[Vegan-commits] r1021 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 22 15:57:24 CEST 2009
Author: jarioksa
Date: 2009-09-22 15:57:24 +0200 (Tue, 22 Sep 2009)
New Revision: 1021
Modified:
pkg/vegan/man/CCorA.Rd
pkg/vegan/man/MOStest.Rd
pkg/vegan/man/add1.cca.Rd
pkg/vegan/man/adonis.Rd
pkg/vegan/man/anosim.Rd
pkg/vegan/man/anova.cca.Rd
pkg/vegan/man/as.mlm.Rd
pkg/vegan/man/beals.Rd
pkg/vegan/man/betadisper.Rd
pkg/vegan/man/bgdispersal.Rd
pkg/vegan/man/capscale.Rd
pkg/vegan/man/cascadeKM.Rd
pkg/vegan/man/cca.object.Rd
pkg/vegan/man/contribdiv.Rd
pkg/vegan/man/decorana.Rd
pkg/vegan/man/designdist.Rd
pkg/vegan/man/goodness.cca.Rd
pkg/vegan/man/isomap.Rd
pkg/vegan/man/kendall.global.Rd
pkg/vegan/man/make.cepnames.Rd
pkg/vegan/man/mantel.Rd
pkg/vegan/man/metaMDS.Rd
pkg/vegan/man/mrpp.Rd
pkg/vegan/man/multipart.Rd
pkg/vegan/man/nestedtemp.Rd
pkg/vegan/man/oecosimu.Rd
Log:
aspell on documents add1.cca.Rd to oecosimu.Rd
Modified: pkg/vegan/man/CCorA.Rd
===================================================================
--- pkg/vegan/man/CCorA.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/CCorA.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -27,7 +27,7 @@
\item{xlabs}{Row labels. The default is to use row names, \code{NULL}
uses row numbers instead, and \code{NA} suppresses plotting row names
completely}
- \item{which}{ \code{1} plots \code{Y} reseults, and
+ \item{which}{ \code{1} plots \code{Y} results, and
\code{2} plots \code{X1} results }
\item{\dots}{Other arguments passed to functions. \code{biplot.CCorA}
passes graphical arguments to \code{\link{biplot}} and
Modified: pkg/vegan/man/MOStest.Rd
===================================================================
--- pkg/vegan/man/MOStest.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/MOStest.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -35,7 +35,7 @@
\item{x}{The independent variable or plotting object in \code{plot}. }
\item{y}{The dependent variable. }
\item{interval}{The two points at which the test statistic is
- evaluated. If missing, the estremes of \code{x} are used. }
+ evaluated. If missing, the extremes of \code{x} are used. }
\item{which}{Subset of plots produced. Values \code{which=1} and
\code{2} define plots specific to \code{MOStest} (see Details), and
larger values select a graphs of \code{\link{plot.lm}} (minus2). }
@@ -112,7 +112,7 @@
the evaluated points.}
\item{hump}{Sorted vector of location of the hump or the pit and the
points where the test was evaluated.}
- \item{coefficients}{Table of test statistics and their signficances.}
+ \item{coefficients}{Table of test statistics and their significances.}
}
\references{
@@ -147,7 +147,7 @@
the \pkg{MASS} package.
}
-\seealso{The nointeraction model can be fitted with \code{\link{humpfit}}. }
+\seealso{The no-interaction model can be fitted with \code{\link{humpfit}}. }
\examples{
## The Al-Mufti data analysed in humpfit():
mass <- c(140,230,310,310,400,510,610,670,860,900,1050,1160,1900,2480)
Modified: pkg/vegan/man/add1.cca.Rd
===================================================================
--- pkg/vegan/man/add1.cca.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/add1.cca.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -36,7 +36,7 @@
Function \code{add1.cca} will implement a test for single term
additions that is not directly available in \code{\link{anova.cca}}.
