| NEWS | R Documentation |
Bugfixes in plotAttractors() and plotSequence().
Fixed compatibility issues with R 3.0 alpha.
Support for SBML: loadSBML() and toSBML() import from and export to SBML documents with the sbml-qual extension package.
saveNetwork() stores networks in the BoolNet file format.
The DNF generator employed by generateRandomNKNetwork() and simplifyNetwork() (as well as by the new functions saveNetwork() and toSBML()) now supports minimizing the canonical DNFs.
BoolNet now supports the modified interface of igraph 0.6 in all plotting functions, but is still compatible with older versions of igraph.
loadNetwork() supports comment lines in the network files.
generateTimeSeries() generates random state sequences from an existing network.
plotSequence() and sequenceToLaTeX() plot and export sequences of states similar to plotAttractors() and attractorsToLaTeX().
getAttractorSequence() extracts the states of a single synchronous attractor from an attractor information structure as a data frame.
generateState() provides a simple way to specify network states using partial assignments.
getPathToAttractor() has an additional parameter includeAttractorStates specifying which attractor states should be included in the path. The default behaviour has been changed to include all attractor states.
generateRandomNKNetwork() now supports the generation of networks using specific classes of functions. For this purpose, it has two new parameters validationFunction and failureIterations.
By default, loadNetwork() no longer changes gene names to lower case. If this behaviour is desired, it can be reactivated using the new lowercaseGenes parameter.
stateTransition() now names the state vector using the gene names.
plotAttractors() has a new parameter drawLegend to disable the legend.
The randomChainLength parameter of getAttractors() now defaults to 10000.
getAttractors(), reconstructNetwork() and markovSimulation() can now be interrupted by the user.