[Vegan-commits] r660 - in pkg/vegan: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 15 09:33:14 CET 2009
Author: jarioksa
Date: 2009-01-15 09:33:14 +0100 (Thu, 15 Jan 2009)
New Revision: 660
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/cascadeKM.Rd
pkg/vegan/man/cca.object.Rd
pkg/vegan/man/mso.Rd
pkg/vegan/man/vegdist.Rd
Log:
Corrected problems in Rd files reported by stricter Rd parser v2 in R 2.9.0 unstable (2009-01-13 r47593)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2009-01-14 19:31:02 UTC (rev 659)
+++ pkg/vegan/inst/ChangeLog 2009-01-15 08:33:14 UTC (rev 660)
@@ -4,21 +4,29 @@
Version 1.16-9 (opened Jan 7, 2009)
- * permatswap: new algorithm "swsh" is added to keep row/column
- incidences (but not sums) constant. The name refers to the two
- steps: (1) binary *sw*aps are made then (2) individuals in
- non-zero cells are *sh*uffled.
+ * Checked with R version 2.9.0 Under development (unstable)
+ (2009-01-13 r47593) having experimental strict Rd parser, and
+ corrected the reported problems in Rd files so that vegan is R
+ 2.9.0-ready.
- * permat methods: calculations of the Chi-squared statistic is
- added to summary, and the type argument can be used in the plot
- "bray" or "chisq" values.
+ * adonis: uses now canonical (hits+1)/(tries+1) for P-values
+ instead of hits/tries.
+ * permatswap: new algorithm "swsh" is added to keep row/column
+ incidences (but not sums) constant. The name refers to the two
+ steps: (1) binary *sw*aps are made then (2) individuals in
+ non-zero cells are *sh*uffled.
+
+ * permat methods: calculations of the Chi-squared statistic is
+ added to summary, and the type argument can be used in the plot
+ "bray" or "chisq" values.
+
* nestednodf: gained argument 'order = TRUE' allowing tests for
other orderings than using marginal frequencies (default)
following suggestion by Almeida-Neto et al. (2008).
* summary.cca: cumulative "accounted for" statistics failed in
- unconstrained models.
+ unconstrained models.
Version 1.16-8 (closed Jan 7, 2009)
Modified: pkg/vegan/man/cascadeKM.Rd
===================================================================
--- pkg/vegan/man/cascadeKM.Rd 2009-01-14 19:31:02 UTC (rev 659)
+++ pkg/vegan/man/cascadeKM.Rd 2009-01-15 08:33:14 UTC (rev 660)
@@ -75,18 +75,18 @@
literally when the groups are not equal in size. Type \code{"all"} to
obtain both indices. The indices are defined as:
\describe{
- \item \bold{calinski}:
+ \item{calinski:}{
\eqn{(SSB/(K-1))/(SSW/(n-K))}, where \eqn{n} is the
number of data points and \eqn{K} is the number of clusters.
\eqn{SSW} is the sum of squares within the clusters while
\eqn{SSB} is the sum of squares among the clusters. This index
- is simply an \eqn{F} (ANOVA) statistic.
+ is simply an \eqn{F} (ANOVA) statistic.}
- \item \bold{ssi}:
+ \item{ssi:}{
the \dQuote{Simple Structure Index} multiplicatively combines
several elements which influence the interpretability of a
partitioning solution. The best partition is indicated by the
- highest SSI value.
+ highest SSI value.}
}
In a simulation study, Milligan and Cooper (1985) found
Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd 2009-01-14 19:31:02 UTC (rev 659)
+++ pkg/vegan/man/cca.object.Rd 2009-01-15 08:33:14 UTC (rev 660)
@@ -42,12 +42,13 @@
component.
Items \code{pCCA}, \code{CCA} and \code{CA} have similar
structure, and contain following items:
+ \describe{
\item{\code{alias}}{The names of the aliased constraints or conditions.
