[Vegan-commits] r2589 - in branches/2.0: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 23 13:49:17 CEST 2013
Author: jarioksa
Date: 2013-08-23 13:49:17 +0200 (Fri, 23 Aug 2013)
New Revision: 2589
Modified:
branches/2.0/R/adipart.default.R
branches/2.0/R/betadiver.R
branches/2.0/R/hiersimu.default.R
branches/2.0/R/multipart.default.R
branches/2.0/R/orditkplot.R
branches/2.0/R/vegandocs.R
branches/2.0/R/vegdist.R
branches/2.0/inst/ChangeLog
branches/2.0/man/SSarrhenius.Rd
branches/2.0/man/adipart.Rd
branches/2.0/man/adonis.Rd
branches/2.0/man/anova.cca.Rd
branches/2.0/man/betadisper.Rd
branches/2.0/man/cca.Rd
branches/2.0/man/clamtest.Rd
branches/2.0/man/density.adonis.Rd
branches/2.0/man/eventstar.Rd
branches/2.0/man/make.cepnames.Rd
branches/2.0/man/mantel.correlog.Rd
branches/2.0/man/model.matrix.cca.Rd
branches/2.0/man/monoMDS.Rd
branches/2.0/man/mrpp.Rd
branches/2.0/man/multipart.Rd
branches/2.0/man/nobs.adonis.Rd
branches/2.0/man/ordistep.Rd
branches/2.0/man/ordisurf.Rd
branches/2.0/man/pcnm.Rd
branches/2.0/man/prc.Rd
branches/2.0/man/predict.cca.Rd
branches/2.0/man/radfit.Rd
branches/2.0/man/specaccum.Rd
branches/2.0/man/vegan-package.Rd
branches/2.0/man/vegdist.Rd
Log:
merge to 2.0-9 all itsy bitsy teenie weenie things that do not trigger conflicts
Modified: branches/2.0/R/adipart.default.R
===================================================================
--- branches/2.0/R/adipart.default.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/adipart.default.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -24,7 +24,7 @@
## check proper design of the model frame
l1 <- sapply(rhs, function(z) length(unique(z)))
if (!any(sapply(2:nlevs, function(z) l1[z] <= l1[z-1])))
- stop("number of levels are inapropriate, check sequence")
+ stop("number of levels are inappropriate, check sequence")
rval <- list()
rval[[1]] <- rhs[,nlevs]
nCol <- nlevs - 1
Modified: branches/2.0/R/betadiver.R
===================================================================
--- branches/2.0/R/betadiver.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/betadiver.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -11,8 +11,8 @@
}
beta <- list("w"="(b+c)/(2*a+b+c)", "-1"="(b+c)/(2*a+b+c)", "c"="(b+c)/2",
"wb"="b+c", "r"="2*b*c/((a+b+c)^2-2*b*c)",
- "I"="log(2*a+b+c)-2*a*log(2)/(2*a+b+c)-((a+b)*log(a+b)+(a+c)*log(a+c))/(2*a+b+c)",
- "e"="exp(log(2*a+b+c)-2*a*log(2)/(2*a+b+c)-((a+b)*log(a+b)+(a+c)*log(a+c))/(2*a+b+c))-1",
+ "I"="log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c)",
+ "e"="exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c))-1",
"t"="(b+c)/(2*a+b+c)", "me"="(b+c)/(2*a+b+c)",
"j"="a/(a+b+c)", "sor"="2*a/(2*a+b+c)",
"m"="(2*a+b+c)*(b+c)/(a+b+c)",
@@ -27,8 +27,9 @@
"z"="(log(2)-log(2*a+b+c)+log(a+b+c))/log(2)"
)
if (help) {
- for (i in 1:length(beta))
- cat(i, " \"", names(beta[i]),"\" = ", beta[[i]], "\n", sep="")
+ for (i in 1:length(beta))
+ writeLines(strwrap(paste(i, " \"", names(beta[i]),
+ "\" = ", beta[[i]], "\n", sep="")))
return(invisible(NULL))
}
x <- ifelse(x > 0, 1, 0)
Modified: branches/2.0/R/hiersimu.default.R
===================================================================
--- branches/2.0/R/hiersimu.default.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/hiersimu.default.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -18,7 +18,7 @@
## check proper design of the model frame
l1 <- sapply(rhs, function(z) length(unique(z)))
if (!any(sapply(2:nlevs, function(z) l1[z] <= l1[z-1])))
- stop("number of levels are inapropriate, check sequence")
+ stop("number of levels are inappropriate, check sequence")
