Version: 1.53.2 Date: 2021-07-28 Text: rmarkdown added as a dependency to fix Bioc build Version: 1.5.1 Date: 2012-06-28 Text: Removed ICMg functionality due to C code errors with BioC Version: 1.5.1 Date: 2012-06-28 Text: Downgraded version number to sync with bioc (yes, not very good practice, sorry) Version: 1.9.17 Date: 2012-06-28 Text: added remove.negative.edges function Version: 1.9.17 Date: 2012-06-28 Text: added positive.edges argument to detect.responses Version: 1.9.15 Date: 2012-05-23 Text: igraph dependency moved to igraph0 Version: 1.9.14 Date: 2012-05-14 Text: dmt added to dependencies Version: 1.9.13 Date: 2012-05-04 Category: USER-VISIBLE CHANGES Text: added PlotMixtureMultivariate function Version: 1.9.12 Date: 2012-05-03 Category: USER-VISIBLE CHANGES Text: added parallelization on update.model.pair step Version: 1.9.12 Date: 2012-05-03 Category: BUG FIXES Text: removed merge updates for potential subnet merges that would exceed max size Version: 1.9.10 Date: 2012-04-30 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added bic.threshold option in detect responses and downstream functions Version: 1.9.10 Date: 2012-04-30 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: latent.class.analysis function replaced with mixture.model Version: 1.9.10 Date: 2012-04-30 Category: BUG FIXES Text: Rd conflicts resolved Version: 1.9.07 Date: 2012-04-25 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: changed all documentation into Roxygen Version: 1.9.07 Date: 2012-04-25 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added bic.mixture.univariate function Version: 1.9.07 Date: 2012-04-25 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added argument mixture.method in detect.responses and to consecutive downstream functions Version: 1.9.07 Date: 2012-04-25 Category: BUG FIXES Text: added information.criterion option to edge.delta costind.ab calculation Version: 1.9.07 Date: 2012-04-25 Category: BUG FIXES Text: "c.max <- max.responses - 1"--> "c.max <- max.responses" in vdp.mixt Version: 1.9.05 Date: 2012-04-24 Text: added the plot.mode = "pca" in plot.responses function Version: 1.9.05 Date: 2012-04-24 Text: added tests/mclust-mixture.R example Version: 1.9.04 Date: 2012-04-21 Text: removed the redundant network.nodes parameter from independent.models input Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added the option to ignore network in detect.responses (netw=NULL); then the methods assumes fully connected network. Without speedups the performance may be very slow. Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added (optional) initial mutual information based filtering of the network edges also in the first stage where pairwise similarities are calculated for all node pairs This can give considerable speedups with large networks Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: merged netresponse.visualization package in the netresponse main package Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added mode = hard in sample2response function Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: plot.associations -> plotAssociations Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: plot.pca -> plotPCA Version: 1.7.38 Date: 2012-03-28 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: get.gofz -> getqofz Version: 1.7.38 Date: 2012-03-28 Category: BUG FIXES Text: changed dependency RBGL into RColorBrewer Version: 1.7.38 Date: 2012-03-28 Category: BUG FIXES Text: changed dependencies multicore and doMC into parallel Version: 1.7.38 Date: 2012-03-28 Category: BUG FIXES Text: Modified mk.hp.posterior so as to accommodate 'max number of responses' (c.max) option. Validations in tests/vdpmixture.R ok Version: 1.7.38 Date: 2012-03-28 Category: BUG FIXES Text: now allowing max.subnet.size = 1 in detect.responses Version: 1.7.38 Date: 2012-03-28 Category: BUG FIXES Text: order.responses: fixed minor bug which occurs when no enrichments are detected Version: 1.7.34 Date: 2012-03-28 Text: changed dependency RBGL into RColorBrewer Version: 1.7.33 Date: 2012-03-13 Text: Modified mk.hp.posterior so as to accommodate 'max number of responses' (c.max) option. Validations in tests/vdpmixture.R ok Version: 1.7.32 Date: 2012-02-21 Text: added the option to ignore network in detect.responses (netw=NULL); then the methods assumes fully connected network. Without speedups the performance may be very slow. Version: 1.7.03 Date: 2012-02-02 Text: merged netresponse.visualization package in the netresponse main package Version: 1.7.02 Date: 2012-02-01 Text: switched to R-2.14.1 Version: 1.7.02 Date: 2012-02-01 Text: now allowing max.subnet.size = 1 in detect.responses Version: 1.7.02 Date: 2012-02-01 