[Vegan-commits] r1965 - in branches/2.0: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 30 08:07:07 CET 2011
Author: jarioksa
Date: 2011-10-30 08:07:03 +0100 (Sun, 30 Oct 2011)
New Revision: 1965
Modified:
branches/2.0/R/metaMDSdist.R
branches/2.0/inst/ChangeLog
branches/2.0/inst/NEWS.Rd
branches/2.0/man/goodness.metaMDS.Rd
branches/2.0/man/metaMDS.Rd
Log:
merge r1961 ('noshrink' default in metaMDSdist) and r1964 (clarify stress scaling)
Modified: branches/2.0/R/metaMDSdist.R
===================================================================
--- branches/2.0/R/metaMDSdist.R 2011-10-29 17:22:16 UTC (rev 1964)
+++ branches/2.0/R/metaMDSdist.R 2011-10-30 07:07:03 UTC (rev 1965)
@@ -1,7 +1,7 @@
`metaMDSdist` <-
- function (comm, distance = "bray", autotransform = TRUE, noshare = 0.1,
- trace = 1, commname, zerodist = "ignore", distfun = vegdist,
- ...)
+ function (comm, distance = "bray", autotransform = TRUE,
+ noshare = TRUE, trace = 1, commname,
+ zerodist = "ignore", distfun = vegdist, ...)
{
## metaMDSdist should get a raw data matrix, but if it gets a
## 'dist' object return that unchanged and quit silently.
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2011-10-29 17:22:16 UTC (rev 1964)
+++ branches/2.0/inst/ChangeLog 2011-10-30 07:07:03 UTC (rev 1965)
@@ -4,6 +4,9 @@
Version 2.0-2 (opened October 20, 2011)
+ * merge r1964: clarify stress scaling in iso/monoMDS.
+ * merge r1961: consinstent 'noshrink' defaults in metaMDSdist()
+ and metaMDS(..., engine="isoMDS")
* merge r1959: capscale zero-rank constraints bug fix.
Version 2.0-1 (released October 20, 2011)
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2011-10-29 17:22:16 UTC (rev 1964)
+++ branches/2.0/inst/NEWS.Rd 2011-10-30 07:07:03 UTC (rev 1965)
@@ -16,6 +16,13 @@
\href{https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html}{R-News
mailing list}.
+ \item \code{stressplot} sometimes failed when \code{metaMDS} was
+ based on \code{isoMDS} because \code{metaMDSdist} did not use same
+ defaults for step-across (extended) dissimilarities as
+ \code{metaMDS(..., engine = "isoMDS")}. The change of defaults
+ can also influence triggering of step-across in
+ \code{capscale(..., metaMDSdist = TRUE)}.
+
}
} % end bug fixes
} %end version 2.0-2
Modified: branches/2.0/man/goodness.metaMDS.Rd
===================================================================
--- branches/2.0/man/goodness.metaMDS.Rd 2011-10-29 17:22:16 UTC (rev 1964)
+++ branches/2.0/man/goodness.metaMDS.Rd 2011-10-30 07:07:03 UTC (rev 1965)
@@ -20,7 +20,7 @@
\arguments{
\item{object}{A result object from \code{\link{metaMDS}},
\code{\link{monoMDS}} or \code{\link[MASS]{isoMDS}}. }
- \item{dis}{Dissimilarities. This should not used with
+ \item{dis}{Dissimilarities. This should not be used with
\code{\link{metaMDS}} or \code{\link{monoMDS}}, but must be used with
\code{\link[MASS]{isoMDS}}.}
\item{pch}{Plotting character for points. Default is dependent on the
@@ -32,9 +32,14 @@
\item{\dots}{Other parameters to functions, e.g. graphical parameters.}
}
\details{
- Function \code{goodness.metaMDS} finds a goodness of fit statistic for
- observations (points). This is defined so that sum of squared values
- is equal to squared stress. Large values indicate poor fit.
