New version of vegan released to CRAN (1.17-9)

April 1, 2011
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(This article was first published on From the bottom of the heap » R, and kindly contributed to R-bloggers)

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 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: rarefy(), rrarefy(), and 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).

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