NEWS
GeneNet 1.2.17 (2025-04-07)
- updated Authors@R field.
- missing package anchors added in documentation.
GeneNet 1.2.16 (2021-11-14)
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).