Changes in version 1.2.17 (2025-04-07)                 

    o   updated Authors@R field.

    o   missing package anchors added in documentation.

                 Changes in version 1.2.16 (2021-11-14)                 

    o   updated URLs.

                 Changes in version 1.2.15 (2020-06-14)                 

    o   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 version 1.2.14 (2020-02-06)                 

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

                 Changes in version 1.2.13 (2015-08-02)                 

    o   added import statement as required by R-devel.

    o   removed dependency on igraph, as igraph now has too many
	subsequent mandatory dependencies (>20 packages).

    o   instead use we now use again the "graph" and "Rgraphviz" from Bioconductor
	for graph modeling and plotting. 

    o   All example scripts and related functions
	in GeneNet have been updated and modified accordingly.

                 Changes in version 1.2.12 (2015-01-21)                 

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

                 Changes in version 1.2.11 (2014-11-16)                 

    o   the example files have been converted into R notebook format.

    o   change of maintainer email address.

                 Changes in version 1.2.10 (2014-07-28)                 

    o   change of maintainer email address.

    o   corrections to index.html file in inst/doc folder.

                 Changes in version 1.2.9 (2014-04-16)                  

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

                 Changes in version 1.2.8 (2013-09-15)                  

    o   small changes to get rid of warnings in R-devel

    o   updated dependencies

                 Changes in version 1.2.7 (2013-06-16)                  

    o   ggm.simulate.data() now uses eigen() to simulate multinormal data.

    o   No dependency on Rgraphviz any more. Instead, igraph is used for plotting.

    o   new function ggm.make.igraph() and network.make.igraph() to generate 
	igraph objects have been added.

    o   correspondingly, the old functions ggm.make.graph() and show.edge.weights() 
	are removed, and all examples have been adapted to igraph.

                 Changes in version 1.2.6 (2013-03-08)                  

    o   License file removed.

    o   Dependencies updated.

                 Changes in version 1.2.5 (2012-01-22)                  

    o   NAMESPACE file added.

    o   Dependencies updated.

                 Changes in version 1.2.4 (2009-10-11)                  

    o   small changes to pass the tests of R version 2.10.

    o   GeneNet now requires corpcor (>= 1.5.3) and longitudinal (>= 1.1.5).

                 Changes in version 1.2.3 (2008-11-17)                  

    o   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 version 1.2.2 (2008-08-18)                  

    o   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 version 1.2.1 (2007-10-21)                  

    o   a number of small internal changes were needed to adjust
	GeneNet to the new version of the fdrtool package (version 1.2.0).

    o   the licence was changed from "GNU GPL 2 or later" to "GNU GPL 3 or later".

    o   some parts of the documentation were updated.

                 Changes in version 1.2.0 (2007-05-26)                  

Newly added

    o   this version implements the approach described in Opgen-Rhein and 
	Strimmer (2007) for estimating partially directed graphs.
	See the arbidopsis example script for illustration.

    o   new utility function extract.network() to simplify the extraction
	of significant edges.

Changes

    o   the plot function ggm.make.dot() resp. network.make.dot() now
	produce dot code for partially directed graphs.

    o   the function ggm.plot.graph() was removed.

    o   all example scripts were updated accordingly.

    o   ggm.test.edges now has option "fdr" to allow to skip fdr 
	computations if necessary.

                 Changes in version 1.1.0 (2007-02-20)                  

Newly added

    o   arth800:         new example data from A. thaliana Affymetrix 
	                 time series experiment

    o   ggm.make.dot:    utility function for network plotting 
	                 (produces dot files for use with graphviz)

Removed

    o   dcor0:           the density and distribution function for correlation
	                 have been moved into the "fdrtool" package 

    o   cor.fit.mixture: this function is not necessary any more, as a similar
	                 function is available in the "fdrtool" package

Changes

    o   examples scripts were changed to include examples for A.thaliana
	and for plotting using ggm.make.dot() 

    o   the function ggm.test.edges() was changed internally to use fdrtool()
	rather than cor.fit.mixture() and locfdr() 

    o   all fdr/Fdr calculations for edge testing are now done using 
	the "fdrtool" package, so the dependency from "locfdr" was removed

                 Changes in version 1.0.1 (2006-08-18)                  

    o   function cor.fit.mixture() was adapted to API changes
	in "locfdr" package

    o   new dependency requirement: locfdr >= 1.1-1

                 Changes in version 1.0.0 (2006-08-09)                  

    o   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).