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).