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

Version: 0.8.0-9000 [2015-10-24]
o ROBUSTNESS: Importing core R functions.


Version: 0.8.0 [2015-02-23]
o ROBUSTNESS: Package test coverage is 49%.
o BUG FIX: plot() for SnpNmfFit used undefined variable 'fit'.


Version: 0.7.1 [2014-04-27]
o DOCUMENTATION: Rebuilt help pages which drop references to a
  few deprecated/private methods.
o DOCUMENTATION: Clarified the example(fitSnpNmfArray).
o ROBUSTNESS: Added package system tests.
o Bumped package dependencies.


Version: 0.7.0 [2013-10-17]
o Added argument 'drop' to doACNE() to be more consistent with
  similar methods in aroma.affymetrix, e.g. doRMA() and doCRMAv2().
o CLEANUP: Removed all explicit calls to gc() and replaced all
  rm() with faster NULL assignments.
o DOCUMENTATION: Added a help page for doACNE().
o DOCUMENTATION: Added references to ACNE article.
o ROBUSTNESS: Now importing only what needs to be imported and
  formally declaring all S3 methods in NAMESPACE.
o Bumped the package dependencies.
o Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].


Version: 0.6.2 [2013-09-16]
o Bumped the package dependencies.


Version: 0.6.1 [2013-08-23]
o Now formally declaring S3 methods in NAMESPACE.


Version: 0.6.0 [2013-08-21]
o CLEANUP: Now package no longer attaches ("loads") several of the
  dependent packages, e.g. R.methods, R.oo, matrixStats, MASS.
o CLEANUP: Added .Rbuildignore to package so that incl/ and other
  directories/files are not included in the source build.
o Bumped the package dependencies.


Version: 0.5.1 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
  R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
  for you; missing documentation, a bug or just me?' on Oct 16, 2012.
o Now package imports utils, R.methodsS3 and R.oo.


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.