rval <- list()
rval[[1]] <- rhs[,nlevs]
nCol <- nlevs - 1
Modified: branches/2.0/R/multipart.default.R
===================================================================
--- branches/2.0/R/multipart.default.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/multipart.default.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -26,7 +26,7 @@
## check proper design of the model frame
l1 <- sapply(rhs, function(z) length(unique(z)))
if (!any(sapply(2:nlevs, function(z) l1[z] <= l1[z-1])))
- stop("number of levels are inapropriate, check sequence")
+ stop("number of levels are inappropriate, check sequence")
rval <- list()
rval[[1]] <- rhs[,nlevs]
nCol <- nlevs - 1
Modified: branches/2.0/R/orditkplot.R
===================================================================
--- branches/2.0/R/orditkplot.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/orditkplot.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -241,9 +241,6 @@
## Should work also in R < 2.8.0 with no capabilities("tiff")
if (!isTRUE(unname(capabilities("tiff"))))
falt["tiff"] <- FALSE
- ## bmp lives only in Windows
- if (.Platform$OS.type != "windows")
- falt["bmp"] <- FALSE
ftypes <- ftypes[falt]
fname <- tkgetSaveFile(filetypes=ftypes)
if(tclvalue(fname) == "")
Modified: branches/2.0/R/vegandocs.R
===================================================================
--- branches/2.0/R/vegandocs.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/vegandocs.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -17,11 +17,11 @@
helptype <- getOption("help_type")
if (length(helptype) && helptype == "html") {
if (!tools:::httpdPort)
- tools:::startDynamicHelp()
+ startDynamicHelp()
browseURL(paste("http://127.0.0.1:", tools:::httpdPort,
"/library/vegan/doc/NEWS.html", sep=""))
} else {
- file.show(tools:::Rd2txt(file.path(system.file(package="vegan"),
+ file.show(Rd2txt(file.path(system.file(package="vegan"),
"NEWS.Rd"), tempfile()))
}
} else {
Modified: branches/2.0/R/vegdist.R
===================================================================
--- branches/2.0/R/vegdist.R 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/R/vegdist.R 2013-08-23 11:49:17 UTC (rev 2589)
@@ -21,7 +21,7 @@
warning("results may be meaningless because data have negative entries in method ",
dQuote(inm))
if (method == 11 && any(colSums(x) == 0))
- warning("data have empty species which influence the results im method ",
+ warning("data have empty species which influence the results in method ",
dQuote(inm))
if (method == 6) # gower, but no altGower
x <- decostand(x, "range", 2, na.rm = TRUE, ...)
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/inst/ChangeLog 2013-08-23 11:49:17 UTC (rev 2589)
@@ -2,8 +2,22 @@
VEGAN RELEASE VERSIONS at http://cran.r-project.org/
-Version 2.0-8 (opened March 19, 2013)
+Version 2.0-9 (opened August 23, 2013)
+ * merge r2588: remove unneeded utils::: in vegandocs (some remain).
+ * merge r2583,7: remove cross-references to disappear in R-3.0-2.
+ * merge r2580,1: literature refs in specaccum.Rd and
+ betadisper.Rd.
+ * merge r2571: aspell fixes in Rd files (stressplot.wmcscale.Rd,
+ commsim.Rd and nullmodel.Rd did not exist in 2.0 and were
+ excluded).
+ * merge r2570: aspell fixes in R files.
+ * merge r2568: aspell fixes in Rd files.
+ * merge r2564: line wrapping in betadiver(help=TRUE).
+ * merge r2558: ordiktplot bmp device in all platforms.
+
+Version 2.0-8 (released July 10, 2013)
+
* merge r2540: remove hard-coded inconsolata fonts.
* merge r2539: stressplot return data in input order.
* merge r2538: use expression(R^2) in stressplot.