- Functions are used implicity in \code{\link{step}}. The
+ Functions are used implicitly in \code{\link{step}}. The
\code{\link{deviance.cca}} and \code{\link{deviance.rda}} used in
\code{\link{step}} have no firm basis, and setting argument
\code{test = "permutation"} may help in getting useful insight into
Modified: pkg/vegan/man/adonis.Rd
===================================================================
--- pkg/vegan/man/adonis.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/adonis.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -21,7 +21,7 @@
where \code{Y} is either a dissimilarity object (inheriting from
class \code{"dist"}) or data frame or a matrix; \code{A}, \code{B}, and
\code{C} may be factors or continuous variables. If a dissimilarity
- object is supplied, no species cofficients can be calculated (see
+ object is supplied, no species coefficients can be calculated (see
Value below).}
\item{data}{ the data frame from which \code{A}, \code{B}, and
\code{C} would be drawn.}
Modified: pkg/vegan/man/anosim.Rd
===================================================================
--- pkg/vegan/man/anosim.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/anosim.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -63,7 +63,7 @@
\code{varwidth=TRUE}.
}
\value{
- The function returs a list of class \code{"anosim"} with following
+ The function returns a list of class \code{"anosim"} with following
items:
\item{call }{Function call.}
\item{statistic}{The value of ANOSIM statistic \eqn{R}}
Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/anova.cca.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -72,7 +72,7 @@
differ significantly from \code{alpha} of the alternative hypothesis,
the permutations are
continued with \code{step} new permutations (at the first step, the
- number of permuations is \code{step - 1}). However, with \code{by =
+ number of permutations is \code{step - 1}). However, with \code{by =
"terms"} a fixed number of permutations will be used, and this
is given by argument \code{permutations}, or if this is missing,
by \code{step}.
@@ -110,7 +110,7 @@
constrained axes will be used as conditions (\dQuote{partialled
out}) and a test for the first constrained eigenvalues is
performed. You can stop permutation tests after exceeding a given
- signficance level with argument \code{cutoff} to speed up
+ significance level with argument \code{cutoff} to speed up
calculations in large models. Setting \code{by = "terms"} will
perform separate significance test for each term (constraining
variable). The terms are assessed sequentially from first to last,
Modified: pkg/vegan/man/as.mlm.Rd
===================================================================
--- pkg/vegan/man/as.mlm.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/as.mlm.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -8,7 +8,7 @@
\code{\link{rda}}, \code{\link{capscale}}) as a multiple response
linear model (\code{\link{lm}}). This allows finding influence
statistics (\code{\link{influence.measures}}). This also allows
- deriving several other statitics, but most of these are biased and
+ deriving several other statistics, but most of these are biased and
misleading, since refitting ignores a major component of variation in
constrained ordination.
}
Modified: pkg/vegan/man/beals.Rd
===================================================================
--- pkg/vegan/man/beals.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/beals.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -39,12 +39,12 @@
Sum(k) N[jk] I[ik] / N[k]}, where \eqn{S_i}{S[i]} is the number of
species on site \eqn{i}, \eqn{N_{jk}}{N[jk]} is the number of joint
occurrences of species \eqn{j} and \eqn{k}, \eqn{N_k}{N[k]} is the
- number of occurences of species \eqn{k}, and \eqn{I} is the incidence
+ number of occurrences of species \eqn{k}, and \eqn{I} is the incidence
(0 or 1) of species (this last term is usually omitted from the
equation, but it is necessary). As \eqn{N_{jk}}{N[jk]} can be
interpreted as a mean of conditional probability, the \code{beals}
- fucntion can be interpred as a mean of conditioned probabilities (De
- \enc{Cáceres}{Caceres} & Legendre 2008). The currrent function is
+ function can be interpreted as a mean of conditioned probabilities (De
+ \enc{Cáceres}{Caceres} & Legendre 2008). The current function is
generalized to abundance values (De \enc{Cáceres}{Caceres} & Legendre
2008).
@@ -66,7 +66,7 @@
belong to the species pool (Ewald 2002) or to identify suitable
unoccupied patches in metapopulation analysis
(\enc{Münzbergová}{Munzbergova} & Herben
- 2004). In this case, the function shold be called with \code{include
+ 2004). In this case, the function should be called with \code{include
= FALSE} for cross-validatory smoothing for species, and argument
\code{species} can be used if only one species was studied.
