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
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 by
gam()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 new
plot()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:
specnumber()) 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).