Modified: branches/2.0/man/SSarrhenius.Rd
===================================================================
--- branches/2.0/man/SSarrhenius.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/SSarrhenius.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -58,8 +58,8 @@
The Lomolino model (\code{SSlomolino}) is
\code{Asym/(1 + slope^log(xmid/area))} (Lomolino 2000, Dengler 2009).
Parameter \code{Asym} is the asymptotic maximum number of species,
- \code{slope} is the maximum slope of increse of richness, and
- \code{xmid} is the area where half of the maximum richess is
+ \code{slope} is the maximum slope of increase of richness, and
+ \code{xmid} is the area where half of the maximum richness is
achieved.
In addition to these models, several other models studied by Dengler
Modified: branches/2.0/man/adipart.Rd
===================================================================
--- branches/2.0/man/adipart.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/adipart.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -36,7 +36,7 @@
gamma diversities.}
\item{formula}{A two sided model formula in the form \code{y ~ x},
where \code{y} is the community data matrix with samples as rows and
- species as column. Right hand side (\code{x}) must grouping vaiables
+ species as column. Right hand side (\code{x}) must grouping variables
referring to levels of sampling hierarchy, terms from right to left
will be treated as nested (first column is the lowest, last is the
highest level, at least two levels specified). Interaction terms are
Modified: branches/2.0/man/adonis.Rd
===================================================================
--- branches/2.0/man/adonis.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/adonis.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -127,7 +127,7 @@
\item{coef.sites}{ matrix of coefficients of the linear model, with
rows representing sources of variation and columns representing
sites; each column represents a fit of a sites distances (from all
- other sites) to the linear model.These are what you get when you
+ other sites) to the linear model. These are what you get when you
fit distances of one site to
your predictors. }
\item{f.perms}{ an \eqn{N} by \eqn{m} matrix of the null \eqn{F}
Modified: branches/2.0/man/anova.cca.Rd
===================================================================
--- branches/2.0/man/anova.cca.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/anova.cca.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -132,9 +132,8 @@
\code{"permutest.cca"}, which has its own \code{print} method. The
distribution of permuted \eqn{F} values can be inspected with
\code{\link{density.permutest.cca}} function. The function
- \code{anova.cca} calls \code{permutest.cca}, fills an
- \code{\link{anova}} table and uses \code{\link{print.anova}} for
- printing.
+ \code{anova.cca} calls \code{permutest.cca} and fills an
+ \code{\link{anova}} table.
}
\note{
Modified: branches/2.0/man/betadisper.Rd
===================================================================
--- branches/2.0/man/betadisper.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/betadisper.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -128,7 +128,7 @@
comparison of group dispersions, is to calculate Tukey's Honest
Significant Differences between groups, via
\code{TukeyHSD.betadisper}. This is a simple wrapper to
- \code{\link{TukeyHSD.aov}}. The user is directed to read the help file
+ \code{\link{TukeyHSD}}. The user is directed to read the help file
for \code{\link{TukeyHSD}} before using this function. In particular,
note the statement about using the function with
unbalanced designs.
@@ -146,7 +146,7 @@
will be biased downward. This bias matters most when comparing diversity
among treatments with small, unequal numbers of samples. Setting
\code{bias.adjust=TRUE} when using \code{betadisper} imposes a
- \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2012).
+ \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2013).
}
\value{
The \code{anova} method returns an object of class \code{"anova"}
@@ -214,9 +214,9 @@
Test of Homogeneity of Variance. \emph{Australian & New Zealand Journal of
Statistics} \strong{42}, 81-–100.
- Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2012) Predator
- density and timing of arrival affect reef fish community assembly. Ms.
- in revision, \emph{Oikos}.
+ Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2013) Predator
+ density and timing of arrival affect reef fish community
+ assembly. \emph{Ecology} \strong{94}, 1057--1068.
}
\author{Gavin L. Simpson; bias correction by Adrian Stier and Ben Bolker.}
\seealso{\code{\link{permutest.betadisper}}, \code{\link[stats]{anova.lm}},
Modified: branches/2.0/man/cca.Rd
===================================================================
--- branches/2.0/man/cca.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/cca.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -228,7 +228,7 @@
finding influence statistics (\code{\link{lm.influence}},
\code{\link{cooks.distance}} etc.).
