RELEASE HISTORY OF GeneNet PACKAGE
             ========================================


		CHANGES IN GeneNet VERSION 1.2.16

- updated URLs.


		CHANGES IN GeneNet VERSION 1.2.15

- new option "stdprec" in ggm.simulate.pcor() to choose between 
  returning the positive definite standardized precision matrix
  or the corresponding partial correlation matrix with diagonal 1.


		CHANGES IN GeneNet VERSION 1.2.14

- bug-fix in documentation to fix warnings/error by R-devel.


 		CHANGES IN GeneNet VERSION 1.2.13

- added import statement as required by R-devel.
- removed dependency on igraph, as igraph now has too many
  subsequent mandatory dependencies (>20 packages).
- instead use we now use again the "graph" and "Rgraphviz" from Bioconductor
  for graph modeling and plotting. 
- All example scripts and related functions
  in GeneNet have been updated and modified accordingly.


  		CHANGES IN GeneNet VERSION 1.2.12

- maintainance update to fix bad URL (as requested by R core team).


  		CHANGES IN GeneNet VERSION 1.2.11

- the example files have been converted into R notebook format.
- change of maintainer email address.


  		CHANGES IN GeneNet VERSION 1.2.10

- change of maintainer email address.
- corrections to index.html file in inst/doc folder.


  		CHANGES IN GeneNet VERSION 1.2.9

- added import() statement in NAMESPACE file to get rid of warning
  of R 3.1.0.


  		CHANGES IN GeneNet VERSION 1.2.8

- small changes to get rid of warnings in R-devel
- updated dependencies


  		CHANGES IN GeneNet VERSION 1.2.7

- ggm.simulate.data() now uses eigen() to simulate multinormal data.
- No dependency on Rgraphviz any more. Instead, igraph is used for plotting.
- new function ggm.make.igraph() and network.make.igraph() to generate 
  igraph objects have been added.
- correspondingly, the old functions ggm.make.graph() and show.edge.weights() 
  are removed, and all examples have been adapted to igraph.


  		CHANGES IN GeneNet VERSION 1.2.6

- License file removed.
- Dependencies updated.


   		CHANGES IN GeneNet VERSION 1.2.5

- NAMESPACE file added.
- Dependencies updated.


   		CHANGES IN GeneNet VERSION 1.2.4

- small changes to pass the tests of R version 2.10.
- GeneNet now requires corpcor (>= 1.5.3) and longitudinal (>= 1.1.5).


   		CHANGES IN GeneNet VERSION 1.2.3

- small bug fixed in the plotting routine in ggm.test.edges().  
  In current versions of R you need to use dev.new() to open a new graphics device.

    		CHANGES IN GeneNet VERSION 1.2.2

- a small bug in ggm.make.dot() was corrected. Now variable names
  such as "1776837_at" can be plotted properly with graphviz 
  (this bug fix was kindly provided by Colin Gillespie, Newcastle).
  

     		CHANGES IN GeneNet VERSION 1.2.1


- a number of small internal changes were needed to adjust
  GeneNet to the new version of the fdrtool package (version 1.2.0).
- the licence was changed from "GNU GPL 2 or later" to "GNU GPL 3 or later".
- some parts of the documentation were updated.

	
     		CHANGES IN GeneNet VERSION 1.2.0


Newly added:
- this version implements the approach described in Opgen-Rhein and 
  Strimmer (2007) for estimating partially directed graphs.
  See the arbidopsis example script for illustration.
- new utility function extract.network() to simplify the extraction
  of significant edges.

Changes:
- the plot function ggm.make.dot() resp. network.make.dot() now
  produce dot code for partially directed graphs.
- the function ggm.plot.graph() was removed.
- all example scripts were updated accordingly.
- ggm.test.edges now has option "fdr" to allow to skip fdr 
  computations if necessary.


		CHANGES IN GeneNet VERSION 1.1.0

Newly added:
- arth800:         new example data from A. thaliana Affymetrix 
                   time series experiment
- ggm.make.dot:    utility function for network plotting 
                   (produces dot files for use with graphviz)
Removed:
- dcor0:           the density and distribution function for correlation
                   have been moved into the "fdrtool" package 
- cor.fit.mixture: this function is not necessary any more, as a similar
                   function is available in the "fdrtool" package

Changes:
- examples scripts were changed to include examples for A.thaliana
  and for plotting using ggm.make.dot() 
- the function ggm.test.edges() was changed internally to use fdrtool()
  rather than cor.fit.mixture() and locfdr() 
- all fdr/Fdr calculations for edge testing are now done using 
  the "fdrtool" package, so the dependency from "locfdr" was removed



		CHANGES IN GeneNet VERSION 1.0.1


- function cor.fit.mixture() was adapted to API changes
  in "locfdr" package
- new dependency requirement: locfdr >= 1.1-1


		CHANGES IN GeneNet VERSION 1.0.0


This is the first standalone release (9 August 2006).
Previously, the functions available in this package were part of
the GeneTS package (version 2.10.2).