MEFA VERSIONS

Version 2.1-0 -- November 12, 2008 (opened - r???)

Version 2.0-2 -- November 12, 2008 (closed - r252)

    * intro text: mefa gives date info when loaded.
    * mefaCompare: compares 2 objects of class mefa,
      based on dimnames and numeric values. Sample
      and taxa tables are not compared.
    * demo: added, based on the vignette (also a tests
      directory to check the demo script).
    * vignette: added to inst/doc based on a manuscript
      submitted to JSS. Dependencies are excluded and
      a verbatim code is placed in the vignette instead.
    * DOLINA data sets: reworked. A more simple example
      is given: dol.count, dol.samp, dol.taxa. The previous
      full data set is available at: hdl:1902.1/12060.
    * extract.mefa: nested segment indexing convention
      introduced when extracted.
    * mefaNestedless: makes an object with non-nested
      segments, bo be used in melt.
    * as.mefa: if class is mefa, the object can be
      rebuilt with new arguments (e.g. drop.zero,
      nested, segment).
    * mefaCrosstab: xtabs function is now used for
      crosstabulation internally, instead of the
      inflate function. This implementation allows
      non integer values as 'count'. All other
      functions (stcs, melt, aggregate) accept it, too.
      The inflate function is in use for integer counts
      used by stcs when expand is TRUE. Help pages and
      examples modified accordingly.
    * boxplot: new argument 'all' for plotting all
      segments and the separate segments in the same graph.
    * melt.mefa: now accepts mefa object with xtab
      element without dimnames. In this case, rows and
      columns are names by integers. When only melt(x)
      is used and x has original segments, those are
      used to build the stcs object. This can however be
      avoided by melt(as.mefa(x, segment = FALSE)).
      As a result, ordering of dimnames can be different.
    * mefa: the restriction of at least 2 columns for
      samp and taxa tables is no longer necessary.
    * qvector: na.rm and ... arguments added.
    * plot: labels corrected.
    * melt.mefa: takes care of zero.pseudo flags silently,
      and returns call attribute as well of raw=FALSE.
    * print.mefa: returns segment names to avoid confusion
      when all other details are the same.
    * mefaTables: xtab.fixed argument now works properly.
    * stcs: argument zero.pseudo now accepts a two element
      vector for species and segments, respectively.
    * summary.mefa: returns list with different names
      for [1:4] elements due to consistency with
      samples/taxa sides: s.rich, s.abu, t.occ, t.abu,
      and these are used in the print.summary method, too.
      Accordingly, the class has now a call attribute to
      return it by the summary.
    * help pages: lots of minor improvements.
    * R code: annotated with comments.
    * summary.stcs: returns same info as summary.mefa,
      but print.stcs remained the default data frame method.
    * plot, boxplot, image methods for stcs: also added
      for avoiding the use of calls like plot(mefa(x)).


Version 2.0-1 -- November 8, 2008 (closed - r205)

    * extract.mefa: now accepts negative indexing
      for exclusion (not as character), and
      column extraction bug fixed
    * type arg of plot.mefa: "hist" replaced by "bar"


Version 2.0-0 -- September 29, 2008 (closed - r200)

    * The package was extensively rewritten
      (started on September 16, 2008).
      It is more easy and efficient than
      < 2.0 versions. The number of object
      classes reduced. The new class stcs
      is almost equivalent to the old sscount.
      The new class mefa can be used either
      as the old xcount and mefa classes
      (and the xclist and mflist classes
      only provided with the undocumented
      patch file). The old xorder class
      is bow useless, too.
    * New methods are provided for manipulating
      pbjects. The "[.mefa" replaces the old
      exclmf function, the aggregate method
      replaces the old strify function.
    * plot, print and summary methods only
      provided for the class mefa. For the
      stcs class, methods for data frames can
      be used (because an stcs object is
      essentially a data frame with some
      conventions and additional attributes).
    * The melt method is provided to convert
      a mefa object into stcs, or redefine
      new segments.
    * dim and dimnames methods also available
      for mefa objects.
    * the mefalogo function depicts the
      general representation of an object
      of class mefa.


Version 1.1-4 -- September 20, 2008 (closed)

    * inflate: arguments of any() corrected


Version 1.1-3 -- September 15, 2008 (closed)

    * citation entry added


Version 1.1-2 -- June 24, 2008 (closed)

    * several minor fixes in .Rd files
    * xytrend moved to sedar
    * preliminary modifications made according to later
      introduction of 'list' objects
    * report as generic function added for methods
    * as.mefa added
    * startup message is added


Version 1.1-1 -- June 12, 2008 (closed)
                 April 02, 2008 (started)

	* accumulate was rewritten
	* vignette is corrected and updated
	* help pages are corrected and updated


Version 1.1-0 -- March 14, 2008

	* vignette is made available
	  and can be used as reference for the
	  dolina demo
	* add.attrib can now handle mefa objects
	  containing NULL attribute table
	* logscale argument inserted into plot methods
	* cutoff argument inserted into print methods
	* report.mefa bug fixed & help corrected
	* new functions: qdef, mapmf, accumulate,
	  ivgen, xytrend
	* mefa from now depends on other packages
	  (xytrend requires vegan)
	* mefa developement is now on R-Forge


Version 1.0-4 -- February 11, 2008

	* the demo was rewritten
	  (and still under construction...)
	* amf function is provided
	* class definitions are rewritten
	* print and plot S3 methods provided for classes
	* digits argument is placed into sscount 
	  and related functions


Version 1.0-3 -- January 4, 2008

	* mefa object can be used in function as.xcount
	* default setting of index argument
	  in add.attrib was changed
	* "SampleReport" option is available 
	  in mefadocs function, showing options for 
	  Sweave report generation.
	* bug fixed in exclmf
	* bug fixed in dolina demo.
	* warning message is placed in strify code


Version 1.0-2 -- December 18, 2007

	* new function: exclmf
	* default setting of index argument 
	  in xorder and check.attrib has changed
	* thus manual was modified inseveral pages
	* There is a mefadocs function, 
	  based on J. Oksanen's vegandocs function
	* currently only "changelog" is active
	* A bug is present in report.mefa, 
	  a WARNING is placed in the manual 
	  will be fixed later


Version 1.0-1 -- December 7, 2007

	* bugs fixed in function stify


Version 1.0 -- November 13, 2007

	* the first public version