- Permutation based signficance for the overall model, single
+ Permutation based significance for the overall model, single
constraining variables or axes can be found with
\code{\link{anova.cca}}. Automatic model building with \R{}
\code{\link{step}} function is possible with
@@ -239,7 +239,7 @@
\code{\link{simulate.cca}}.
Separate methods based on constrained ordination model are principal
- response curves (\code{\link{prc}}) and variance partioning between
+ response curves (\code{\link{prc}}) and variance partitioning between
several components (\code{\link{varpart}}).
Design decisions are explained in \code{\link{vignette}}
Modified: branches/2.0/man/clamtest.Rd
===================================================================
--- branches/2.0/man/clamtest.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/clamtest.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -132,7 +132,7 @@
\item The original authors suggest that multiple testing adjustment
for multiple testing should be based on the number of points
(\code{npoints}) used to draw the critical lines on the plot,
- whereas the adjustment should be based on the number tests (i.e,
+ whereas the adjustment should be based on the number tests (i.e.,
tested species). The function uses the same numerical values as
the original paper, but there is no automatic connection between
\code{npoints} and \code{alpha} arguments, but you must work out
Modified: branches/2.0/man/density.adonis.Rd
===================================================================
--- branches/2.0/man/density.adonis.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/density.adonis.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -72,10 +72,10 @@
standard \code{plot} of \code{densiy} objects, but can also add a
vertical line for the observed statistic.
- Functions that can return several permuted statistics simultaenously
+ Functions that can return several permuted statistics simultaneously
also have \code{\link[lattice]{densityplot}} method
- (\code{\link{adonis}}, \code{\link{oecosimu}} and diversity partioning
- functions based on \code{oecosimu}). The standard
+ (\code{\link{adonis}}, \code{\link{oecosimu}} and diversity
+ partitioning functions based on \code{oecosimu}). The standard
\code{\link{density}} can only handle univariate data, and a warning
is issued if the function is used for a model with several observed
statistics. The \code{\link[lattice]{densityplot}} method is available
Modified: branches/2.0/man/eventstar.Rd
===================================================================
--- branches/2.0/man/eventstar.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/eventstar.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -34,7 +34,7 @@
The \eqn{q^\ast}{q*} index represents the scale parameter of
the one parameter Tsallis diversity family that leads to
the greatest deviation from the maximum equitability given the relative
-abundance vactor of a community.
+abundance vector of a community.
The value of \eqn{q^\ast}{q*} is found by identifying the minimum
of the evenness profile over scaling factor \eqn{q}{q} by
Modified: branches/2.0/man/make.cepnames.Rd
===================================================================
--- branches/2.0/man/make.cepnames.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/make.cepnames.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -26,7 +26,7 @@
formed by taking four first letters of the generic name and four
first letters of the specific or subspecific epithet. The current
function first makes valid \R names using \code{\link{make.names}},
- and then splits these into elemets. The CEP name is made by taking
+ and then splits these into elements. The CEP name is made by taking
the four first letters of the first element, and four first letters
of the last (default) or the second element (with
\code{seconditem = TRUE}). If there was only one name element, it is
Modified: branches/2.0/man/mantel.correlog.Rd
===================================================================
--- branches/2.0/man/mantel.correlog.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/mantel.correlog.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -168,4 +168,5 @@
}
-\keyword{ multivariate }
\ No newline at end of file
+\keyword{ multivariate }
+
Modified: branches/2.0/man/model.matrix.cca.Rd
===================================================================
--- branches/2.0/man/model.matrix.cca.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/model.matrix.cca.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -37,8 +37,8 @@
of the original model are unavailable.
}
\value{
- Returns a data frame (\code{model.frame}) or an unnnamed matrix or a list
- of two matrices called \code{Constraints} and \code{Conditions}
+ Returns a data frame (\code{model.frame}) or an unnamed matrix or a
+ list of two matrices called \code{Constraints} and \code{Conditions}
(\code{model.matrix}).
}
\author{
Modified: branches/2.0/man/monoMDS.Rd
===================================================================
--- branches/2.0/man/monoMDS.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/monoMDS.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -137,7 +137,7 @@
square and to rotate the axes (argument \code{pc}) to principal
components so that the first dimension shows the major variation.
It is possible to rotate the solution so that the first axis is
- parallel to a given environmental variable using fuction
+ parallel to a given environmental variable using function
\code{\link{metaMDSrotate}}.
