VEGAN STABLE VERSIONS 

Version 1.4-3 (Luova)
=====================

Based on devel version 1.5-30

* `cca' and `rda' use canonical expansion of the formula and return
  the `terms' component.  Functions like `terms', `formula' and
  `update' magically started to work with cca and rda (and eight lines
  of code would allow `step' and `stepAIC' to work magically in model
  building... but it's so much magic that I don't trust it). Some of
  the allowed things are now `mod <- cca(dune ~ . - Use, dune.env)'
  (all variables but `Use' in dune.env), and `update(mod, . ~ . -
  Manure)' (remove `Manure' from the previous).

* `cca' and `rda' find centroids of factor levels with factor
  constraints (only with formula interface). These can be accessed
  with `display="cn"' in `scores', `summary' and `plot'.  If
  `display="cn"' is requested in `plot', biplot arrows are still drawn
  unless there is a class centroid with the same name: continuous
  variables are still shown as arrows and ordered factors both as
  arrows as centroids.

* Enhanced user control of many ordination plots. Some accept more
  graphical parameters (`ordiplot', `plot.procrustes'). New functions
  `points.cca' and `text.cca' to add these items into CCA/RDA
  plots (documented separately).

* `identify.ordiplot' knows more alternatives, among them
  `plot.procrustes'.  This was helped with new, very generic
  `scores.ordiplot'.

* New functions to add graphical items in ordination diagrams:
  `ordihull' draws convex hulls for groups,  `ordiarrows' draws
  arrows, `ordisegments' segments, `ordigrid' combines points in to a
  grid, `ordispider' combines points to their (weighted) centroids or
  WA scores to the corresponding LC score in cca/rda, `ordiellipse'
  draws dispersion or confidence ellipses for points. All these take a
  groups argument for selecting subsets of points. `ordispider'
  obsoletes `spider.cca' (introduced in the previous release). 

* Implemented simple ``deshrinking'' of weighted averages in
  `wascores'.

* A new diversity function `fisher.alpha' that estimates the diversity
  as the alpha parameter of Fisher's log-series. Thanks to Bob O'Hara
  <bob.ohara@helsinki.fi> for the main code.

* `summary.decorana' now in canonical form so that printing is done by
  `print.summary.decorana' and user can intercept and catch the
  result.  Several users had been surprised of the earlier
  non-canonical behaviour. `summary' knows again the prior weights
  used in downweighting of rare species (these evaporated in 1.4-0).

* rda summary/scores/plot bugfix: Scaling of site scores was wrong
  with scaling alternatives 1 and 3.

* envfit (vectorfit, factorfit) bug fixes: Can now handle single
  vectors (labelling, permutation). Recognize now `choices' so that
  the user can select ordination axes.

* Checked with released R-1.7.0.

Version 1.4-2
=============

Based on devel version 1.5-18

New functions and data sets:

* dune: A new data set -- the classic Dune Meadow data with the
  environmental data.

* ordiplot, identify.ordiplot: New functions to plot "any" ordination
  result and identify plotted points. Intended to provide similar
  functionality as `plot', `plotid' and `specid' functions in `labdsv'
  without name clashes. Functions `plot.cca' and `plot.decorana'
  return (invisibly) `ordiplot' objects as well, and these can be used
  by `identify' to label species and sites.

* rda: Redundancy Analysis, or optionally, yet another PCA. This is a
  spin-off from cca(), and it is documented together with cca. The
  only new functions are rda, rda.default, rda.formula and
  summary.rda. Otherwise rda uses cca methods which were changed to be
  aware of rda.

* read.cep: A function to read Cornell Ecology Package or CEP
  formatted files into R. This has been in devel versions since 1.1-1,
  but it never made to the releases, since this worked only in Linux,
  but crashed R in Windows. It seemed to work in R-1.6.1 with gcc 3.2
  (MinGW) in Windows, so it is included. Treat with caution.

* spider.cca: A tiny function that joins each WA score to the
  corresponding LC score in cca/rda plots.

Minor changes:

* Checked with R-1.7.0 (unstable devel version, snapshot 2003-02-05)
  and corrected as needed. 

* Added symmetric scaling (=3) to alternitves in cca and rda.

* Minor improvements and bug fixes in vegemite.

Version 1.4-1 (Logan)
=====================

Based on devel version 1.5-10.

New features:

* Permutation tests added to envfit (vectorfit, factorfit) and
  procrustes (called protest).

* All permutation tests take now argument strata: If given,
  permutations made only within strats. Concerns anosim, anova.cca
  (permutest.cca), mantel, envfit (factorfit, envfit) and protest (in
  procrustes). 