Text: order.responses: fixed minor bug which occurs when no enrichments are detected Version: 1.7.02 Date: 2012-02-01 Text: added mode = hard in sample2response function Version: 1.7.02 Date: 2012-02-01 Text: added (optional) initial mutual information based filtering of the network edges also in the first stage where pairwise similarities are calculated for all node pairs This can give considerable speedups with large networks Version: 1.7.02 Date: 2012-02-01 Text: plot.associations -> plotAssociations Version: 1.7.02 Date: 2012-02-01 Text: plot.pca -> plotPCA Version: 1.7.02 Date: 2012-02-01 Text: get.gofz -> getqofz Version: 1.5.14 Date: 2011-10-28 Text: removed compiler package and functions as they are included in R-2.14 Version: 1.5.12 Date: 2011-06-29 Text: added options for read.network Version: 1.5.11 Date: 2011-06-28 Text: compiler added Version: 1.5.11 Date: 2011-06-28 Text: corrected weight estimation from vdp.mixt Version: 1.5.09 Date: 2011-06-13 Text: updated toydata Version: 1.5.09 Date: 2011-06-13 Text: compute.weights: now operating in log-domain to avoid occasional floating point errors Version: 1.5.08 Date: 2011-05-27 Text: added plot.pca function to visualize subnets in 2D with ellipsoid confidence intervals and annotation colors Version: 1.5.04 Date: 2011-05-27 Category: BUG FIXES Text: fixed discretization NAMESPACE issues Version: 1.5.02 Date: 2011-05-18 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added speedup option speedup.max.edges in detect.responses. To consider only this many most similar neighborghs in merging, similarity is evaluated by empirical mutual information estimate with sqrt(n) bins where n is data sample size Version: 1.5.02 Date: 2011-05-18 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: changed AIC to default information criterion (previously BIC). Both remain to be available through information.criterion argument Version: 1.3.43 Date: 2011-04-13 Text: updated vignette Version: 1.3.41 Date: 2011-04-08 Text: updated documentation for ICMg functions Version: 1.3.39 Date: 2011-04-07 Text: optimized the code (vdp.mixt, compute.weight, detect.responses:subgraph) Version: 1.3.37 Date: 2011-04-06 Text: read.sif function improved Version: 1.3.36 Date: 2011-04-04 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: added default speedups (speedup, speedup.max.edges options in detect.responses) Version: 1.3.35 Date: 2011-04-04 Text: added functions for the ICMg (Interaction Component Model for finding Gene modules) package by Juuso Parkkinen Version: 1.1.34 Date: 2011-04-03 Text: fixed a bug in updatePosterior which caused halt; now trying to increase implicit noise for calculating free energy, if this does not help, merging of the investigated subnetwork pair is prevented (previously all calculations were stopped at this point, which is not practical) Version: 1.1.33 Date: 2011-03-30 Text: added various information criteria for model selection to detect.responses and find.similar.features (AIC, AICc, BIC) Version: 1.1.33 Date: 2011-03-30 Text: added vignette PDF windows buildcheck seems to require it Version: 1.1.31 Date: 2011-03-26 Text: polished vignette Version: 1.1.31 Date: 2011-03-26 Text: optimized memory usage Version: 1.1.29 Date: 2011-03-23 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: package: xadded support for reading in SIF network files through read.sif function Version: 1.1.29 Date: 2011-03-23 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: detect.responses: added support for igraph and graphNEL network formats; in detect.responses output the network is now also outputted in graphNEL format. This is more memory-efficient than previous implementation. Version: 1.1.29 Date: 2011-03-23 Category: OTHER CHANGES Text: within detect.responses now handling the network through edge list; this is considerably more memory-efficient than previous implementation Version: 1.1.29 Date: 2011-03-23 Category: OTHER CHANGES Text: added dependencies to graph and igraph packages Version: 1.1.28 Date: 2011-03-23 Text: made mixture density functions visible in NAMESPACE as this seems to be required in the new R version even if the functions are used internally. Version: 1.1.27 Date: 2011-03-22 Text: removed nodes and samples from NetResponseModel output Version: 1.1.26 Date: 2011-03-22 Text: moved NetResponseModel functions in AllGenerics.R Version: 1.1.26 Date: 2011-03-22 Text: removed intermediate matrices from detect.responses.R (costs, Nparams, bic.ind, bic.joint) Version: 1.1.26 Date: 2011-03-22 Text: added two fields in pick.model.parameters: free.energy and Nparams Version: 1.1.26 Date: 2011-03-22 Text: added internal function bic for bic calculations Version: 