[Vegan-commits] r1022 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 23 08:51:30 CEST 2009
Author: jarioksa
Date: 2009-09-23 08:51:30 +0200 (Wed, 23 Sep 2009)
New Revision: 1022
Modified:
pkg/vegan/man/RsquareAdj.Rd
pkg/vegan/man/ordihull.Rd
pkg/vegan/man/ordilabel.Rd
pkg/vegan/man/ordiplot3d.Rd
pkg/vegan/man/ordipointlabel.Rd
pkg/vegan/man/ordiresids.Rd
pkg/vegan/man/orditkplot.Rd
pkg/vegan/man/ordixyplot.Rd
pkg/vegan/man/permatfull.Rd
pkg/vegan/man/permuted.index2.Rd
pkg/vegan/man/permutest.betadisper.Rd
pkg/vegan/man/plot.permat.Rd
pkg/vegan/man/predict.cca.Rd
pkg/vegan/man/renyi.Rd
pkg/vegan/man/spantree.Rd
pkg/vegan/man/specaccum.Rd
pkg/vegan/man/specpool.Rd
pkg/vegan/man/taxondive.Rd
pkg/vegan/man/treedive.Rd
pkg/vegan/man/tsallis.Rd
pkg/vegan/man/varechem.Rd
pkg/vegan/man/varpart.Rd
pkg/vegan/man/vegan-internal.Rd
pkg/vegan/man/vegdist.Rd
pkg/vegan/man/vegemite.Rd
Log:
aspell on ordihull.Rd to wcmdscale.Rd
Modified: pkg/vegan/man/RsquareAdj.Rd
===================================================================
--- pkg/vegan/man/RsquareAdj.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/RsquareAdj.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -37,7 +37,7 @@
methods find this information from the fitted result
object. There are specific methods for \code{\link{rda}},
\code{\link{cca}}, \code{\link{lm}} and \code{\link{glm}}. Adjusted,
- or even unandjusted, R-squared may not be available in some cases,
+ or even unadjusted, R-squared may not be available in some cases,
and then the functions will return \code{NA}. There is no adjusted
R-squared in \code{\link{cca}}, in partial \code{\link{rda}}, and
R-squared values are available only for \code{\link{gaussian}}
@@ -50,7 +50,7 @@
\references{
Peres-Neto, P., P. Legendre, S. Dray and D. Borcard. 2006. Variation
- partioning of species data matrices: estimation and comparison of
+ partitioning of species data matrices: estimation and comparison of
fractions. \emph{Ecology} 87: 2614-2625. }
\seealso{
Modified: pkg/vegan/man/ordihull.Rd
===================================================================
--- pkg/vegan/man/ordihull.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/ordihull.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -61,7 +61,7 @@
groups. }
\item{label}{Label the centre of the points in hull or the ellipse with
the group name.}
- \item{startmark}{plotting characer used to mark the first
+ \item{startmark}{plotting character used to mark the first
item. The default is to use no mark, and for instance,
\code{startmark = 1} will draw a circle. For other plotting characters,
see \code{pch} in \code{\link{points}}. }
@@ -126,7 +126,7 @@
\code{\link{decorana}} or if the user gives the weights in the
call. If \code{ordispider} is called with \code{\link{cca}} or
\code{\link{rda}} result without \code{groups} argument, the function
- connects each `WA' scores to the correspoding `LC' score.
+ connects each `WA' scores to the corresponding `LC' score.
Function \code{ordicluster} overlays a cluster dendrogram onto
ordination. It needs the result from a hierarchic clustering such as
@@ -146,7 +146,7 @@
you may wish to change the default values in \code{\link{arrows}},
\code{\link{lines}}, \code{\link{segments}} and
\code{\link{polygon}}. You can pass
- parameters to \code{\link{scores}} as well. Umderlying function for
+ parameters to \code{\link{scores}} as well. Underlying function for
\code{ordihull} is \code{\link{chull}}.