Modified: pkg/vegan/man/betadisper.Rd
===================================================================
--- pkg/vegan/man/betadisper.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/betadisper.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -116,7 +116,7 @@
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 also be performed
+ Pairwise comparisons of group mean dispersions can also be performed
using \code{\link{permutest.betadisper}}. An alternative to the classical
comparison of group dispersions, is to calculate Tukey's Honest
Significant Differences between groups, via
Modified: pkg/vegan/man/bgdispersal.Rd
===================================================================
--- pkg/vegan/man/bgdispersal.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/bgdispersal.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -86,7 +86,7 @@
\note{The function uses a more powerful alternative for the McNemar test
than the classical formula. The classical formula was constructed in
- the spririt of Pearson's Chi-square, but the formula in this function
+ the spirit of Pearson's Chi-square, but the formula in this function
was constructed in the spirit of Wilks Chi-square or the \eqn{G}
statistic. Function \code{\link{mcnemar.test}} uses the classical
formula. The new formula was introduced in \pkg{vegan} version
Modified: pkg/vegan/man/capscale.Rd
===================================================================
--- pkg/vegan/man/capscale.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/capscale.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -87,7 +87,7 @@
Redundancy Analysis of results of Metric (Classical) Multidimensional
Scaling (Anderson & Willis 2003). Function capscale uses two steps:
(1) it ordinates the dissimilarity matrix using
- \code{\link{cmdscale}} and (2) analyzes these results using
+ \code{\link{cmdscale}} and (2) analyses these results using
\code{\link{rda}}. If the user supplied a community data frame instead
of dissimilarities, the function will find the needed dissimilarity
matrix using \code{\link{vegdist}} with specified
@@ -134,7 +134,7 @@
constant on the left hand side, or \code{comm ~ 1}. With
\code{metaMDSdist = TRUE}, the function can do automatic data
standardization and use extended dissimilarities using function
- \code{\link{stepacross}} similary as in non-metric multidimensional
+ \code{\link{stepacross}} similarly as in non-metric multidimensional
scaling with \code{\link{metaMDS}}.
}
Modified: pkg/vegan/man/cascadeKM.Rd
===================================================================
--- pkg/vegan/man/cascadeKM.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/cascadeKM.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -48,10 +48,10 @@
displayed.}
\item{grpmts.plot}{Show the plot (\code{TRUE} or \code{FALSE}).}
\item{sortg}{Sort the objects as a function of their group membership
- to produce a more easily interpretatable graph. See Details. The
+ to produce a more easily interpretable graph. See Details. The
original object names are kept; they are used as labels in the
output table \code{x}, although not in the graph. If there were no
- rownames, sequential row numbers are used to keep track of the
+ row names, sequential row numbers are used to keep track of the
original order of the objects.}
\item{gridcol}{The colour of the grid lines in the plots. \code{NA},
which is the default value, removes the grid lines.}
@@ -59,7 +59,7 @@
}
\details{
- The function creates several partitions formimg a cascade from a small
+ The function creates several partitions forming a cascade from a small
to a large number of groups formed by \code{\link{kmeans}}. Most
of the work is performed by function \code{cIndex} which is based on the
\code{\link[cclust]{clustIndex}} function (package \pkg{cclust}).
Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/cca.object.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -32,7 +32,7 @@
with \code{formula}.}
\item{terminfo}{Further information on terms with three subitems:
\code{terms} which is like the \code{terms} component above, but
- lists conditions and constrainst similarly; \code{xlev}
+ lists conditions and constraints similarly; \code{xlev}
which lists the factor levels, and \code{ordered} which is
\code{TRUE} to ordered factors.