}
Modified: branches/2.0/man/mrpp.Rd
===================================================================
--- branches/2.0/man/mrpp.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/mrpp.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -98,7 +98,7 @@
counts. Function \code{summary} finds the within-class, between-class
and overall means of these dissimilarities, and the MRPP statistics
with all \code{weight.type} options and the Classification Strength,
- CS (Van Sickle and Hughes, 2000). CS is defined for dissimiliraties as
+ CS (Van Sickle and Hughes, 2000). CS is defined for dissimilirities as
\eqn{\bar{B} - \bar{W}}{Bbar-Wbar}, where \eqn{\bar{B}}{Bbar} is the
mean between cluster dissimilarity and \eqn{\bar{W}}{Wbar} is the mean
within cluster dissimilarity with \code{weight.type = 1}. The function
@@ -113,7 +113,7 @@
function \code{\link{hclust}}. The terminal segments hang to
within-cluster dissimilarity. If some of the clusters are more
heterogeneous than the combined class, the leaf segment are reversed.
- The histograms are based on dissimilarites, but ore otherwise similar
+ The histograms are based on dissimilarities, but ore otherwise similar
to those of Van Sickle and Hughes (2000): horizontal line is drawn at
the level of mean between-cluster dissimilarity and vertical lines
connect within-cluster dissimilarities to this line. }
Modified: branches/2.0/man/multipart.Rd
===================================================================
--- branches/2.0/man/multipart.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/multipart.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -25,7 +25,7 @@
all rows are in the same group in the second level.}
\item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y}
is the community data matrix with samples as rows and species as column. Right
- hand side (\code{x}) must grouping vaiables referring to levels of sampling hierarchy,
+ hand side (\code{x}) must grouping variables referring to levels of sampling hierarchy,
terms from right to left will be treated as nested (first column is the lowest,
last is the highest level, at least two levels specified). Interaction terms are not allowed.}
\item{data}{A data frame where to look for variables defined in the right hand side
Modified: branches/2.0/man/nobs.adonis.Rd
===================================================================
--- branches/2.0/man/nobs.adonis.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/nobs.adonis.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -38,7 +38,7 @@
\code{\link{isomap}}, \code{\link{metaMDS}}, \code{\link{pcnm}},
\code{\link{procrustes}}, \code{\link{radfit}},
\code{\link{varpart}} and \code{\link{wcmdscale}}. } \value{ A
- single number, normally an interger, giving the number of
+ single number, normally an integer, giving the number of
observations. }
\author{
Modified: branches/2.0/man/ordistep.Rd
===================================================================
--- branches/2.0/man/ordistep.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/ordistep.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -99,7 +99,7 @@
al. 2008). The second criterion is ignored with option
\code{R2step = FALSE}, and the third criterion can be ignored setting
\code{Pin = 1} (or higher). The \code{direction} has choices
- \code{"forward"} and \code{"both"}, but it is very excepctional that a
+ \code{"forward"} and \code{"both"}, but it is very exceptional that a
term is dropped with the adjusted \eqn{R^2}{R2} criterion. Function
uses adjusted \eqn{R^2}{R2} as the criterion, and it cannot be used if
the criterion cannot be calculated. Therefore it is unavailable for
Modified: branches/2.0/man/ordisurf.Rd
===================================================================
--- branches/2.0/man/ordisurf.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/ordisurf.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -42,7 +42,7 @@
if \code{knots = 2} the function will fit a quadratic trend surface
instead of a smooth surface. A vector of length 2 is allowed when
\code{isotropic = FALSE}, with the first and second elements of
- \code{knots} refering to the first and second of ordination
+ \code{knots} referring to the first and second of ordination
dimensions (as indicated by \code{choices}) respectively.}
\item{family}{Error distribution in \code{\link[mgcv]{gam}}.}
\item{col}{ Colour of contours. }
Modified: branches/2.0/man/pcnm.Rd
===================================================================
--- branches/2.0/man/pcnm.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/pcnm.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -33,9 +33,9 @@
distance has a huge influence on the PCNM vectors. The default is to
use the longest distance to keep data connected. The distances above
truncation threshold are given an arbitrary value of 4 times
- threshold. For regular data, the first PCNM vectorsshow a wide scale
+ threshold. For regular data, the first PCNM vectors show a wide scale
variation and later PCNM vectors show smaller scale variation (Borcard
- & Legendre 2002), but for irregular data the intepretation is not as
+ & Legendre 2002), but for irregular data the interpretation is not as
clear.