}
Modified: pkg/vegan/man/ordilabel.Rd
===================================================================
--- pkg/vegan/man/ordilabel.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/ordilabel.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -24,7 +24,7 @@
\item{cex}{ Character expansion for the text (passed to \code{\link{text}}). }
\item{fill}{ Background colour of the labels (the \code{col} argument of
\code{\link{polygon}}).}
- \item{border}{The colour and visibilit of the border of the label as defined in
+ \item{border}{The colour and visibility of the border of the label as defined in
\code{\link{polygon}}).}
\item{\dots}{Other arguments (passed to \code{\link{text}}). }
}
Modified: pkg/vegan/man/ordiplot3d.Rd
===================================================================
--- pkg/vegan/man/ordiplot3d.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/ordiplot3d.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -48,10 +48,10 @@
\item{xlab, ylab, zlab}{Axis labels passed to
\code{\link[scatterplot3d]{scatterplot3d}}. If missing, labels are
taken from the
- ordination result. Set to \code{NA} to supress labels. }
+ ordination result. Set to \code{NA} to suppress labels. }
\item{justify, adj}{Text justification passed to
\code{\link[rgl]{rgl.texts}}. One of these is used depending on the
- versionof \pkg{rgl} installed.}
+ version of \pkg{rgl} installed.}
\item{groups}{Factor giving the groups for which the graphical item is
drawn.}
\item{w}{Weights used to find the average within group. Weights are
@@ -93,7 +93,7 @@
environmental variables will be plotted, and the ordination scores can
be added with \code{\link{text.ordiplot}} or
\code{\link{points.ordiplot}}. Further, you can use any functions from
- the \code{\link{ordihull}} family with the invisble result of
+ the \code{\link{ordihull}} family with the invisible result of
\code{\link{ordiplot3d}}, but you must remember to specify the
\code{display} as \code{"points"} or \code{"arrows"}. To change the
viewing angle, orientation etc. you must see
@@ -152,7 +152,7 @@
\note{The user interface of \pkg{rgl} changed in version 0.65, but
the \code{ordirgl} functions do not yet fully use the new
- capablities. However, they should work both in old and new versions
+ capabilities. However, they should work both in old and new versions
of \pkg{rgl}.
}
Modified: pkg/vegan/man/ordipointlabel.Rd
===================================================================
--- pkg/vegan/man/ordipointlabel.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/ordipointlabel.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -7,7 +7,7 @@
points and text label to the points. The points are in the exact
location given by the ordination, but the function tries to optimize
the location of the text labels to minimize overplotting text. The
- function may be useful with moderatly crowded ordination plots.
+ function may be useful with moderately crowded ordination plots.
}
\usage{
ordipointlabel(x, display = c("sites", "species"), choices = c(1, 2),
@@ -24,7 +24,7 @@
plot. These should be vectors of the same length as the number of
items in \code{display}.}
\item{add}{ Add to an existing plot. }
- \item{\dots}{Other rguments passed to \code{\link{points}} and
+ \item{\dots}{Other arguments passed to \code{\link{points}} and
\code{\link{text}}.}
}
\details{
Modified: pkg/vegan/man/ordiresids.Rd
===================================================================
--- pkg/vegan/man/ordiresids.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/ordiresids.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -40,7 +40,7 @@
The default plots are similar as in \code{\link{plot.lm}}, but they
use \code{\link[lattice]{Lattice}} functions
\code{\link[lattice]{xyplot}} and \code{\link[lattice]{qqmath}}. The
- alternatives have default formulas but these can be replaced by the
+ alternatives have default formulae but these can be replaced by the
user. The elements available in formula or in the \code{groups} argument
are \code{Fitted}, \code{Residuals}, \code{Species} and \code{Sites}.
}
Modified: pkg/vegan/man/orditkplot.Rd
===================================================================
--- pkg/vegan/man/orditkplot.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/orditkplot.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -72,12 +72,12 @@
In addition there are buttons
for the following tasks: \strong{Copy to EPS} copies the current plot
to an encapsulated postscript (eps) file using standard Tcl/Tk
- utilities. The faithfullness of this copy is system dependent. Button
+ utilities. The faithfulness of this copy is system dependent. Button
\strong{Export plot} uses \code{plot.orditkplot} function to redraw
the plot into graphical file formats. Depending on the system, the
following graphical formats may be available: eps, pdf, png, jpeg or
bmp. The file type is deduced from the file suffix or the selection of
- the file type in the dialog box. Alternatively, the same dialog can be
+ the file type in the dialogue box. Alternatively, the same dialogue can be
used to save the plot to an editable \code{\link{xfig}} file. Button
\strong{Dump to R} writes the edited coordinates of labels and points
to the \R session for further processing, and the
@@ -101,7 +101,7 @@
The function only displays one set of scores. However, you can use
\code{\link{ordipointlabel}} to produce a result object that has
different points and text types for several sets of scores and this
- can further edited fith \code{orditkplot}. For a good starting
+ can further edited with \code{orditkplot}. For a good starting
solution you need to scale the \code{\link{ordipointlabel}} result so
that the points span over the whole horizontal axis.