This is produced by \pkg{vegan} internal function
@@ -110,7 +110,7 @@
\code{v} with weights \code{Xbar}, but the multiplying effect of
eigenvalues removed. These often are known as WA scores in
\code{cca}. Only in \code{CCA}.}
- \item{\code{wa.eig}}{The direct result of weighted avaraging or weighted
+ \item{\code{wa.eig}}{The direct result of weighted averaging or weighted
summation (matrix multiplication)
with the resulting eigenvalue inflation.}
\item{\code{wa.excluded, u.excluded}}{WA scores for rows removed by
@@ -127,7 +127,7 @@
}
\seealso{The description here provides a hacker's interface. For more
- user friendly acces to the \code{cca} object see
+ user friendly access to the \code{cca} object see
\code{\link{alias.cca}}, \code{\link{coef.cca}},
\code{\link{deviance.cca}}, \code{\link{predict.cca}},
\code{\link{scores.cca}},
Modified: pkg/vegan/man/contribdiv.Rd
===================================================================
--- pkg/vegan/man/contribdiv.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/contribdiv.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -15,7 +15,7 @@
\item{comm}{The community data matrix with samples as rows and species as column.}
\item{index}{Character, the diversity index to be calculated.}
\item{relative}{Logical, if \code{TRUE} then contribution diversity values are expressed as their signed deviation from their mean. See details.}
- \item{scaled}{Logical, if \code{TRUE} then relative contribution diversity values are scaled by the sum of gamma values (if \code{index = "richness"}) or by sum of gamma values times the number of rowx in \code{comm} (if \code{index = "simpson"}). See details.}
+ \item{scaled}{Logical, if \code{TRUE} then relative contribution diversity values are scaled by the sum of gamma values (if \code{index = "richness"}) or by sum of gamma values times the number of rows in \code{comm} (if \code{index = "simpson"}). See details.}
\item{drop.zero}{Logical, should empty rows dropped from the result? If empty rows are not dropped, their corresponding results will be \code{NA}s.}
\item{x}{An object of class \code{"contribdiv"}.}
\item{sub, xlab, ylab, ylim, col}{Graphical arguments passed to plot.}
Modified: pkg/vegan/man/decorana.Rd
===================================================================
--- pkg/vegan/man/decorana.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/decorana.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -98,7 +98,7 @@
space, so that the results look non-curved in two-dimensional projections
(`lolly paper effect'). As a result, the points usually have an
easily recognized triangular or diamond shaped pattern, obviously an
- artefact of detrendingt. Rescaling works differently than commonly
+ artefact of detrending. Rescaling works differently than commonly
presented, too. \code{decorana} does not use, or even evaluate, the
widths of species responses. Instead, it tries to equalize the
weighted variance of species scores on axis segments (parameter
@@ -173,7 +173,7 @@
\code{\link{cca}}. Orthogonal correspondence analysis can be
made with \code{\link[MASS]{corresp}}, or with \code{decorana} or
\code{\link{cca}}, but the scaling of results vary (and the one in
- \code{decorana} correspondes to \code{scaling = -1} in
+ \code{decorana} corresponds to \code{scaling = -1} in
\code{\link{cca}}.).
See \code{\link{predict.decorana}} for adding new points to an
ordination.
Modified: pkg/vegan/man/designdist.Rd
===================================================================
--- pkg/vegan/man/designdist.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/designdist.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -73,7 +73,7 @@
If you want to implement binary dissimilarities based on the 2x2
contingency table notation, you can set \code{abcd = TRUE}. In this
notation \code{a = J}, \code{b = A-J}, \code{c = B-J}, \code{d =
- P-A-B+J}. This notation is often used instead fo the more more
+ P-A-B+J}. This notation is often used instead of the more more
tangible default notation for reasons that are opaque to me.
