Package: ACNE
=============

Version: 0.5.0 [2011-10-24]
o Added a NAMESPACE.


Version: 0.4.3 [2011-08-01]
o WORKAROUND: In order for the package to work with the most recent
  version of R devel, which automatically add namespaces to packages
  who do not have one, we explicitly have specify that this package
  should use, for instance, cat() of R.utils (instead of 'base').


Version: 0.4.2 [2010-09-28]
o ROBUSTIFICATION: Improved validation of argument 'refs'.


Version: 0.4.1 [2010-06-21]
o Added more biocViews to the DESCRIPTION file.
o Added argument 'refs' to NmfPlm() and fitSnpNmf().


Version: 0.4.0 [2010-05-18]
o BUG FIX: The NmfSnp class would use a way too large threshold
  for deciding when the NMF algorithm has converged.  The
  default accuracy 0.02 was replaced with 10.0 due to a "stray"
  argument in an internal function call.  This bug has been there
  since March 24, 2009.
o CLEAN UP: All flavors of NMF algorithms but the default one
  ("v4") is deprecated and no longer available in NmfPlm.


Version: 0.3.0 [2010-05-17]
o Added doACNE().  Added also redundancy tests for it.
o CLEAN UP: Now a flavor tag is added to NmfPlm:s only 
  if flavor != "v4" (default).


Version: 0.2.0 [2010-05-04]
o Bumped up the version of the package dependencies.
o Set the license to LGPL v2.1 or newer.


Version: 0.1.2 [2009-11-18]
o SPEED UP/CLEAN UP: For debug purposes, the internal NmfPlm
  fit function as well as fitSnpNmf() used to save the input
  data for each SNP fitted.  This is now removed, and should
  speed up the processing substantially.


Version: 0.1.1 [2009-11-11]
o BUG FIX: One of the testScripts/ had a type.
o CLEAN UP: Removed an obsolete testScripts/.


Version: 0.1.0 [2009-11-03]
o Moved the package to the r-forge.r-project.org repository.
o Renamed package to ACNE (from aroma.affymetrix.nmf)


Version: 0.0.5 [2009-03-25]
o Added example code with example data for fitSnpNmfArray().
o Added fitSnpNmfArray(), which takes an Kx2xI array.
  fitSnpNmfArray() returns a list object of class SnpNmfFit
  for which there is a plot() function.
  Note, fitSnpNmf() takes a 2KxI matrix.
o Added snpMatrixToArray() and snpArrayToMatrix().


Version: 0.0.4 [2009-03-24]
o Added sanity checks of all input and output to functions.
o Added Rdoc comments (Rd help pages).
o Removed obsolete dependency on the 'impute' package.
o Cleaned up code.


Version: 0.0.3 [2009-02-02]


Version: 0.0.2 [2009-01-28]
o CLEAN UP: Removed old MyProbeLevelModel class.
o NmfPlm now inherits from ProbeLevelModel.
o Created temporary package.


Version: 0.0.1 [2008-xx-xx]
o Created.