Modified: pkg/vegan/man/ordixyplot.Rd
===================================================================
--- pkg/vegan/man/ordixyplot.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/ordixyplot.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -75,7 +75,7 @@
these functions work with all \pkg{vegan} ordinations and many others.
The \code{formula} is used to define the models. All functions have
- simple default formulas which are used if \code{formula} is missing.
+ simple default formulae which are used if \code{formula} is missing.
If formula is omitted in \code{ordisplom} it
produces a pairs plot of ordination axes and variables in
\code{data}. If \code{formula} is given, ordination results must be
Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/permatfull.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -56,21 +56,21 @@
The \code{shuffle} argument only have effect if the \code{mtype = "count"} and \code{permatfull} function is used with \code{"none", "rows", "columns"} values of \code{fixedmar}. All other cases for count data are individual based randomisations. The \code{"samp"} and \code{"both"} options result fixed matrix fill. The \code{"both"} option means that individuals are shuffled among non zero cells ensuring that there are no cell with zeros as a result, than cell (zero and new valued cells) are shuffled.
-The function \code{permatswap} is useful when bith matrix fill (i.e. the proportion of empty cells) and row/columns sums should be kept constant. \code{permatswap} uses different kinds of swap algorithms, and row and columns sums are fixed in all cases.
+The function \code{permatswap} is useful when with matrix fill (i.e. the proportion of empty cells) and row/columns sums should be kept constant. \code{permatswap} uses different kinds of swap algorithms, and row and columns sums are fixed in all cases.
For presence-absence data, the \code{swap} and \code{tswap} methods of \code{\link{commsimulator}} can be used.
For count data, a special swap algorithm ('swapcount') is implemented that results in permuted matrices with
fixed marginals and matrix fill at the same time.
-The 'quasiswapcount' algorithm (\code{method="quasiswap"} and \code{mtype="count"}) uses the same trick as Carsten Dormann's \code{\link[bipartite]{swap.web}} function in the package 'bipartite'. First, a random matrix is generated by the \code{\link{r2dtable}} function retaining row and column sums. Than the original matrix fill is reconstructed by sequential steps to increase or decrease matrix fill in the random matrix. These steps are based on swaping 2x2 submatrices (see 'swapcount' algorithm for details) to maintain row and column totals. This algorithm generates independent matrices in each step, so \code{burnin} and \code{thin} arguments are not considered. This is the default method, because this is not sequential (as 'swapcount' is) so independence of subsequent matrices does not have to be checked.
+The 'quasiswapcount' algorithm (\code{method="quasiswap"} and \code{mtype="count"}) uses the same trick as Carsten Dormann's \code{\link[bipartite]{swap.web}} function in the package 'bipartite'. First, a random matrix is generated by the \code{\link{r2dtable}} function retaining row and column sums. Than the original matrix fill is reconstructed by sequential steps to increase or decrease matrix fill in the random matrix. These steps are based on swapping 2x2 submatrices (see 'swapcount' algorithm for details) to maintain row and column totals. This algorithm generates independent matrices in each step, so \code{burnin} and \code{thin} arguments are not considered. This is the default method, because this is not sequential (as 'swapcount' is) so independence of subsequent matrices does not have to be checked.
-The 'swapcount' algorithm (\code{method="swap"} and \code{mtype="count"}) tries to find 2x2 submatrices (identified by 2 random row and 2 random column indices), that can be swapped in order to leave column and row totals and fill unchanged. First, the algorithm finds the largest value in the submatrix that can be swapped (\eqn{d}) and whether in diagonal or antidiagonal way. Submatrices that contain values larger than zero in either diagonal or antidiagonal position can be swapped. Swap means that the values in diagonal or antidiagonal positions are decreased by \eqn{d}, while remaining cells are increased by \eqn{d}. A swap is made only if fill doesn't change. This algorithm is sequential, subsequent matrices are not independent, because swaps modify little if the matrix is large. In these cases many burnin steps and thinning is needed to get independent random matrices. Although this algorithm is implemented in C, large burmin and thin values can slow it down considerably. WARNING: according to simulations, this algorithm seems to be biased and non random, thus its use should be avoided!
