===============
version 1.65.1
===============

o new feature:
--allow parameter `Prefix' in `run.plgem' to be passed down to
  `plgem.fit' when `writeFiles=TRUE'

o bug fix:
--only check existence of `fittingEvalFileName' when both `fittingEval' and
  `plot.file' are TRUE in `plgem.fit'

===============
version 1.65.1
===============

o new feature:
--added parameter `Prefix' to `run.plgem' to be passed down to
  `plgem.write.summary' when `writeFiles=TRUE'

o bug fix:
--fixed error occurring when running `run.plgem' with `plotFile=TRUE'

===============
version 1.59.2
===============

o bug fixes:
--fixed syntax error in `plgem.obsStn'
--imported function `is' into NAMESPACE

===============
version 1.59.1
===============

o bug fixes:
--updated class-checks to avoid package failures in R 4.0, as reported in
  https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html
  and
  http://bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq
--imported several functions into NAMESPACE from `grDevices', `graphics' and
  `stats'

===============
version 1.37.1
===============

o minor changes:
--added biocViews `GeneExpression' and `MassSpectrometry'
--moved Biobase and MASS from `Depends' to `Imports'

===============
version 1.33.1
===============

o minor changes:
--removed unnecessary calls to `which' within subsetting operations, to avoid
  potential unintended consequences pointed out by Wolfgang Huber:
  <https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004353.html>

===============
version 1.31.2
===============

o new features:
--added a parameter `prefix' to function `plgem.fit' so that multiple PLGEM
  fitting evaluation plots could be saved under different names.
--added a file existence test in function `plgem.fit' to avoid overwriting of
  PLGEM fitting evaluation plot files.
--added new parameter `gPar' to function `plgem.fit' to define plotting
  boundaries of PLGEM fitting evaluation plot.
--added new function `setGpar' to facilitate passing graphical parameters to
  `plgem.fit'.

===============
version 1.31.1
===============

o fixed bug:
--corrected call to `png' in function `plgem.fit' to avoid partial argument
  match of `file' to `filename'.

o minor changes:
--improved readability of progress report outputted by `plgem.resampledStn'
  when `verbose=TRUE'.
--changed call to `packageStartupMessage' from an `.onLoad' to an
  `.onAttach' hook.
--moved source of the vignette in new subfolder `vignettes'.

===============
version 1.21.1
===============

o fixed bug:
--corrected call to `plgem.write.summary' within function `run.plgem'.

===============
version 1.19.3
===============

o minor changes:
--welcome message at package start-up is now delivered via a call to
  `packageStartupMessage', rather than via `message'.
--added sessionInfo() at the end of vignette.

===============
version 1.19.2
===============

o minor changes:
--updated author contact information in man pages.

===============
version 1.19.1
===============

o minor changes:
--updated maintainer contact information in DESCRIPTION file.
--improved package title and description.

===============
version 1.17.3
===============

o minor changes:
--added information about what baseline was used to generate the observed STN
  values in the colnames of the PLGEM.STN matrix outputted by function
  `plgem.obsStn'.
--added information about what baseline was used to generate the the p-values
  in the colnames of the matrix outputted by function `plgem.pValue'.

===============
version 1.17.2
===============

o fixed bug:
--updated LPSeset object to match new object definition of eSet in Bioconductor.

===============
version 1.17.1
===============

o fixed bug:
--in case that more than one condition had the highest number of replicates,
  function `run.plgem' was picking the wrong condition to fit the model.

===============
version 1.15.13
===============

o minor change:
--changed maintainer information.

===============
version 1.15.12
===============

o minor changes:
--added a check in function `plgem.write.summary' to test for existence of files
  with identical names in the working directory and to prompt the user to decide
  whether to abort the writing process or to overwrite the existing files;
--amended the documentation for function `plgem.write.summary' to update the
  different types of files that are now written to the working directory.

===============
version 1.15.11
===============

o minor changes:
--added warnings in function `plgem.fit', displayed if the fitting parameters
  are outside the normally observed range of values;
--removed `library' calls from source code (NAMESPACE should take care of
  package dependencies).

===============
version 1.15.10
===============

o minor changes:
--added `NEWS' file.

