/usr/lib/R/site-library/BoolNet/NEWS.Rd is in r-cran-boolnet 1.61-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 | \name{NEWS}
\title{NEWS file for the \pkg{BoolNet} package}
\section{Changes in version 1.61}{
\subsection{Modified functions}{
\itemize{
\item{Bugfixes in \code{plotAttractors()} and \code{plotSequence()}.}
\item{Fixed compatibility issues with R 3.0 alpha.}
}
}
}
\section{Changes in version 1.60}{
\subsection{New functions}{
\itemize{
\item{Support for SBML: \code{loadSBML()} and \code{toSBML()} import from and export to SBML documents with the \code{sbml-qual} extension package.}
\item{\code{saveNetwork()} stores networks in the \pkg{BoolNet} file format.}
}
}
\subsection{Modified functions}{
\itemize{
\item{The DNF generator employed by \code{generateRandomNKNetwork()} and \code{simplifyNetwork()} (as well as by the new functions \code{saveNetwork()} and \code{toSBML()}) now supports minimizing the canonical DNFs.}
}
}
}
\section{Changes in version 1.51}{
\subsection{Modified functions}{
\itemize{
\item{\pkg{BoolNet} now supports the modified interface of \pkg{igraph} 0.6 in all plotting functions, but is still compatible with older versions of \pkg{igraph}.}
\item{\code{loadNetwork()} supports comment lines in the network files.}
}
}
}
\section{Changes in version 1.50}{
\subsection{New functions}{
\itemize{
\item{\code{generateTimeSeries()} generates random state sequences from an existing network.}
\item{\code{plotSequence()} and \code{sequenceToLaTeX()} plot and export sequences of states similar to \code{plotAttractors()} and \code{attractorsToLaTeX()}.}
\item{\code{getAttractorSequence()} extracts the states of a single synchronous attractor from an attractor information structure as a data frame.}
\item{\code{generateState()} provides a simple way to specify network states using partial assignments.}
}
}
\subsection{Modified functions}{
\itemize{
\item{\code{getPathToAttractor()} has an additional parameter \code{includeAttractorStates} specifying which attractor states should be included in the path. The default behaviour has been changed to include all attractor states.}
\item{\code{generateRandomNKNetwork()} now supports the generation of networks using specific classes of functions. For this purpose, it has two new parameters \code{validationFunction} and \code{failureIterations}.}
\item{By default, \code{loadNetwork()} no longer changes gene names to lower case. If this behaviour is desired, it can be reactivated using the new \code{lowercaseGenes} parameter.}
\item{\code{stateTransition()} now names the state vector using the gene names.}
\item{\code{plotAttractors()} has a new parameter \code{drawLegend} to disable the legend.}
\item{The \code{randomChainLength} parameter of \code{getAttractors()} now defaults to 10000.}
\item{\code{getAttractors()}, \code{reconstructNetwork()} and \code{markovSimulation()} can now be interrupted by the user.}
}
}
}
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