+The 'swapcount' algorithm (\code{method="swap"} and \code{mtype="count"}) tries to find 2x2 submatrices (identified by 2 random row and 2 random column indices), that can be swapped in order to leave column and row totals and fill unchanged. First, the algorithm finds the largest value in the submatrix that can be swapped (\eqn{d}) and whether in diagonal or antidiagonal way. Submatrices that contain values larger than zero in either diagonal or antidiagonal position can be swapped. Swap means that the values in diagonal or antidiagonal positions are decreased by \eqn{d}, while remaining cells are increased by \eqn{d}. A swap is made only if fill doesn't change. This algorithm is sequential, subsequent matrices are not independent, because swaps modify little if the matrix is large. In these cases many burnin steps and thinning is needed to get independent random matrices. Although this algorithm is implemented in C, large burnin and thin values can slow it down considerably. WARNING: according to simulations, this algorithm seems to be biased and non random, thus its use should be avoided!
The algorithm \code{"swsh"} in the function \code{permatswap} is a hybrid algorithm. First, it makes binary quasiswaps to keep row and column incidences constant, then non-zero values are modified according to the \code{shuffle} argument (only \code{"samp"} and \code{"both"} are available in this case, because it is applied only on non-zero values).
-The algorithm \code{"abuswap"} produces two kinds of null models (based on \code{fixedmar="columns"} or \code{fixedmar="rows"}) as described in Hardy (2008; randomization sheme 2x and 3x, respectively).
+The algorithm \code{"abuswap"} produces two kinds of null models (based on \code{fixedmar="columns"} or \code{fixedmar="rows"}) as described in Hardy (2008; randomization scheme 2x and 3x, respectively).
These preserve column and row occurrences, and column or row sums at the same time.
-Constraints on row/colum sums, matrix fill, total sum and sums within
+Constraints on row/column sums, matrix fill, total sum and sums within
strata can be checked by the \code{summary} method. \code{plot} method is for
visually testing the randomness of the permuted matrices, especially for the
sequential swap algorithms. If there are any tendency in the graph, higher \code{burnin} and
@@ -83,9 +83,9 @@
for restricted permutations. Each strata should contain at least 2 rows
in order to perform randomization (in case of low row numbers, swap algorithms
can be rather slow). If the design is not well balanced
-(i.e. same number of observations within each stratum), permutad matrices may be biased
+(i.e. same number of observations within each stratum), permuted matrices may be biased
because same constraints are forced on submatrices of different dimensions. This
-often means, that the munber of potential permutations will decrease with their dimensions.
+often means, that the number of potential permutations will decrease with their dimensions.
So the more constraints we put, the less randomness can be expected.
The function \code{permat.control} is used to set up quantitative matrix permutations in other functions
Modified: pkg/vegan/man/permuted.index2.Rd
===================================================================
--- pkg/vegan/man/permuted.index2.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/permuted.index2.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -48,7 +48,7 @@
each level of strata? If \code{FALSE} a separate, possibly restricted,
permutation is produced for each level of \code{strata}.}
\item{ncol, nrow}{numeric; the number of columns and rows of samples
- in the spatial grid respectiavly.}
+ in the spatial grid respectively.}
\item{all.perms}{an object of class \code{allPerms}, the result of a
call to \code{\link{allPerms}}.}
\item{i}{integer; row of \code{control$all.perms} to return.}
Modified: pkg/vegan/man/permutest.betadisper.Rd
===================================================================
--- pkg/vegan/man/permutest.betadisper.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/permutest.betadisper.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -1,7 +1,7 @@
\name{permutest.betadisper}
\alias{permutest.betadisper}
\alias{print.permutest.betadisper}
-\title{Permutation test of ultivariate homogeneity of groups dispersions
+\title{Permutation test of multivariate homogeneity of groups dispersions
(variances)}
\description{
Implements a permutation-based test of multivariate homogeneity of
@@ -30,10 +30,10 @@
residuals to generate a permutation distribution of F under the Null
hypothesis of no difference in dispersion between groups.
- Pairwise comprisons of group mean dispersions can be performed by
- setting argument \code{pairwise} to \code{TRUE}. A classicial t test
+ Pairwise comparisons of group mean dispersions can be performed by
+ setting argument \code{pairwise} to \code{TRUE}. A classical t test
is performed on the pairwise group dispersions. This is combined with a
- permutation test based on the t statistic calculated on pariwise group
+ permutation test based on the t statistic calculated on pairwise group
dispersions. An alternative to the classical comparison of group
dispersions, is to calculate Tukey's Honest Significant Differences
between groups, via \code{\link{TukeyHSD.betadisper}}.