The PCNM functions are used to express distances in rectangular form
@@ -51,7 +51,7 @@
The function is based on \code{pcnm} function in Dray's unreleased
\pkg{spacemakeR} package. The differences are that the current
- function usesr \code{\link{spantree}} as an internal support
+ function uses \code{\link{spantree}} as an internal support
function. The current function also can use prior weights for rows by
using weighted metric scaling of \code{\link{wcmdscale}}. The use of
row weights allows finding orthonormal PCNMs also for correspondence
Modified: branches/2.0/man/prc.Rd
===================================================================
--- branches/2.0/man/prc.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/prc.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -102,7 +102,7 @@
\section{Warning }{The first level of \code{treatment} must be the
control: use function \code{\link{relevel}} to guarantee the correct
- refence level. The current version will ignore user setting of
+ reference level. The current version will ignore user setting of
\code{\link{contrasts}} and always use treatment contrasts
(\code{\link{contr.treatment}}). The \code{time} must be an unordered
factor. }
Modified: branches/2.0/man/predict.cca.Rd
===================================================================
--- branches/2.0/man/predict.cca.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/predict.cca.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -112,7 +112,7 @@
for sites from environmental data. In that case the new data frame
must contain all constraining and conditioning environmental variables
of the model formula. With \code{type = "response"} or
- \code{type = "working"} the new data must contain envinronmental variables
+ \code{type = "working"} the new data must contain environmental variables
if constrained component is desired, and community data matrix if
residual or unconstrained component is desired. With these types, the
function uses \code{newdata} to find new \code{"lc"} (constrained) or
Modified: branches/2.0/man/radfit.Rd
===================================================================
--- branches/2.0/man/radfit.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/radfit.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -197,7 +197,7 @@
\code{\link{coef}}, \code{\link{deviance}}, \code{\link{logLik}}. In
addition the fit results can be accessed with \code{\link{fitted}},
\code{\link{predict}} and \code{\link{residuals}} (inheriting from
- \code{\link{residuals.glm}}).The graphical functions were discussed
+ \code{\link{residuals.glm}}). The graphical functions were discussed
above in Details.
}
Modified: branches/2.0/man/specaccum.Rd
===================================================================
--- branches/2.0/man/specaccum.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/specaccum.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -191,8 +191,8 @@
Kindt R., Van Damme, P. & Simons, A.J. (2006) Patterns of species
richness at varying scales in western Kenya: planning for
- agroecosystem diversification. \emph{Biodiversity and Conservation}, online
- first: DOI 10.1007/s10531-005-0311-9
+ agroecosystem diversification. \emph{Biodiversity and Conservation},
+ 10: 3235--3249.
Ugland, K.I., Gray, J.S. & Ellingsen, K.E. (2003). The
species-accumulation curve and estimation of species richness. \emph{Journal
Modified: branches/2.0/man/vegan-package.Rd
===================================================================
--- branches/2.0/man/vegan-package.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/vegan-package.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -107,4 +107,5 @@
\keyword{ spatial }
\keyword{ nonparametric }
\keyword{ htest }
-\keyword{ regression }
\ No newline at end of file
+\keyword{ regression }
+
Modified: branches/2.0/man/vegdist.Rd
===================================================================
--- branches/2.0/man/vegdist.Rd 2013-08-23 06:45:23 UTC (rev 2588)
+++ branches/2.0/man/vegdist.Rd 2013-08-23 11:49:17 UTC (rev 2589)
@@ -175,7 +175,7 @@
prob(j)}, or based on the probability of observing at least \eqn{j}
species in shared in compared communities. The current function uses
analytic result from hypergeometric distribution
- (\code{\link{phyper}}) to find the probablities. This probability
+ (\code{\link{phyper}}) to find the probabilities. This probability
(and the index) is dependent on the number of species missing in both
sites, and adding all-zero species to the data or removing missing
species from the data will influence the index. The probability (and
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