==============
version 1.15.9
==============

o major changes:
--Modified output of function `plgem.obsStn' to contain also the output of
  function `plgem.fit';
--Modified output of functions `plgem.deg' and `run.plgem' to contain also the
  output of functions `plgem.obsStn' and `plgem.pValue'; significant features
  are now listed by their names only (no more associated observed STN value) as
  a separate element of the output list, called `significant';
--Modified functions `plgem.deg' and `plgem.pValue' to deal with the new output
  of function `plgem.obsStn';
--Modified function `plgem.write.summary' to deal with the new output of
  functions `plgem.deg' and `run.plgem'.

o minor changes:
--due to more complex outputs of functions `plgem.obsStn' and
  `plgem.resampledStn', splitted the documentation into two independent man
  file;
--enhanced status message printed out by function `run.plgem' about the
  condition being selected for fitting the model;
--added argument `prefix' to function `plgem.write.summary' to allow user to
  specify a prefix to prepend to the file names;
--modified documentation to reflect all above changes.


==============
version 1.15.8
==============

o minor changes:
--added clear statements throughout the vignette and other package documentation
  that two replicates are required and sufficient to fit a PLGEM (although, of
  course, having more replicates can only improve the fitting);
--changed URL in reference to MCP paper to point to the abstract, rather than
  the to full text (which not everyone might have access to);
--further improved rendering of math equations in documentation;
--added a check for consistency of input baseline condition in functions
  `plgem.obsStn', `plgem.resampledStn' and `run.plgem';
--improved error messages from private check functions. 


==============
version 1.15.7
==============

o minor changes:
--fixed a documentation bug that was causing a CHECK error in the manual page of
  function `run.plgem';
--added a private function to perform a consistency check for the input
  ExpressionSet;
--improved display of math expressions in PDF versions of manual pages.


==============
version 1.15.6
==============

o major changes:
--replaced argument `covariateNumb' with `covariate' and allowed to specify the
  covariate also by its name (rather than only by its number);
--replaced argument `fit.condition' and `baseline.condition' with `fitCondition'
  and `baselineCondition', respectively, and allowed to specify the condition
  also by its name (rather than only by its number);
--added arguments `trimAllZeroRows' and `zeroMeanOrSD' also to function
  `run.plgem' to improve fitting in cases with many zero values;

o minor changes:
--updated package documentation to reflect above changes;
--added `COVARIATE' to the value of function `plgem.fit';
--added file `privateFunctions.R' to have small auxiliary functions all in one
  place, improving modularity and readability of source code;
--fixed a bug when more than one condition had the highest number of replicates
  (argument `covariate' was not passed to function `plgem.fit');
--overall code optimization.


==============
version 1.15.5
==============

o major changes:
--added arguments `trimAllZeroRows' and `zeroMeanOrSD' to function `plgem.fit'
  to improve fitting in cases with many zero values;

o minor changes:
--minor amendments to the vignette.


==============
version 1.15.4
==============

o minor changes:
--overall reformatting of vignette for improved readability.


==============
version 1.15.3
==============

o major changes:
--fixed dependencies in NAMESPACE that were causing check errors when trying to
  load the namespace.


==============
version 1.15.2
==============

o minor changes:
--replaced `.First.lib' with `.onLoad' in zzz.r file (due to adding a NAMESPACE
  to the package);
--updated e-mail address in man files.


==============
version 1.15.1
==============

o major changes:
--added NAMESPACE.

o minor changes:
--updated references in vignette and man pages.


==============
version 1.11.3
==============

o minor changes:
--added a few argument checks to generate meaningful error messages in case
  argument `covariateNumb' was not a number, or arguments `q' or `signLev' were
  outside the allowed range (i.e. between 0 and 1).


==============
version 1.11.2
==============

o minor changes:
--fixed documentation bug (missing link to `ExpressionSet' class);
--overall improvement of help files and vignettes.


==============
version 1.11.1
==============

o major changes:
--added function `plgem.pValue' to calculate p-values for given observed STN
  values.


==============
version 1.11.0
==============

o major changes:
--corrected the object class for LPSeset, which is now an `ExpressionSet' rather
  than an `exprSet'.


==============
version 1.9.1
==============

o major changes:
--`LPSeset' dataset has been updated from `exprSet' to `ExpressionSet' class;
--the requirement of the `conditionName' covariate in the `phenoData' of the
  `ExpressionSet' has been eliminated; now a numeric index (`covariateNumb')
  needs to be provided to indicate which covariate has to be used to identify
  the different experimental conditions and set of replicated arrays on the
  `ExpressionSet';
--updated functions to deal with the switch from the `exprSet' to the
  `ExpressionSet' class and on the addition of the `covariateNumb' argument;
--added new function `plgem.write.summary',  providing a simple wrapper for
  writing on the disk the list(s) of differentially expressed genes.

o minor changes:
--updated package documentation to reflect all above changes;