Modified: pkg/vegan/man/plot.permat.Rd
===================================================================
--- pkg/vegan/man/plot.permat.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/plot.permat.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -33,7 +33,7 @@
}
\value{
-The \code{plot} creates aplor as a side effect.
+The \code{plot} creates a plot as a side effect.
The \code{as.ts} method returns an object of class 'ts'.
}
Modified: pkg/vegan/man/predict.cca.Rd
===================================================================
--- pkg/vegan/man/predict.cca.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/predict.cca.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -50,7 +50,7 @@
standardization in \code{\link{cca}} and scaling and centring in
\code{\link{rda}}. In \code{\link{capscale}} the \code{"response"} gives
the dissimilarities, and \code{"working"} the scaled scores that produce
- the dissimlarities as Euclidean distances.
+ the dissimilarities as Euclidean distances.
In \code{predict} \code{"response"}
gives an approximation of the original data matrix or dissimilarities,
\code{"wa"} the site scores as weighted averages of the community data,
@@ -84,7 +84,7 @@
unconstrained part of the ordination.
Function \code{predict} can find the estimate of the original data
- matrix or dissimilarites (\code{type = "response"}) with any rank.
+ matrix or dissimilarities (\code{type = "response"}) with any rank.
With \code{rank = "full"} it is identical to \code{fitted}.
In addition, the function
can find the species scores or site scores from the community data
Modified: pkg/vegan/man/renyi.Rd
===================================================================
--- pkg/vegan/man/renyi.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/renyi.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -80,7 +80,7 @@
Function \code{renyi} returns a data frame of selected
indices. Function \code{renyiaccum} with argument \code{raw = FALSE}
returns a three-dimensional array, where the first dimension are the
- accumulated sites, second dimension are the diveristy scales, and
+ accumulated sites, second dimension are the diversity scales, and
third dimension are the summary statistics \code{mean}, \code{stdev},
\code{min}, \code{max}, \code{Qnt 0.025} and \code{Qnt 0.975}. With
argument \code{raw = TRUE} the statistics on the third dimension are
@@ -102,7 +102,7 @@
\author{ Roeland Kindt \email{r.kindt at cgiar.org} and Jari Oksanen }
\seealso{\code{\link{diversity}} for diversity indices, and
- \code{\link{specaccum}} for ordinaty species accumulation curves, and
+ \code{\link{specaccum}} for ordinary species accumulation curves, and
\code{\link[lattice]{xyplot}}, \code{\link{persp}} and
\code{\link[rgl]{rgl}} for controlling graphics. }
\examples{
Modified: pkg/vegan/man/spantree.Rd
===================================================================
--- pkg/vegan/man/spantree.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/spantree.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -27,7 +27,7 @@
\item{toolong}{ Shortest dissimilarity regarded as \code{NA}.
The function uses a fuzz factor, so
that dissimilarities close to the limit will be made \code{NA}, too.
- If \code{toolong = 0} (or negative), no dissimmilarity is regarded
+ If \code{toolong = 0} (or negative), no dissimilarity is regarded
as too long.
}
\item{x}{A \code{spantree} result object.}
Modified: pkg/vegan/man/specaccum.Rd
===================================================================
--- pkg/vegan/man/specaccum.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/specaccum.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -89,7 +89,7 @@
\item{sites}{Number of sites. For \code{method = "rarefaction"} this
is the number of sites corresponding to a certain number of
individuals and generally not an integer, and the average
- number of individuals is also retunred in item \code{individuals}.}
+ number of individuals is also returned in item \code{individuals}.}
\item{richness}{The number of species corresponding to number of
sites. With \code{method = "collector"} this is the observed
richness, for other methods the average or expected richness.}
@@ -138,7 +138,7 @@
\seealso{\code{\link{rarefy}} and \code{\link{rrarefy}} are related
individual based models. Other accumulation models are
- \code{\link{poolaccum}} for extrapoltated richenss, and
+ \code{\link{poolaccum}} for extrapoltated richness, and
\code{\link{renyiaccum}} and \code{\link{tsallisaccum}} for
diversity indices. Underlying graphical functions are
\code{\link{boxplot}}, \code{\link{matlines}},
Modified: pkg/vegan/man/specpool.Rd
===================================================================
--- pkg/vegan/man/specpool.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/specpool.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -121,12 +121,12 @@
developed by Bob O'Hara (unpublished).
