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Yesterday Jari packaged up the latest release in the current stable branch of the vegan package. Version 1.17-9 of vegan is now on CRAN as a source tarball with binaries for MS Windows and MacOS X to follow soon. New releases in the current, stable branch of the package tend to be for bug fixes but we sometimes include new functionality considered low impact and important enough to warrant early release. This release sees a fix to a bug in the anova() method for rda(), cca() and capscale(), which would produce incorrect results when partial models were supplied and testing was performed by axes [e.g. anova.cca(..., by = "axis") ].
From a user’s perspective, there were three important additions to vegan with this release:
ordisurf()gained several new arguments to allow control of the methods used bygam()when fitting response surfaces to ordination configurations. The smoothness selection method can now be specified via a new argument'method'and an additional penalty can be applied to smooth terms so that they can be penalized out (i.e. removed from) the model if there really is no relationship between the response and the ordination configuration. If this happens,ordisurf()won’t draw a response surface at all.- Automatic plotting of the fitted surface as a side-effect of
ordisurf()can now be turned off, and a newplot()method allows later plotting of response surfaces without having to refit the entire model again. metaMDSrotate()can now rotate an nMDS ordination with an arbitrary dimensional solution whereas before it would only rotate 2-D solutions.diversity()(and related functions:rarefy(),rrarefy(), andspecnumber()) are now more intuitive and work with vector inputs. As a result many sites/samples can be analysed at once now.
Full details of the release can be seen in the NEWS file, the relevant portion of which appears at the bottom of this post.
We’ve got some exciting new features planned for the next version of vegan, which I’ll blog about when they start appearing in the development version on R-forge.
VEGAN RELEASE VERSIONS
======================
CHANGES IN VEGAN 1.17-9
- anova of cca/rda/capscale results gave wrong results in partial
models. The bug was introduced in vegan 1.17-7.
- diversity and related functions rarefy, rrarefy and specnumber
now accept vector input. Earlier a single site had to be
analysed either as a single-row matrix or using the non-default
setting MARGIN = 2.
- drarefy: new function that returns a matrix of probabilities
that a species occurs in a rarefied sample of a given size.
- metaMDS: it is possible to supply a starting configuration with
argument 'previous.best'. A previous metaMDS or isoMDS result can
also be given as a starting configuration. If the starting
configuration has a higher number of dimensions than requested,
the extra ones are dropped, and if the starting configuration
has fewer dimensions, random scores for extra dimensions will be
added. This may help in running metaMDS over a range of
dimensionalities.
- metaMDSrotate: can now rotate metaMDS solutions with any number
of dimensions so that the first axis is parallel to a fitted
environmental vector. Previously, only two dimensional solutions
worked.
- ordilabel: gained argument 'xpd' that allows labels outside the
plot area. This allows labels above axes, for instance.
- ordisurf: gained several new arguments to control the mgcv::gam
fitting. Also gained an argument to suppress plotting, and a new
plot method. The fitted model can be specified with a formula.
- prestonfit and friends: default is now 'tiesplit = TRUE' (which
was a new feature introduced in vegan 1.17-8).
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