}
Modified: pkg/vegan/man/goodness.cca.Rd
===================================================================
--- pkg/vegan/man/goodness.cca.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/goodness.cca.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -37,7 +37,7 @@
\item{choices}{Axes shown. Default is to show all axes of the \code{"model"}. }
\item{model}{Show constrained (\code{"CCA"}) or unconstrained
(\code{"CA"}) results. }
- \item{statistic}{Stastic used: \code{"explained"} gives the cumulative
+ \item{statistic}{Statistic used: \code{"explained"} gives the cumulative
percentage accounted for, \code{"distance"} shows the residual
distances. Distances are not available for sites in constrained or
partial analyses. }
Modified: pkg/vegan/man/isomap.Rd
===================================================================
--- pkg/vegan/man/isomap.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/isomap.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -11,7 +11,7 @@
\description{
The function performs isometric feature mapping which consists of
three simple steps: (1) retain only some of the shortest
- dissimilarities among objects, (2) estimate all dissimilarites as
+ dissimilarities among objects, (2) estimate all dissimilarities as
shortest path distances, and (3) perform metric scaling (Tenenbaum et
al. 2000).
}
@@ -24,11 +24,11 @@
}
\arguments{
- \item{dist}{Dissimilariies. }
+ \item{dist}{Dissimilarities. }
\item{ndim}{Number of axes in metric scaling (argument \code{k} in
\code{\link{cmdscale}}).}
\item{epsilon}{Shortest dissimilarity retained. }
- \item{k}{Number of shortest dissimilariteis retained for a point. If
+ \item{k}{Number of shortest dissimilarities retained for a point. If
both \code{epsilon} and \code{k} are given, \code{epsilon} will be used. }
\item{path}{Method used in \code{\link{stepacross}} to estimate the
shortest path, with alternatives \code{"shortest"} and \code{"extended"}. }
Modified: pkg/vegan/man/kendall.global.Rd
===================================================================
--- pkg/vegan/man/kendall.global.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/kendall.global.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -81,10 +81,10 @@
The corrections used for multiple testing are applied to the list of
P-values (P); they take into account the number of tests (k) carried
- out simulatenously (number of groups in \code{kendall.global}, or
+ out simultaneously (number of groups in \code{kendall.global}, or
number of species in \code{kendall.post}). The corrections are
- performed using funtion \code{\link{p.adjust}}; see that function
- for the describtion of the correction methods. In addition, there is
+ performed using function \code{\link{p.adjust}}; see that function
+ for the description of the correction methods. In addition, there is
\enc{Šidák}{Sidak} correction which defined as
\eqn{P_{corr} = 1 -(1 - P)^k}.
}
Modified: pkg/vegan/man/make.cepnames.Rd
===================================================================
--- pkg/vegan/man/make.cepnames.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/make.cepnames.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -6,7 +6,7 @@
A standard CEP name has four first letters of the generic name and
four first letters of the specific epithet of a Latin name. The last
epithet, that may be a subspecific name, is used in the current
- function. If the name has only one component, it is abbreaviated to
+ function. If the name has only one component, it is abbreviated to
eight characters (see \code{\link{abbreviate}}).
The returned names are made unique with function
\code{\link{make.unique}} which adds numbers to the end of CEP names if needed.
Modified: pkg/vegan/man/mantel.Rd
===================================================================
--- pkg/vegan/man/mantel.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/mantel.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -8,7 +8,7 @@
Function \code{mantel} finds the Mantel statistic as a matrix
correlation between two dissimilarity matrices, and function
\code{mantel.partial} finds the partial Mantel statistic as the
- partial matrix correlation between three dissimilarity matricies. The
+ partial matrix correlation between three dissimilarity matrices. The
significance of the statistic is evaluated by permuting rows and
columns of the first dissimilarity matrix.
@@ -68,7 +68,7 @@
\note{
Legendre & Legendre (1998) say that partial Mantel correlations
- often are difficult to interpet.
+ often are difficult to interpret.
}
\author{Jari Oksanen }
Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/metaMDS.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -241,7 +241,7 @@
Function \code{metaMDS} is a simple wrapper for
\code{\link[MASS]{isoMDS}} and some support functions.
You can call these support functions separately for better control
- of results. Data transformation, dissmilarities and possible
+ of results. Data transformation, dissimilarities and possible
\code{\link{stepacross}} are made in function \code{metaMDSdist}
which returns a dissimilarity result. Iterative search (with starting
values from \code{initMDS}) is made in \code{metaMDSiter}.