1.1.26 Date: 2011-03-22 Text: removed costs from NetResponseModel output Version: 1.1.22 Date: 2011-03-13 Category: USER-VISIBLE CHANGES Text: added support for sparse matrices with the Matrix package (from CRAN) Version: 1.1.19 Date: 2011-01-25 Category: BUG FIXES Text: now providing names for the elements in model@params list Version: 1.1.19 Date: 2011-01-25 Category: USER-VISIBLE CHANGES Text: renamed result.stats into model.stats Version: 1.1.19 Date: 2011-01-25 Category: USER-VISIBLE CHANGES Text: now NetResponseModel also return the recalculated models for the responses. No need to recalculate them which speeds up analysis of the end results. Also useful since the result is not completely deterministic due to stochastic initializations in model learning etc., and relearning the models can sometimes produce slightly different results. Version: 1.1.19 Date: 2011-01-25 Category: NEW FEATURE Text: added find.similar.features function which can be used to find features (genes) that are similar to the subnetwork but not directly interacting with it Version: 1.1.18 Date: 2011-01-25 Category: USER-VISIBLE CHANGES Text: in get.subnets function now using default min.responses=2 and subnet.size=2 (at least 2 genes in a subnetwork) Version: 1.1.18 Date: 2011-01-25 Category: USER-VISIBLE CHANGES Text: added 'subnets' field to the NetResponseModel class. This lists the subnetworks by feature names. Version: 1.1.18 Date: 2011-01-25 Category: BUG FIXES Text: NetResponseModel class now returns the original network used in the experiment (diagonal set to zero, however), previous version returned the agglomerated network Version: 1.1.18 Date: 2011-01-25 Category: NEW FEATURES Text: added functions order.responses and order.samples Version: 1.1.18 Date: 2011-01-25 Category: BUG FIXES Text: in result.stats function corrected the minimum responses filtering part Version: 1.1.17 Date: 2011-01-19 Text: users can now give the expression data D in either matrix or data.frame format to detect.responses function, which will automatically convert non-matrix inputs into matrix format. Version: 1.1.16 Date: 2011-01-16 Category: BUG FIXES Text: in the last step of the merging stage the network reduced into a numeric which caused error, now corrected by rejecting further operations with completely merged nets in detect.responses Version: 1.1.15 Date: 2011-01-15 Category: BUG FIXES Text: in split.qofz minimum cluster size check added. clusters smaller than min.size cannot be splitted any more; this caused problems Version: 1.1.13 Date: 2011-01-07 Category: BUG FIXES Text: in split.qofz speedup function added the line 'indices <- indices[rinds]'. Without this, an erroneous subset is selected and the program will eventually fail. Version: 1.1.12 Date: 2011-01-02 Category: BUG FIXES Text: in internals.R some functions (mk.qOFz, mk.E.log.q.p.eta, mk.free.energy, mk.hp.posterior, mk.hp.prior, mk.log.lambda) were defined multiple times. Removed multiple copies. Also ensuring that no empty clusters are returned; this caused problems in split.qOFz and updatePosterior Version: 1.1.12 Date: 2011-01-02 Category: OTHER CHANGES Text: Version: 1.1.12 Date: 2011-01-02 Category: o Code has been optimized for speed Text: Version: 1.1.12 Date: 2011-01-02 Category: o updated citation info Text: Version: 0.99.3 Date: 2010-10-03 Text: Added slots 'datamatrix' and 'network' into NetResponseModel class. These are used to store the input data used to learn the model. Subsequently, removed data inputs from functions such as get.parameters etc. since now they can fetch the data matrix directly from the model object. Version: 0.99.3 Date: 2010-10-03 Text: Added project URL address to DESCRIPTION file Version: 0.99.3 Date: 2010-10-03 Text: Added 'speedup' option to vdp.mixt Version: 0.99.2 Date: 2010-09-28 Text: Fixed bug in C code. The previous version had convergence problems related to PCA initialization of component split during stick-breaking process, and mixture component centroids were subsequently not retrieved optimally Version: 0.99.2 Date: 2010-09-28 Text: changed the output format of function vdp.mixt to focus on variables relevant for the end user. Version: 0.99.2 Date: 2010-09-28 Text: updated toydata and man pages according to the change to vdp.mixt output Version: 0.99.2 Date: 2010-09-28 Text: added test/demo.R testing and demonstrating vdp.mixt Version: 0.99.0 Date: 2010-09-23 Text: Improved man pages and examples Version: 0.99.0 Date: 2010-09-23 Text: Removed greedy and find.best.splitting from user-visible function space Version: 0.99.0 Date: 2010-09-23 Text: Added pre-calculated NetResponseModel object to toydata Version: 0.4.4 Date: 2010-09-17 Text: Initial release.