
                 RELEASE HISTORY OF THE "st" PACKAGE
               =======================================

		CHANGES IN `st' PACKAGE VERSION 1.2.7

- update URLs.


		CHANGES IN `st' PACKAGE VERSION 1.2.6

- change modt.fun() to use limma::eBayes() rather than limma::ebayes().


		CHANGES IN `st' PACKAGE VERSION 1.2.5

- added import statements required by R-devel.


		CHANGES IN `st' PACKAGE VERSION 1.2.4

- fixed the "please use :: or requireNamespace() instead" warnings.


		CHANGES IN `st' PACKAGE VERSION 1.2.3

- change of maintainer email address.
- fixed the  "no visible global function definition" warnings.


		CHANGES IN `st' PACKAGE VERSION 1.2.2

- added import statement in NAMESPACE to address corresponding warnings
  in R 3.1.0.


		CHANGES IN `st' PACKAGE VERSION 1.2.1

- package update necessary due to updated functions in sda version 1.3.1.
  In particular, sda::centroids() and sda::catscore() functions now 
  use shrinkage estimates of frequencies. 

  Correspondingly, diffmean.fun(), studentt.fun(), samL1.R(), lait.R()
  efront.R() and cst.R() have been modified internally to continue to
  use empirical frequencies.  In addition, shrinkt.fun(), shrinkt.stat()
  and shrinkcat.stat() now have a new "lambda.freqs" option. 
  

		CHANGES IN `st' PACKAGE VERSION 1.2.0

- one-sample shrinkage CAT scores and paired shrinkage CAT scores are now
  implemented, as well as CAT scores with unequal variances. In addition,
  the regularization parameters lambda and lambda.var can now be specified.
- similary, estimation of one-sample shrinkage t-scores and paired 
  shrinkage t-scores is now available, as well as optional specification 
  of lambda.var regularization parameter.
- in addtion, computation of the paired student t statistics as well as 
  student t scores with unequal variance is now possible.


		CHANGES IN `st' PACKAGE VERSION 1.1.8

- changes to work with the updated centroids() and catscore()
  functions in sda version 1.2.2


		CHANGES IN `st' PACKAGE VERSION 1.1.7

- NAMESPACE file added


		CHANGES IN `st' PACKAGE VERSION 1.1.6

- small change in studentt.fun and diffmean.fun to avoid uncessary
  verbose output


		CHANGES IN `st' PACKAGE VERSION 1.1.5

- small changes in the code needed to work with the modified centroids 
  function from the sda package version 1.2.0 
- neighborhood options removed from shrinkcat.stat()
- shrinkcat.stat() now uses catscore() function from sda package
  (this is much faster than the version previously implemented in "st")


		CHANGES IN `st' PACKAGE VERSION 1.1.4

- added option "group.method".  Now groups are determined either
  by the correlation neighborhood (possibly overlapping groups) or 
  by the clusters on the correlation graph (disjoint groups). 


		CHANGES IN `st' PACKAGE VERSION 1.1.3

- added option "group.thresh" to allow the specification of 
  correlation neighborhoods around features and the computation
  of the grouped cat score.


		CHANGES IN `st' PACKAGE VERSION 1.1.2

- correlation-shared t-statistic of Tibshirani and Wasserman 
  (2006) added: new functions cst.stat() and cst.fun().
- correlation-predicted t-statistic of Lai (2008) added:
  new functions lait.stat(), lait.fun() and lai.tscore().


		CHANGES IN `st' PACKAGE VERSION 1.1.1

- rankprod.stat() and rankprod.fun() added for calculation of the
  two-sided rank products statistic.
- reference to Zuber and Strimmer (2009) added.
- small corrections in the help pages, to pass the more stringent
  checks on .Rd files introduced in R in January 2009.


		CHANGES IN `st' PACKAGE VERSION 1.1.0

- new functions shrinkcat.stat() und shrinkcat.fun() implementing
  a shrinkage estimate of the "correlation-adjusted t-score" described
  in Zuber and Strimmer (2009).
- part of the code was rewritten to share code with the "sda" package 
  (exploiting the link between discriminant analysis and gene ranking). 


		CHANGES IN `st' PACKAGE VERSION 1.0.3

- the class labels can now be specified as arbitrary factors,
  the argument L is not any more restricted to be a vector containing
  only 1s and  2s.


		CHANGES IN `st' PACKAGE VERSION 1.0.2

- some corrections and extensions have been made in the documentation,
  in particular, how to compute q-values and local FDR values
- shrinkt() now returns a proper vector (one for which is.vector() is TRUE).
- the license was changed from "GNU GPL 2 or later" to "GNU GPL 3 or later".


		CHANGES IN `st' PACKAGE VERSION 1.0.1

- reference to Opgen-Rhein and Strimmer (2007) updated.
- updated email address
- updated minimum R versions and version of corpcor package


		CHANGES IN `st' PACKAGE VERSION 1.0.0


This is the first standalone release (31 August 2006).

This package implements the "shrinkage t" statistic described
in Opgen-Rhein and Strimmer (2007).  It also offers a convenient
interface to a number of other regularized t-type statistics often
used in high-dimensional case-control studies.    