Functions \code{poolaccum} and \code{estaccumR} are similar to
- \code{\link{specaccum}}, but estimateextrapolated richness indices
+ \code{\link{specaccum}}, but estimate extrapolated richness indices
of \code{specpool} or \code{estimateR} in addition to number of
species for random ordering of sampling units. Function
\code{specpool} uses presence data and \code{estaccumR} count
data. The functions share \code{summary} and \code{plot}
- methods. The \code{summary} returns quantile envilopes of
+ methods. The \code{summary} returns quantile envelopes of
permutations corresponding the given level of \code{alpha} and
standard deviation of permutations for each sample size. The
\code{plot} function shows the mean and envelope of permutations
Modified: pkg/vegan/man/taxondive.Rd
===================================================================
--- pkg/vegan/man/taxondive.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/taxondive.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -8,7 +8,7 @@
\title{ Indices of Taxonomic Diversity and Distinctness }
\description{
- Function finds indices of taxonomic diversity and distinctiness,
+ Function finds indices of taxonomic diversity and distinctness,
which are averaged taxonomic distances among species or individuals in
the community (Clarke & Warwick 1998, 2001)
}
@@ -27,7 +27,7 @@
order in both.}
\item{x}{Classification table with a row for each species or other
basic taxon, and columns
- for identifiers of its classication at higher levels.}
+ for identifiers of its classification at higher levels.}
\item{varstep}{Vary step lengths between successive levels
relative to proportional loss of the number of distinct classes.}
\item{check}{If \code{TRUE}, remove all redundant levels which are
@@ -80,7 +80,7 @@
With \code{check = TRUE}, the function removes classes which are distinct for all
species or which combine all species into one class, and assumes that
each row presents a distinct basic taxon. The function scales
- the distances so that longesth path length between
+ the distances so that longest path length between
taxa is 100 (not necessarily when \code{check = FALSE}).
Function \code{plot.taxondive} plots \eqn{\Delta^+} against Number of
Modified: pkg/vegan/man/treedive.Rd
===================================================================
--- pkg/vegan/man/treedive.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/treedive.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -39,7 +39,7 @@
2006). The subset of the dendrogram is found by first calculating
\code{\link{cophenetic}} distances from the input dendrogram, then
reconstructing the dendrogram for the subset of the cophenetic
- distance matrix for species occuring in each site.
+ distance matrix for species occurring in each site.
The functions need a dendrogram of species traits as an input. If
species traits contain \code{\link{factor}} or \code{\link{ordered}}
@@ -58,7 +58,7 @@
A vector of diversity values or a single tree height.
}
\references{
- Petchey, O.L. and Gaston, K.J. 2002. Funcional diversity (FD), species
+ Petchey, O.L. and Gaston, K.J. 2002. Functional diversity (FD), species
richness and community composition. \emph{Ecology Letters} 5,
402--411.
Modified: pkg/vegan/man/tsallis.Rd
===================================================================
--- pkg/vegan/man/tsallis.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/tsallis.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -46,7 +46,7 @@
Details on plotting methods and accumulating values can be found on the help pages of the functions \code{\link{renyi}} and \code{\link{renyiaccum}}.
}
\value{
-Function \code{tsallis} returns a data frame of selected indices. Function \code{tsallisaccum} with argument \code{raw = FALSE} returns a three-dimensional array, where the first dimension are the accumulated sites, second dimension are the diveristy scales, and third dimension are the summary statistics \code{mean}, \code{stdev}, \code{min}, \code{max}, \code{Qnt 0.025} and \code{Qnt 0.975}. With argument \code{raw = TRUE} the statistics on the third dimension are replaced with individual permutation results.
+Function \code{tsallis} returns a data frame of selected indices. Function \code{tsallisaccum} with argument \code{raw = FALSE} returns a three-dimensional array, where the first dimension are the accumulated sites, second dimension are the diversity scales, and third dimension are the summary statistics \code{mean}, \code{stdev}, \code{min}, \code{max}, \code{Qnt 0.025} and \code{Qnt 0.975}. With argument \code{raw = TRUE} the statistics on the third dimension are replaced with individual permutation results.
}
\references{
Tsallis, C. (1988) Possible generalization of Boltzmann-Gibbs statistics.