Function \code{\link{alias.cca}} does not access this item
directly, but it finds the aliased variables and their defining
equations from the \code{QR} item.}
\item{\code{biplot}}{Biplot scores of constraints. Only in \code{CCA}.}
- \item{centroids}{(Weighted) centroids of factor levels of
+ \item{\code{centroids}}{(Weighted) centroids of factor levels of
constraints. Only in \code{CCA}. Missing if the ordination was not
called with \code{formula}.}
\item{\code{eig}}{Eigenvalues of axes. In \code{CCA} and \code{CA}.}
@@ -104,7 +105,7 @@
after both \code{pCCA} and \code{CCA}. In \code{\link{cca}} the
standardization is Chi-square, and in \code{\link{rda}} centring
and optional scaling by species standard deviations using function
- \code{\link{scale}}. }
+ \code{\link{scale}}.} }
}
}
Modified: pkg/vegan/man/mso.Rd
===================================================================
--- pkg/vegan/man/mso.Rd 2009-01-14 19:31:02 UTC (rev 659)
+++ pkg/vegan/man/mso.Rd 2009-01-15 08:33:14 UTC (rev 660)
@@ -59,8 +59,8 @@
\value{
The function \code{mso} returns an amended \code{cca} or \code{rda}
object with the additional attributes \code{grain}, \code{H},
- \code{H.test} and \code{vario}.
- \item{grain }{ The grain attribute defines the interval size of the
+ \code{H.test} and \code{vario}.
+ \item{grain}{The grain attribute defines the interval size of the
distance classes .}
\item{H }{ H is an object of class 'dist' and contains the geographic
distances between observations.}
@@ -69,27 +69,30 @@
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
- brackets):
- \item{H }{ Distance class as multiples of grain.}
- \item{Dist }{ Average distance of pairs of observations in distance class H.}
- \item{n }{ Number of unique pairs of observations in distance class
- H.}
- \item{All }{ Empirical (chi-square) variogram of total variance
- (inertia).}
- \item{Sum }{ Sum of empirical (chi-square) variograms of explained
- and residual variance (inertia).}
- \item{CA }{ Empirical (chi-square) variogram of residual variance
- (inertia).}
- \item{CCA }{ Empirical (chi-square) variogram of explained variance
- (inertia).}
- \item{pCCA }{ Empirical (chi-square) variogram of conditioned
- variance (inertia).}
- \item{se }{ Standard error of the empirical (chi-square) variogram
- of total variance (inertia).}
- \item{CA.signif }{P-value of permutation test for spatial
- independence of residual variance (inertia).}
+ brackets):
+ \describe{
+ \item{\code{H}}{Distance class as multiples of grain.}
+ \item{\code{Dist}}{ Average distance of pairs of observations in distance class H.}
+ \item{n }{ Number of unique pairs of observations in distance class
+ H.}
+ \item{\code{All}}{ Empirical (chi-square) variogram of total variance
+ (inertia).}
+ \item{\code{Sum}}{ Sum of empirical (chi-square) variograms of explained
+ and residual variance (inertia).}
+ \item{\code{CA}}{ Empirical (chi-square) variogram of residual variance
+ (inertia).}
+ \item{\code{CCA}}{ Empirical (chi-square) variogram of explained variance
+ (inertia).}
+ \item{\code{pCCA}}{ Empirical (chi-square) variogram of conditioned
+ variance (inertia).}
+ \item{\code{se}}{ Standard error of the empirical (chi-square) variogram
+ of total variance (inertia).}
+ \item{\code{CA.signif}}{P-value of permutation test for spatial
+ independence of residual variance (inertia).}
+ }
}
}
+
\references{ Wagner, H.H. 2004. Direct multi-scale ordination with
canonical correspondence analysis. \emph{Ecology} 85: 342--351. }
\author{ The responsible author was Helene Wagner.}
Modified: pkg/vegan/man/vegdist.Rd
===================================================================
--- pkg/vegan/man/vegdist.Rd 2009-01-14 19:31:02 UTC (rev 659)
+++ pkg/vegan/man/vegdist.Rd 2009-01-15 08:33:14 UTC (rev 660)
@@ -73,10 +73,10 @@
min(x[ij],x[ik])/(sum x[ik]))}
\cr
\code{morisita}
- \tab {\eqn{d_{jk} = \frac{2 \sum_i x_{ij} x_{ik}}{(\lambda_j +
+ \tab \eqn{d_{jk} = \frac{2 \sum_i x_{ij} x_{ik}}{(\lambda_j +
\lambda_k) \sum_i x_{ij} \sum_i
x_{ik}}}{d[jk] = 2*sum(x[ij]*x[ik])/((lambda[j]+lambda[k]) *
- sum(x[ij])*sum(x[ik]))} }
+ sum(x[ij])*sum(x[ik]))}
\cr
\tab where \eqn{\lambda_j = \frac{\sum_i x_{ij} (x_{ij} - 1)}{\sum_i
x_{ij} \sum_i (x_{ij} - 1)}}{lambda[j] =
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