NEWS

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GeneNet 1.2.17 (2025-04-07)

• updated Authors@R field.
• missing package anchors added in documentation.

GeneNet 1.2.16 (2021-11-14)

• updated URLs.

GeneNet 1.2.15 (2020-06-14)

• 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.

GeneNet 1.2.14 (2020-02-06)

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

GeneNet 1.2.13 (2015-08-02)

• 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.

GeneNet 1.2.12 (2015-01-21)

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

GeneNet 1.2.11 (2014-11-16)

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

GeneNet 1.2.10 (2014-07-28)

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

GeneNet 1.2.9 (2014-04-16)

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

GeneNet 1.2.8 (2013-09-15)

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

GeneNet 1.2.7 (2013-06-16)

• 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.

GeneNet 1.2.6 (2013-03-08)

• License file removed.
• Dependencies updated.

GeneNet 1.2.5 (2012-01-22)

• NAMESPACE file added.
• Dependencies updated.

GeneNet 1.2.4 (2009-10-11)

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

GeneNet 1.2.3 (2008-11-17)

• 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.

GeneNet 1.2.2 (2008-08-18)

• 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).

GeneNet 1.2.1 (2007-10-21)

• 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.

GeneNet 1.2.0 (2007-05-26)

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.

GeneNet 1.1.0 (2007-02-20)

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

GeneNet 1.0.1 (2006-08-18)

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

GeneNet 1.0.0 (2006-08-09)

• 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).