NEWS

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netresponse 1.53.2 (2021-07-28)

• rmarkdown added as a dependency to fix Bioc build

netresponse 1.9.17 (2012-06-28)

• added remove.negative.edges function
• added positive.edges argument to detect.responses

netresponse 1.9.15 (2012-05-23)

• igraph dependency moved to igraph0

netresponse 1.9.14 (2012-05-14)

• dmt added to dependencies

netresponse 1.9.13 (2012-05-04)

USER-VISIBLE CHANGES

• added PlotMixtureMultivariate function

netresponse 1.9.12 (2012-05-03)

USER-VISIBLE CHANGES

• added parallelization on update.model.pair step

BUG FIXES

• removed merge updates for potential subnet merges that would exceed max size

netresponse 1.9.10 (2012-04-30)

SIGNIFICANT USER-VISIBLE CHANGES

• added bic.threshold option in detect responses and downstream functions
• latent.class.analysis function replaced with mixture.model

BUG FIXES

• Rd conflicts resolved

netresponse 1.9.07 (2012-04-25)

SIGNIFICANT USER-VISIBLE CHANGES

• changed all documentation into Roxygen
• added bic.mixture.univariate function
• added argument mixture.method in detect.responses and to consecutive downstream functions

BUG FIXES

• added information.criterion option to edge.delta costind.ab calculation
• "c.max <- max.responses - 1"--> "c.max <- max.responses" in vdp.mixt

netresponse 1.9.05 (2012-04-24)

• added the plot.mode = "pca" in plot.responses function
• added tests/mclust-mixture.R example

netresponse 1.9.04 (2012-04-21)

• removed the redundant network.nodes parameter from independent.models input

netresponse 1.7.38 (2012-03-28)

SIGNIFICANT USER-VISIBLE CHANGES

• 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.
• 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
• merged netresponse.visualization package in the netresponse main package
• added mode = hard in sample2response function
• plot.associations -> plotAssociations
• plot.pca -> plotPCA
• get.gofz -> getqofz

BUG FIXES

• changed dependency RBGL into RColorBrewer
• changed dependencies multicore and doMC into parallel
• Modified mk.hp.posterior so as to accommodate 'max number of responses' (c.max) option. Validations in tests/vdpmixture.R ok
• now allowing max.subnet.size = 1 in detect.responses
• order.responses: fixed minor bug which occurs when no enrichments are detected

netresponse 1.7.34 (2012-03-28)

• changed dependency RBGL into RColorBrewer

netresponse 1.7.33 (2012-03-13)

• Modified mk.hp.posterior so as to accommodate 'max number of responses' (c.max) option. Validations in tests/vdpmixture.R ok

netresponse 1.7.32 (2012-02-21)

• 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.

netresponse 1.7.03 (2012-02-02)

• merged netresponse.visualization package in the netresponse main package

netresponse 1.7.02 (2012-02-01)

• switched to R-2.14.1
• now allowing max.subnet.size = 1 in detect.responses
• order.responses: fixed minor bug which occurs when no enrichments are detected
• added mode = hard in sample2response function
• 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
• plot.associations -> plotAssociations
• plot.pca -> plotPCA
• get.gofz -> getqofz

netresponse 1.5.14 (2011-10-28)

• removed compiler package and functions as they are included in R-2.14

netresponse 1.5.12 (2011-06-29)

• added options for read.network

netresponse 1.5.11 (2011-06-28)

• compiler added
• corrected weight estimation from vdp.mixt

netresponse 1.5.09 (2011-06-13)

• updated toydata
• compute.weights: now operating in log-domain to avoid occasional floating point errors

netresponse 1.5.08 (2011-05-27)

• added plot.pca function to visualize subnets in 2D with ellipsoid confidence intervals and annotation colors

netresponse 1.5.04 (2011-05-27)

BUG FIXES

• fixed discretization NAMESPACE issues

netresponse 1.5.02 (2011-05-18)

SIGNIFICANT USER-VISIBLE CHANGES

• 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
• changed AIC to default information criterion (previously BIC). Both remain to be available through information.criterion argument

netresponse 1.5.1 (2012-06-28)

