[Vegan-commits] r1254 - in pkg/vegan: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 13 13:39:02 CEST 2010
Author: jarioksa
Date: 2010-08-13 13:39:00 +0200 (Fri, 13 Aug 2010)
New Revision: 1254
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/decostand.Rd
pkg/vegan/man/mso.Rd
pkg/vegan/man/permCheck.Rd
pkg/vegan/man/permuted.index2.Rd
pkg/vegan/man/radfit.Rd
pkg/vegan/man/specpool.Rd
pkg/vegan/man/wcmdscale.Rd
Log:
remove \ that is visible in rendereing Rd files
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/inst/ChangeLog 2010-08-13 11:39:00 UTC (rev 1254)
@@ -20,7 +20,9 @@
* msoplot: legend mixed symbols and labels.
- * Rd (help) files: use real UTF-8 instead of \'-escapes.
+ * Rd (help) files: removed some superfluous \-characters that were
+ visible in rendering text (accented letters, Latex notation in
+ wrong places).
Version 1.18-8 (closed August 12, 2010)
Modified: pkg/vegan/man/decostand.Rd
===================================================================
--- pkg/vegan/man/decostand.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/decostand.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -54,16 +54,16 @@
1}).
\item \code{hellinger}: square root of \code{method = "total"}
(Legendre & Gallagher 2001).
- \item \code{log}: logarithmic transformation as suggested by Anderson
- et al. (2006): \eqn{\log_b (x) + 1} for \eqn{x > 0}, where \eqn{b} is
- the base of the logarithm; zeros are left as zeros. Higher bases give
- less weight to quantities and more to presences, and \code{logbase = Inf}
- gives the presence/absence scaling. Please note this is \emph{not}
- \eqn{\log(x+1)}.
+ \item \code{log}: logarithmic transformation as suggested by
+ Anderson et al. (2006): \eqn{\log_b (x) + 1}{log_b (x) + 1} for
+ \eqn{x > 0}, where \eqn{b} is the base of the logarithm; zeros are
+ left as zeros. Higher bases give less weight to quantities and more
+ to presences, and \code{logbase = Inf} gives the presence/absence
+ scaling. Please note this is \emph{not} \eqn{\log(x+1)}{log(x+1)}.
Anderson et al. (2006) suggested this for their (strongly) modified
Gower distance, but the standardization can be used independently
of distance indices.
- }
+ }
Standardization, as contrasted to transformation, means that the
entries are transformed relative to other entries.
Modified: pkg/vegan/man/mso.Rd
===================================================================
--- pkg/vegan/man/mso.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/mso.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -22,7 +22,7 @@
\code{\link{rda}} function.}
\item{object.xy}{ A vector, matrix or data frame with the spatial
coordinates of the data represented by object.cca. Must have the
- same number of rows as \code{object.cca\$CA\$Xbar} (see
+ same number of rows as \code{object.cca$CA$Xbar} (see
\code{\link{cca.object}}). }
\item{grain}{ Interval size for distance classes.}
\item{round.up}{ Determines the choice of breaks. If false, distances
@@ -65,7 +65,7 @@
\item{H }{ H is an object of class 'dist' and contains the geographic
distances between observations.}
\item{H.test }{ H.test contains a set of dummy variables that describe
- which pairs of observations (rows = elements of \code{object\$H}) fall in
+ which pairs of observations (rows = elements of \code{object$H}) fall in
which distance class (columns). }
\item{vario }{ The vario attribute is a data frame that contains some
or all of the following components for the rda case (cca case in
Modified: pkg/vegan/man/permCheck.Rd
===================================================================
--- pkg/vegan/man/permCheck.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/permCheck.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -102,12 +102,12 @@
the number of observations and the permutation design. In such cases,
\code{nperm} is reduced to equal the number of possible permutations,
and complete enumeration of all permutations is turned on
- (\code{control\$complete} is set to \code{TRUE}).
+ (\code{control$complete} is set to \code{TRUE}).
