


		CHANGES IN GeneTS VERSION 2.0


NEW FEATURES

    With version 2.0 GeneTS provides functions to infer large sparse graphical
    Gaussian models, following an approach outlined in:

    Schaefer, J., and K. Strimmer. 2003. A practical approach to inferring large
    graphical models from sparse microarray data. Submitted to Bioinformatics.
    [Preprint available from http://www.stat.uni-muenchen.de/~strimmer/]

NEW FUNCTIONS
 
    o ggm.simulate.pcor, ggm.estimate.pcor, ggm.simulate.data, ggm.test.edges
    
    o ggm.make.graph, ggm.plot.graph

    o cor2pcor, pcor2cor, pcor
 
    o bagged.cov, bagged.cor, bagged.pcor  
   
    o cor0.test, cor0.estimate.kappa, cor.fit.mixture, cor.prob.nonzero
    
    o kappa2N, N2kappa
   
    o dcor0, pcor0, rcor0, ibeta functions
 
    o z.transform, hotelling.transform
    
    o robust.boot

    o fdr.estimate.eta0

    o pseudoinverse, rank.condition

    o standardize.cov, rebuild.cov
    
    o sm2vec, sm.indices, vec2sm 
 
    o is.positive.definite, is.symmetric, is.square
   
 
   
    
CHANGES

    o bacteria renamed to caulobacter to avoid collision with MASS package.
    
    o fdr.control renamed from fdr.test,  significant hypothesis are 
      now those with p <= cutoff rather than with p < cutoff,
      q-values are computed, and pi0 < 1 is now allowed.
 
   


		CHANGES IN GeneTS VERSION 1.1


NEW FEATURES

    This version of GeneTS is a maintainance release only.

CHANGES


    o The functions periodogram.spec() and periodogram.freq() are now
      combined in the single function periodogram(). 

    o Rather than using angular frequencies between 0 and pi, GeneTS
      by default now uses frequencies between 0 and the Nyquist critical
      frequency fc = frequency()/2 (i.e. typically between 0 and 0.5). 

    o Given a constant time series fisher.g.test() now returns a p-value
      of 1 instead of issuing an error. The man page for fisher.g.test()
      is changed and slightly extended.

    o Previously, all methods in GeneTS assumed that the *rows* in a matrix
      contain the time series data.  This convention is now changed so that
      each *column* represents one time series (this follows the convention
      used by the ts package).  All functions and data sets in GeneTS are
      also changed accordingly.
    



		CHANGES IN GeneTS VERSION 1.0


NEW FEATURES

    First public release of GeneTS.  This version of GeneTS implements
    all methods for cell cycle analysis described in:

    Wichert, S., K. Fokianos, and K. Strimmer. 2004.  Identifying periodically
    expressed transcripts in microarray time series data. Bioinformatics 20:5-20.

NEW FUNCTIONS
      
      o the average periodogram for multiple time series (avgp)
      
      o Fisher's exact g test as gene selection method (fisher.g.test)
      
      o multiple testing using false discovery rate (fdr.test)
      
      o simplified interface to periodogram (periodogram)
      
      o some other utility function (is.constant, dominant.freqs)
      
      o parts of the bacterial data set by Laub et al. (2000) (caulobacter)
 