@@ -55,7 +55,7 @@
Tothmeresz, B. (1995) Comparison of different methods for diversity
ordering. \emph{Journal of Vegetation Science} \bold{6}, 283--290.
-Patil, G. P. and Taillie, C. (1982) Diversity as a concep and its measurement.
+Patil, G. P. and Taillie, C. (1982) Diversity as a concept and its measurement.
\emph{J. Am. Stat. Ass.} \bold{77}, 548--567.
Keylock, C. J. (2005) Simpson diversity and the Shannon-Wiener index as special cases of a generalized entropy.
@@ -66,7 +66,7 @@
}
\author{\enc{P\'eter S\'olymos}{Peter Solymos}, \email{solymos at ualberta.ca}, based on the code of Roeland Kindt and Jari Oksanen written for \code{renyi}}
\seealso{
-Plotting methods and accumulation routins are based on functions \code{\link{renyi}} and \code{\link{renyiaccum}}. An object of class 'tsallisaccum' can be used with function \code{\link{rgl.renyiaccum}} as well. See also settings for \code{\link{persp}}.
+Plotting methods and accumulation routines are based on functions \code{\link{renyi}} and \code{\link{renyiaccum}}. An object of class 'tsallisaccum' can be used with function \code{\link{rgl.renyiaccum}} as well. See also settings for \code{\link{persp}}.
}
\examples{
data(BCI)
Modified: pkg/vegan/man/varechem.Rd
===================================================================
--- pkg/vegan/man/varechem.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/varechem.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -16,7 +16,7 @@
The \code{varechem} data frame has 24 rows and 14 columns, giving the
soil characteristics of the very same sites as in the \code{varespec}
data frame. The chemical measurements have obvious names.
-\code{Baresoil} gives the estimated cover of bare soil, \code{Humpdepth}
+\code{Baresoil} gives the estimated cover of bare soil, \code{Humdepth}
the thickness of the humus layer.
}
\references{
Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/varpart.Rd 2009-09-23 06:51:30 UTC (rev 1022)
@@ -82,7 +82,7 @@
The identifiable fractions are designated by lower case alphabets. The
meaning of the symbols can be found in the separate document
- "partionining.pdf" (which can be read using \code{\link{vegandocs}}),
+ "partitioning.pdf" (which can be read using \code{\link{vegandocs}}),
or can be displayed graphically using function
\code{showvarparts}.
@@ -140,7 +140,7 @@
\item{nsets}{Number of explanatory tables}
\item{bigwarning}{Warnings on collinearity.}
\item{fract}{Basic fractions from all estimated constrained models.}
- \item{indfract}{Invididual fractions or all possible subsections in
+ \item{indfract}{Individual fractions or all possible subsections in
the Venn diagram (see \code{showvarparts}).}
\item{contr1}{Fractions that can be found after conditioning on single
explanatory table in models with three or four explanatory tables.}
@@ -152,7 +152,7 @@
\code{indfract}, \code{contr1} and \code{contr2} are all data frames with
items:
\itemize{
- \item{Df}{Degrees of freedom of numerator of the \eqn{F}-statististic
+ \item{Df}{Degrees of freedom of numerator of the \eqn{F}-statistic
for the fraction.}
\item{R.square}{Raw R-squared. This is calculated only for
\code{fract} and this is \code{NA} in other items.}
@@ -166,7 +166,7 @@
\references{
-(a) References on variation partioning
+(a) References on variation partitioning
Borcard, D., P. Legendre & P. Drapeau. 1992. Partialling out the spatial
component of ecological variation. Ecology 73: 1045--1055.
@@ -181,7 +181,7 @@
(c) Reference on adjustment of the bimultivariate redundancy statistic
-Peres-Neto, P., P. Legendre, S. Dray and D. Borcard. 2006. Variation partioning
+Peres-Neto, P., P. Legendre, S. Dray and D. Borcard. 2006. Variation partitioning
of species data matrices: estimation and comparison of fractions.
Ecology 87: 2614--2625.
}
Modified: pkg/vegan/man/vegan-internal.Rd
===================================================================
--- pkg/vegan/man/vegan-internal.Rd 2009-09-22 13:57:24 UTC (rev 1021)
+++ pkg/vegan/man/vegan-internal.Rd 2009-09-23 06:51:30 UTC (rev 1022)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1022
More information about the Vegan-commits
mailing list