Modified: pkg/vegan/man/mrpp.Rd
===================================================================
--- pkg/vegan/man/mrpp.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/mrpp.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -94,7 +94,7 @@
\code{\link{vegdist}} also are available.
Function \code{meandist} calculates a matrix of mean within-cluster
-dissimilarities (diagonal) and between-cluster dissimilarites
+dissimilarities (diagonal) and between-cluster dissimilarities
(off-diagonal elements), and an attribute \code{n} of \code{grouping}
counts. Function \code{summary} finds the within-class, between-class
and overall means of these dissimilarities, and the MRPP statistics
@@ -146,7 +146,7 @@
}
\author{
-M. Herny H. Stevens \email{HStevens at muohio.edu} and Jari Oksanen.
+M. Henry H. Stevens \email{HStevens at muohio.edu} and Jari Oksanen.
}
\note{
This difference may be one of location (differences in mean) or one of
Modified: pkg/vegan/man/multipart.Rd
===================================================================
--- pkg/vegan/man/multipart.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/multipart.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -24,7 +24,7 @@
\item{index}{Character, the entropy index to be calculated (see Details).}
\item{relative}{Logical, if \code{TRUE} then beta diversity is
standardized by its maximum (see Details).}
- \item{scales}{Numeroc, of length 1, the order of the generalized diversity index
+ \item{scales}{Numeric, of length 1, the order of the generalized diversity index
to be used.}
\item{global}{Logical, indicates the calculation of beta diversity values, see Details.}
\item{nsimul}{Number of permutation to use if \code{matr} is not of class 'permat'.
Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/nestedtemp.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -27,7 +27,7 @@
nesteddisc(comm)
nestedtemp(comm, ...)
nestednodf(comm, order = TRUE)
-\method{plot}{nestedtemp}(x, kind = c("temperature", "incidendce"),
+\method{plot}{nestedtemp}(x, kind = c("temperature", "incidence"),
col=rev(heat.colors(100)), names = FALSE, ...)
}
@@ -47,7 +47,7 @@
The nestedness functions evaluate alternative indices of nestedness.
The functions are intended to be used together with Null model
communities and used as an argument in \code{\link{oecosimu}} to analyse
- the nonrdanomness of results.
+ the nonrandomness of results.
Function \code{netstedchecker} gives the number of checkerboard units,
or 2x2 submatrices where both species occur once but on different
Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd 2009-09-22 07:23:14 UTC (rev 1020)
+++ pkg/vegan/man/oecosimu.Rd 2009-09-22 13:57:24 UTC (rev 1021)
@@ -119,7 +119,7 @@
but each call produces a matrix that is independent of previous
matrices, and has the same marginal totals as the original data. The
recommended method is \code{quasiswap} which is much faster because
- it is implemented in C. Method \code{bactkracking} is provided for
+ it is implemented in C. Method \code{backtracking} is provided for
comparison, but it is so slow that it may be dropped from future
releases of \pkg{vegan} (or also implemented in C).
Method \code{quasiswap} (\enc{Miklós}{Miklos} & Podani 2004)
@@ -143,8 +143,8 @@
Function \code{as.ts} transforms the simulated results of sequential
methods into a time series or a \code{\link{ts}} object. This allows
using analytic tools for time series in studying the sequences (see
- examples). Function \code{as.mcmc} transformts teh simulated results
- of sequential mehots into an \code{\link[coda]{mcmc}} object of the
+ examples). Function \code{as.mcmc} transforms the simulated results
+ of sequential methods into an \code{\link[coda]{mcmc}} object of the
\pkg{coda} package. The \pkg{coda} package provides functions for
the analysis of stationarity, adequacy of sample size,
autocorrelation, need of burn-in and much more for sequential
@@ -189,7 +189,7 @@
\references{
Gotelli, N.J. & Entsminger, N.J. (2001). Swap and fill algorithms in
- null model analyis: rethinking the knight's tour. \emph{Oecologia}
+ null model analysis: rethinking the knight's tour. \emph{Oecologia}
129, 281--291.
Gotelli, N.J. & Entsminger, N.J. (2003). Swap algorithms in null model
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