CHANGES IN VERSION 2.52.1
- Fixed compilation error from fopen

CHANGES IN VERSION 2.7.0
- Added findgenes.matrix method
- Changed multicore package for parallel

CHANGES IN VERSION 2.5.6
- Changed printf and put statements to Rprintf, error to Rf_error and removed stderr calls to avoid compiler warnings.

CHANGES IN VERSION 2.5.4
- Added function fitNNSingleHyp

CHANGES IN VERSION 2.5.2
- Added function makeEBarraysSingleHyp

CHANGES IN VERSION 2.2.1
- Fixed bug in fitGG which stopped the execution when the levels of argument groups where not ordered.

CHANGES IN VERSION 2.1.0
- Added wrapper for normal-normal model fit
- Added posterior predictive simulation, power calculations and forward simulation for normal-normal model.

CHANGES IN VERSION 1.2.0
- forwsimDiffExpr is now fully operational. Vignette updated with examples.

CHANGES IN VERSION 1.1.2
- Fixed bug in forwsimDiffExpr which caused the C code to crash
- Fixed bug in forwsimDiffExpr which caused it to crash for certain randomSeed values
- Added function buildPatterns to build a matrix indicating which groups are put together under each pattern. 

CHANGES IN VERSION 1.1.1
- Changed specification of S3 class methods in NAMESPACE file so that now e.g. parest.gagafit is not visible, only parest is visible.

CHANGES IN VERSION 1.1.0
- Included routines for sequential design of high-throughput experiments
- Fixed numerical overflow that affected fitGG in some data sets
- Removed warning from powfindgenes when user selects to use all genes
- Fixed bug in classpred cause by specifying 'ngenes' greater than the available number of genes in the input data

CHANGES IN VERSION 1.0.8
- Fixed access to unallocated memory address in C code

CHANGES IN VERSION 1.0.7,1.0.6
- Changes in vignette so that it compiles in all platforms

CHANGES IN VERSION 1.0.5
- Fixed some errors in vignette

CHANGES IN VERSION 1.0.4
- Removed INDEX file so that it can be automatically generated with R CMD BUILD

CHANGES IN VERSION 1.0.3
- Fixed some compiler warnings

CHANGES IN VERSION 1.0.2
- Added function posmeansGG to compute posterior expected expression values and fold changes.
- fitGG method=='EM' and method=='quickEM' have been re-implemented to improve speed, and they now allow nclust>1. method=='quickEM' has been set as the default.
- fixed bug when dcgamma, mcgamma and rcgamma check the validity of the input parameters.
- added option in checkfit to allow expression levels to be shown in log2 scale

CHANGES IN VERSION 1.0.1
- Added function geneclus to perform supervised gene clustering.
- Parameter B in fitGG can be used to specify maximum number of EM iterations
- fitGG with method=='EM' now stops when (i) the absolute change in log-likelihood, (ii) the relative change in log-likelihood or (iii) the change in parameter values is negligible. In previous versions (i)-(iii) had to hold simultaneously for the algorithm to stop, which typically caused an unnecessary increase in computing time.
- Argument 'patterns' in fitGG now must have colnames that match the group codes indicated in the argument 'groups'.
- When printing a gagafit object, the estimated proportion of genes is indicated for each expression pattern

CHANGES IN VERSION 1.0.0
- Added a version of the GaGa and MiGaGa models which assumes a constant coefficient of variation across groups. The two versions of the model are accessible through the parameter 'equalcv' available in most functions.
- Added two new methods to fit the GaGa and MiGaGa models: Simulated Annealing and Metropolis-Hastings. These options are accessible through the parameter 'method' in fitGG. 
- Functions simGG and simnewsamples now return 'ExpressionSet' objects.
- Updated vignette with examples using Simulated Annealing and Metropolis-Hastings to fit the model.
- Updated vignette with information about the two variants of GaGa and MiGaGa models: constant and non-constant coefficient of variation.
- Changed fake code in vignette to real code.
- Changed function names to modern nomenclature: fit.gg to fitGG, sim.gg to simGG

CHANGES IN VERSION 0.99.1
- Fixed warnings due to uninitialized variables in the C code

CHANGES IN VERSION 0.99.0
- Changed word 'library' for 'package' in the Vignette
