VEGAN STABLE VERSIONS 

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.