• Removed ICMg functionality due to C code errors with BioC
• Downgraded version number to sync with bioc (yes, not very good practice, sorry)

netresponse 1.3.43 (2011-04-13)

• updated vignette

netresponse 1.3.41 (2011-04-08)

• updated documentation for ICMg functions

netresponse 1.3.39 (2011-04-07)

• optimized the code (vdp.mixt, compute.weight, detect.responses:subgraph)

netresponse 1.3.37 (2011-04-06)

• read.sif function improved

netresponse 1.3.36 (2011-04-04)

SIGNIFICANT USER-VISIBLE CHANGES

• added default speedups (speedup, speedup.max.edges options in detect.responses)

netresponse 1.3.35 (2011-04-04)

• added functions for the ICMg (Interaction Component Model for finding Gene modules) package by Juuso Parkkinen

netresponse 1.1.34 (2011-04-03)

• 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)

netresponse 1.1.33 (2011-03-30)

• added various information criteria for model selection to detect.responses and find.similar.features (AIC, AICc, BIC)
• added vignette PDF windows buildcheck seems to require it

netresponse 1.1.31 (2011-03-26)

• polished vignette
• optimized memory usage

netresponse 1.1.29 (2011-03-23)

SIGNIFICANT USER-VISIBLE CHANGES

• package: xadded support for reading in SIF network files through read.sif function
• 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.

OTHER CHANGES

• within detect.responses now handling the network through edge list; this is considerably more memory-efficient than previous implementation
• added dependencies to graph and igraph packages

netresponse 1.1.28 (2011-03-23)

• 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.

netresponse 1.1.27 (2011-03-22)

• removed nodes and samples from NetResponseModel output

netresponse 1.1.26 (2011-03-22)

• moved NetResponseModel functions in AllGenerics.R
• removed intermediate matrices from detect.responses.R (costs, Nparams, bic.ind, bic.joint)
• added two fields in pick.model.parameters: free.energy and Nparams
• added internal function bic for bic calculations
• removed costs from NetResponseModel output

netresponse 1.1.22 (2011-03-13)

USER-VISIBLE CHANGES

• added support for sparse matrices with the Matrix package (from CRAN)

netresponse 1.1.19 (2011-01-25)

BUG FIXES

• now providing names for the elements in model@params list

USER-VISIBLE CHANGES

• renamed result.stats into model.stats
• 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.

NEW FEATURE

• 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

netresponse 1.1.18 (2011-01-25)

USER-VISIBLE CHANGES

• in get.subnets function now using default min.responses=2 and subnet.size=2 (at least 2 genes in a subnetwork)
• added 'subnets' field to the NetResponseModel class. This lists the subnetworks by feature names.

BUG FIXES

• NetResponseModel class now returns the original network used in the experiment (diagonal set to zero, however), previous version returned the agglomerated network
• in result.stats function corrected the minimum responses filtering part

NEW FEATURES

• added functions order.responses and order.samples

netresponse 1.1.17 (2011-01-19)

• 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.

netresponse 1.1.16 (2011-01-16)

BUG FIXES

• 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

netresponse 1.1.15 (2011-01-15)

BUG FIXES

• in split.qofz minimum cluster size check added. clusters smaller than min.size cannot be splitted any more; this caused problems

netresponse 1.1.13 (2011-01-07)

BUG FIXES

• in split.qofz speedup function added the line 'indices <- indices[rinds]'. Without this, an erroneous subset is selected and the program will eventually fail.

netresponse 1.1.12 (2011-01-02)

BUG FIXES

• 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

OTHER CHANGES

o Code has been optimized for speed

o updated citation info

netresponse 0.99.3 (2010-10-03)

• 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.
• Added project URL address to DESCRIPTION file
• Added 'speedup' option to vdp.mixt

netresponse 0.99.2 (2010-09-28)

• 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
• changed the output format of function vdp.mixt to focus on variables relevant for the end user.
• updated toydata and man pages according to the change to vdp.mixt output
• added test/demo.R testing and demonstrating vdp.mixt

netresponse 0.99.0 (2010-09-23)

• Improved man pages and examples
• Removed greedy and find.best.splitting from user-visible function space
• Added pre-calculated NetResponseModel object to toydata

netresponse 0.4.4 (2010-09-17)

• Initial release.