* fitted.procrustes(): A new function.

* rarefy(): A new function for rarefaction species richness.

Other changes:


* cca.default(): Handles now NULL matrices X and Z: skips them.

* cca.formula(): Knows now cca(X ~ 1) and permforms unconstrained CA,
  and cca(X ~ ., data) and perfors CCA using all variables in `data'
  as constraints. Has now na.action=na.fail so that cca crashes more
  informatively (used to crash mysteriously). A more graceful
  na.action may come. Assignment "=" corrected to the true blue "<-"
  (used to crash in old R).

* envfit (factorfit, vectorfit): Use `scores' now. Various bugfixes
  and should work now with single factors or vectors.

* plot.envfit(): Options `choices' works now like documented.

* ordisurf(): A new name to surf() to avoid name clash with labdsv.
  
* procrustes(): added option `symmetric' for symmetric rotation and
  goodness of fit statistic. 

* plot.procrustes(): Keyword `axes' changed to `choices' to be
  consistent with other functions.

* vegemite(): A new name to vegetab. The name was chosen because the
  output is so compact (and to avoid confusion with function vegtab in
  labdsv). Function checks now that the cover codes fit in one column
  and splits the output if it does not fit into used page width.

Version 1.4-0
=============

Based on devel version 1.3-19.

New functions:
--------------

* `anosim': Analysis of Similarities.

* `cca': [Partial] [Constrained] Correspondence Analysis.  This is an
  alternative to Dray's `CAIV' (package `CoCoAn').  Differences
  include formula interface, WA scores in addition to LC scores,
  partial CCA, residual CA after constraints, algorithm based on svd
  (and much faster), more standard support functions (`plot',
  `summary', `print').

* `anova.cca' and `permutest.cca': Permutation tests for `cca'.

* `envfit': A new wrapper function which calls either `vectorfit' or
  new `factorfit' function, and `plot.envfit' for easier display of
  results in graphs.

* `mantel': Mantel test for two dissimilarity matrices.

* `scores': A generic function to extract scores from `cca',
  `decorana' or even from some common ordination methods in R.

* `surf': Surface fitting for ordination, intended as an alternative
  to `vectorfit'.

* `vegetab': Prints a compact, ordered vegetation table, together with
  `coverscale' to transform data into compact format.

Other changes:
--------------

* `downweight': directly callable instead of being embedded in
  `decorana'. Now it can be used with other downweighting thresholds
  or with other CA's than `decorana', e.g., `cca', `ca', `CAIV'.

* `plot.decorana': new keyword `type', removed keyword `tol'.

* `vectorfit': centres now ordination before fitting, so it will work
  with other ordinations than MDS.

* Mainly user invisible changes in `plot.decorana', `plot.procrustes',
  `postMDS', `print.summary.procrustes', `vectorfit', `procrustes'.
  One of the main changes was that `eqscplot' of `MASS' library was
  replaced with `plot(..., asp=1)' of standard R (but this is not
  S-plus compliant).

* Edited help files.  More examples run from help files.  

* Tried to improve LabDSV compliance, see http://labdsv.nr.usu.edu/.

* Checked with R-1.5.0.  However, `log' in diversity not changed into
  `logb' (yet), although base is specified, because `logb' won't work
  in R pre-1.5.0. 

Version 1.2-1
=============

* Checked with R-1.4-0 (frozen snapshot) tools: Documentation and
  method consistency corrected (summary.decorana.R, decorana.Rd), and
  file permissions changed.

* decorana.Rd: removed dependence on package `multiv' in the example,
  since it is not a `recommended package' -- replaced with
  `decorana(..., ira=1)'.

Version 1.2-0
=============

Based on experimental version 1.1-6. Doesn't include read.cep() of the
experimental version, because the function is certainly unportable to
all platforms (works on Red Hat Linux 7.1, but perhaps nowhere else).

Major new feature:

* decorana(): R port of Mark Hill's DECORANA for Detrended
  correspondence analysis, with methods print(), summary() and plot().

Minor changes:

* postMDS(): finds isoMDS scores and doesn't destroy list structure.

* vectorfit: finds isoMDS scores and decorana row scores (which are
  uncentred, though).

* Proof reading in documentation.

Version 1.0-3
=============

* `plot.procrustes': selection of axes plotted, improved scaling in
  graphics, control of axis labels.

* `postMDS': added plot to demonstrate half-change scaling. 

* `procrustes': target can now have lower dimensionality than rotated matrix.

Version 1.0-2
=============

* Fixed bugs in documentation.

* `plot.procrustes': Fixed passing `...' to graphics functions.

Version 1.0-1
=============

* The first public version.