Alternatively, if the number of possible permutations is low, and less
- than \code{control\$minperm}, it is better to enumerate all possible
+ than \code{control$minperm}, it is better to enumerate all possible
permutations, and as such complete enumeration of all permutations is
- turned on (\code{control\$complete} is set to \code{TRUE}).
+ turned on (\code{control$complete} is set to \code{TRUE}).
Function \code{numPerms} returns the number of permutations for the
passed \code{object} and the selected permutation
Modified: pkg/vegan/man/permuted.index2.Rd
===================================================================
--- pkg/vegan/man/permuted.index2.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/permuted.index2.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -83,8 +83,8 @@
within a function implementing a permutation test. The main purpose of
\code{permute} is to return the correct permutation in each iteration
of the loop, either a random permutation from the current design or
- the next permutation from \code{control\$all.perms} if it is not
- \code{NULL} and \code{control\$complete} is \code{TRUE}.
+ the next permutation from \code{control$all.perms} if it is not
+ \code{NULL} and \code{control$complete} is \code{TRUE}.
}
\value{
For \code{permuted.index2} a vector of length \code{n} containing a
Modified: pkg/vegan/man/radfit.Rd
===================================================================
--- pkg/vegan/man/radfit.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/radfit.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -54,8 +54,9 @@
be plotted.}
\item{order.by}{A vector used for ordering sites in plots.}
\item{BIC}{Use Bayesian Information Criterion, BIC, instead of
- Akaike's AIC. The penalty for a parameter is \eqn{k = \log(S)} where
- \eqn{S} is the number of species, whereas AIC uses \eqn{k = 2}.}
+ Akaike's AIC. The penalty for a parameter is \eqn{k = \log(S)}{k =
+ log(S)} where \eqn{S} is the number of species, whereas AIC uses
+ \eqn{k = 2}.}
\item{model}{Show only the specified model. If missing, AIC is used to
select the model. The model names (which can be abbreviated) are
\code{Preemption}, \code{Lognormal}, \code{Veiled.LN},
Modified: pkg/vegan/man/specpool.Rd
===================================================================
--- pkg/vegan/man/specpool.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/specpool.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -95,8 +95,8 @@
\eqn{C_{ace} = 1 - \frac{a_1}{N_{rare}}}{C_{ace} = 1- a1/N_{rare}}
\cr
\tab \eqn{\gamma^2_{ace} = \max \left[ \frac{S_{rare} \sum_{i=1}^{10}
- i(i-1)a_i}{C_{ace} N_{rare} (N_{rare} - 1)}-1, 0 \right]}{gamma^2 = \max(
- S_rare/C_ace (sum[i=1..10] i*(i-1)*a_i) / N_rare/(N_rare-1) -1 , 0)}
+ i(i-1)a_i}{C_{ace} N_{rare} (N_{rare} - 1)}-1, 0 \right]}{gamma^2 =
+ max(S_rare/C_ace (sum[i=1..10] i*(i-1)*a_i) / N_rare/(N_rare-1) -1 , 0)}
}
Here \eqn{a_i} refers to number of species with abundance \eqn{i}
and \eqn{S_{rare}}{S_rare} is the number of rare
Modified: pkg/vegan/man/wcmdscale.Rd
===================================================================
--- pkg/vegan/man/wcmdscale.Rd 2010-08-13 10:04:03 UTC (rev 1253)
+++ pkg/vegan/man/wcmdscale.Rd 2010-08-13 11:39:00 UTC (rev 1254)
@@ -18,8 +18,8 @@
\item{d}{a distance structure such as that returned by \code{dist}
or a full symmetric matrix containing the dissimilarities.}
\item{k}{the dimension of the space which the data are to be
- represented in; must be in \eqn{\{1,2,\ldots,n-1\}}. If missing,
- all dimensions with above zero eigenvalue.}
+ represented in; must be in \eqn{\{1,2,\ldots,n-1\}}{{1,2,\ldots,n-1}}.
+ If missing, all dimensions with above zero eigenvalue.}
\item{eig}{indicates whether eigenvalues should be returned.}
\item{add}{logical indicating if an additive constant \eqn{c*} should
be computed, and added to the non-diagonal dissimilarities such that
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