+ Function \code{goodness.metaMDS} finds a goodness of fit statistic
+ for observations (points). This is defined so that sum of squared
+ values is equal to squared stress. Large values indicate poor fit.
+ The absolute values of the goodness statistic depend on the
+ definition of the stress: \code{\link[MASS]{isoMDS}} expresses
+ stress in percents, and therefore its goodness values are 100 times
+ higher than those of \code{\link{monoMDS}} which expresses the
+ stress as a proportion.
Function \code{stressplot} draws a Shepard diagram which is a plot
of ordination distances and monotone or linear fit line against
Modified: branches/2.0/man/metaMDS.Rd
===================================================================
--- branches/2.0/man/metaMDS.Rd 2011-10-29 17:22:16 UTC (rev 1964)
+++ branches/2.0/man/metaMDS.Rd 2011-10-30 07:07:03 UTC (rev 1965)
@@ -37,8 +37,9 @@
choices = c(1,2), shrink = FALSE, select, ...)
\method{scores}{metaMDS}(x, display = c("sites", "species"), shrink = FALSE,
choices, ...)
-metaMDSdist(comm, distance = "bray", autotransform = TRUE, noshare = 0.1,
- trace = 1, commname, zerodist = "ignore", distfun = vegdist, ...)
+metaMDSdist(comm, distance = "bray", autotransform = TRUE,
+ noshare = TRUE, trace = 1, commname, zerodist = "ignore",
+ distfun = vegdist, ...)
metaMDSiter(dist, k = 2, trymax = 20, trace = 1, plot = FALSE,
previous.best, engine = "monoMDS", ...)
initMDS(x, k=2)
@@ -251,17 +252,19 @@
\value{ Function \code{metaMDS} returns an object of class
\code{metaMDS}. The final site ordination is stored in the item
- \code{points}, and species ordination in the item
- \code{species}. The other items store the information on the steps
- taken and the items returned by the \code{engine} function. The
- object has \code{print}, \code{plot}, \code{points} and \code{text}
- methods. Functions \code{metaMDSdist} and \code{metaMDSredist}
- return \code{\link{vegdist}} objects. Function \code{initMDS}
- returns a random configuration which is intended to be used within
+ \code{points}, and species ordination in the item \code{species},
+ and the stress in item \code{stress} (NB, the scaling of the stress
+ depends on the \code{engine}: \code{\link[MASS]{isoMDS}} uses
+ percents, and \code{\link{monoMDS}} proportions in the range \eqn{0
+ \ldots 1}). The other items store the information on the steps taken
+ and the items returned by the \code{engine} function. The object has
+ \code{print}, \code{plot}, \code{points} and \code{text} methods.
+ Functions \code{metaMDSdist} and \code{metaMDSredist} return
+ \code{\link{vegdist}} objects. Function \code{initMDS} returns a
+ random configuration which is intended to be used within
\code{\link[MASS]{isoMDS}} only. Functions \code{metaMDSiter} and
\code{postMDS} returns the result of NMDS with updated
- configuration.
-}
+ configuration. }
\references{
@@ -305,11 +308,10 @@
to \code{FALSE} with a warning.
}
-\section{Warning}{ \code{metaMDS} used \code{\link[MASS]{isoMDS}} as
- its NMDS engine till version 1.18-28, when this was replaced with
- the \code{\link{monoMDS}} function. You can set argument
- \code{engine} to select the old engine.
-}
+\section{Warning}{\code{metaMDS} uses \code{\link{monoMDS}} as its
+ NMDS \code{engine} from \pkg{vegan} version 2.0-0, when it replaced
+ the \code{\link[MASS]{isoMDS}} function. You can set argument
+ \code{engine} to select the old engine.}
\seealso{\code{\link{monoMDS}} (and \code{\link[MASS]{isoMDS}}),
\code{\link{decostand}},
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