discussion). If \code{const} is a vector of two items, the first
- is used for species, and the second item for site scores.}
+ on \sQuote{Design Decisions} with \code{browseVignettes("vegan")}
+ for details and discussion). If \code{const} is a vector of two
+ items, the first is used for species, and the second item for site
+ scores.}
\item{axis.bp}{Draw \code{\link{axis}} for biplot arrows.}
\item{axes}{Number of axes in summaries.}
\item{digits}{Number of digits in output.}
Modified: pkg/vegan/man/simper.Rd
===================================================================
--- pkg/vegan/man/simper.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/simper.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -31,9 +31,7 @@
\item{digits}{Number of digits in output.}
\item{parallel}{Number of parallel processes or a predefined socket
cluster. With \code{parallel = 1} uses ordinary, non-parallel
- processing. The parallel processing is done with \pkg{parallel}
- package. See \code{\link{vegandocs}} \code{decision-vegan} for
- details.}
+ processing.}
\item{...}{Parameters passed to other functions. In \code{simper} the
extra parameters are passed to \code{\link[permute]{shuffleSet}} if
permutations are used.}
Modified: pkg/vegan/man/specpool.Rd
===================================================================
--- pkg/vegan/man/specpool.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/specpool.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -121,18 +121,17 @@
the number
of individuals in rare species.
- Functions estimate the standard errors of the estimates. These
- only concern the number of added species, and assume that there is
- no variance in the observed richness. The equations of standard
- errors are too complicated to be reproduced in this help page, but
- they can be studied in the \R source code of the function and are
- discussed in the \code{\link{vignette}} \dQuote{diversity-vegan}
- that can be read with the \code{\link{vegandocs}} command. The
- standard error are based on the following sources: Chiu et
- al. (2014) for the Chao estimates and Smith and van Belle (1984)
- for the first-order Jackknife and the bootstrap (second-order
- jackknife is still missing). For the variance estimator of
- \eqn{S_{ace}}{S_ace} see O'Hara (2005).
+ Functions estimate the standard errors of the estimates. These only
+ concern the number of added species, and assume that there is no
+ variance in the observed richness. The equations of standard errors
+ are too complicated to be reproduced in this help page, but they can
+ be studied in the \R source code of the function and are discussed
+ in the \code{\link{vignette}} that can be read with the
+ \code{browseVignettes("vegan")}. The standard error are based on the
+ following sources: Chiu et al. (2014) for the Chao estimates and
+ Smith and van Belle (1984) for the first-order Jackknife and the
+ bootstrap (second-order jackknife is still missing). For the
+ variance estimator of \eqn{S_{ace}}{S_ace} see O'Hara (2005).
Functions \code{poolaccum} and \code{estaccumR} are similar to
\code{\link{specaccum}}, but estimate extrapolated richness indices
Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/varpart.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -92,10 +92,9 @@
explained by the explanatory table.
The identifiable fractions are designated by lower case alphabets. The
- meaning of the symbols can be found in the separate document
- "partitioning.pdf" (which can be read using \code{\link{vegandocs}}),
- or can be displayed graphically using function
- \code{showvarparts}.
+ meaning of the symbols can be found in the separate document (use
+ \code{browseVignettes("vegan")}), or can be displayed graphically
+ using function \code{showvarparts}.
A fraction is testable if it can be directly
expressed as an RDA model. In these cases the printed output also
@@ -107,9 +106,9 @@
the number of estimated models.
An abridged explanation of the alphabetic symbols for the individual
- fractions follows, but computational details should be checked in
- "partitioning.pdf" (readable with \code{\link{vegandocs}}) or in the
- source code.
+ fractions follows, but computational details should be checked in the
+ vignette (readable with \code{browseVignettes("vegan")}) or in the
+ source code.
With two explanatory tables, the fractions explained
uniquely by each of the two tables are \code{[a]} and
@@ -209,11 +208,11 @@
\note{
- You can use command \code{\link{vegandocs}} to display document
- "partitioning.pdf" which presents Venn diagrams showing the fraction
- names in partitioning the variation of Y with respect to 2, 3, and 4
- tables of explanatory variables, as well as the equations used in
- variation partitioning.
+ You can use command \code{browseVignettes("vegan")} to display
+ document which presents Venn diagrams showing the fraction names in
+ partitioning the variation of Y with respect to 2, 3, and 4 tables of
+ explanatory variables, as well as the equations used in variation
+ partitioning.
The functions frequently give negative estimates of variation.
Adjusted \eqn{R^2}{R-squared} can be negative for any fraction;
@@ -252,11 +251,6 @@
data(mite.env)
data(mite.pcnm)
-## See detailed documentation:
-\dontrun{
-vegandocs("partition")
-}
-
# Two explanatory matrices -- Hellinger-transform Y
# Formula shortcut "~ ." means: use all variables in 'data'.
mod <- varpart(mite, ~ ., mite.pcnm, data=mite.env, transfo="hel")
Modified: pkg/vegan/man/vegan-package.Rd
===================================================================
--- pkg/vegan/man/vegan-package.Rd 2016-02-25 12:51:13 UTC (rev 2993)
+++ pkg/vegan/man/vegan-package.Rd 2016-02-26 11:04:05 UTC (rev 2994)
@@ -12,31 +12,26 @@
multivariate tools can be used for other data types as well. }
\details{The functions in the \pkg{vegan} package contain tools for
-diversity analysis (see \code{\link{vignette}}
-\code{vegandocs("diversity")}), ordination and analysis of
-dissimilarities (see \code{\link{vignette}}
-\code{vegandocs("intro")}). Together with the \pkg{labdsv} package,
-the \pkg{vegan} package provides most standard tools of descriptive
-community analysis. Package \pkg{ade4} provides an alternative
-comprehensive package, and several other packages complement
-\pkg{vegan} and provide tools for deeper analysis in specific
-fields. Package \pkg{BiodiversityR} provides a GUI for a large subset
-of \pkg{vegan} functionality.
+diversity analysis, ordination methods and tools for the analysis of
+dissimilarities. Together with the \pkg{labdsv} package, the \pkg{vegan}
+package provides most standard tools of descriptive community
+analysis. Package \pkg{ade4} provides an alternative comprehensive
+package, and several other packages complement \pkg{vegan} and provide
+tools for deeper analysis in specific fields. Package
+\pkg{BiodiversityR} provides a GUI for a large subset of \pkg{vegan}
+functionality.
The \pkg{vegan} package is developed at GitHub
(\url{https://github.com/vegandevs/vegan/}). GitHub provides up-to-date
information and forums for bug reports.
-The \pkg{vegan} documents can be read with \code{\link{vegandocs}}
-function. In addition to \code{\link{vignette}}s of basic usage, you
-can read \code{NEWS} on the new features and bug fixes in the release
-version (\code{vegandocs("NEWS")}), and more technical and fine
-grained \code{ChangeLog} (\code{vegandocs("Change")}). Several
-frequently asked questions really are answered in the vegan FAQ
-(\code{vegandocs("FAQ")}). The discussion on design decisions can be
-read with \code{vegandocs("decision")}. A tutorial of the package at
-\url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}
-provides a more thorough introduction to the package.
+Most important changes in \pkg{vegan} documents can be read with
+\code{news(package="vegan")} and vignettes can be browsed with
+\code{browseVignettes("vegan")}. The vignettes include a \pkg{vegan}
+FAQ, discussion on design decisions, short introduction to ordination
+and discussion on diversity methods. A tutorial of the package at
+\url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf} provides
+a more thorough introduction to the package.
To see the preferable citation of the package, type
\code{citation("vegan")}.
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