CHANGES IN VERSION 1.53.2 (2021-07-28)
o rmarkdown added as a dependency to fix Bioc build
CHANGES IN VERSION 1.5.1 (2012-06-28)
o Removed ICMg functionality due to C code errors with BioC
o Downgraded version number to sync with bioc (yes, not very good practice, sorry)
CHANGES IN VERSION 1.9.17 (2012-06-28)
o added remove.negative.edges function
o added positive.edges argument to detect.responses
CHANGES IN VERSION 1.9.15 (2012-05-23)
o igraph dependency moved to igraph0
CHANGES IN VERSION 1.9.14 (2012-05-14)
o dmt added to dependencies
CHANGES IN VERSION 1.9.13 (2012-05-04)
USER-VISIBLE CHANGES
o added PlotMixtureMultivariate function
CHANGES IN VERSION 1.9.12 (2012-05-03)
USER-VISIBLE CHANGES
o added parallelization on update.model.pair step
BUG FIXES
o removed merge updates for potential subnet merges that would exceed max size
CHANGES IN VERSION 1.9.10 (2012-04-30)
SIGNIFICANT USER-VISIBLE CHANGES
o added bic.threshold option in detect responses and downstream functions
o latent.class.analysis function replaced with mixture.model
BUG FIXES
o Rd conflicts resolved
CHANGES IN VERSION 1.9.07 (2012-04-25)
SIGNIFICANT USER-VISIBLE CHANGES
o changed all documentation into Roxygen
o added bic.mixture.univariate function
o added argument mixture.method in detect.responses and to consecutive downstream functions
BUG FIXES
o added information.criterion option to edge.delta costind.ab calculation
o "c.max <- max.responses - 1"--> "c.max <- max.responses" in vdp.mixt
CHANGES IN VERSION 1.9.05 (2012-04-24)
o added the plot.mode = "pca" in plot.responses function
o added tests/mclust-mixture.R example
CHANGES IN VERSION 1.9.04 (2012-04-21)
o removed the redundant network.nodes parameter from independent.models input
CHANGES IN VERSION 1.7.38 (2012-03-28)
SIGNIFICANT USER-VISIBLE CHANGES
o 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.
o 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
o merged netresponse.visualization package in the netresponse main
package
o added mode = hard in sample2response function
o plot.associations -> plotAssociations
o plot.pca -> plotPCA
o get.gofz -> getqofz
BUG FIXES
o changed dependency RBGL into RColorBrewer
o changed dependencies multicore and doMC into parallel
o Modified mk.hp.posterior so as to accommodate 'max number of
responses' (c.max) option. Validations in tests/vdpmixture.R
ok
o now allowing max.subnet.size = 1 in detect.responses
o order.responses: fixed minor bug which occurs when no enrichments are detected
CHANGES IN VERSION 1.7.34 (2012-03-28)
o changed dependency RBGL into RColorBrewer
CHANGES IN VERSION 1.7.33 (2012-03-13)
o Modified mk.hp.posterior so as to accommodate 'max number of
responses' (c.max) option. Validations in tests/vdpmixture.R
ok
CHANGES IN VERSION 1.7.32 (2012-02-21)
o 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.
CHANGES IN VERSION 1.7.03 (2012-02-02)
o merged netresponse.visualization package in the netresponse main
package
CHANGES IN VERSION 1.7.02 (2012-02-01)
o switched to R-2.14.1
o now allowing max.subnet.size = 1 in detect.responses
o order.responses: fixed minor bug which occurs when no enrichments are detected
o added mode = hard in sample2response function
o 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
o plot.associations -> plotAssociations
o plot.pca -> plotPCA
o get.gofz -> getqofz
CHANGES IN VERSION 1.5.14 (2011-10-28)
o removed compiler package and functions as they are included in
R-2.14
CHANGES IN VERSION 1.5.12 (2011-06-29)
o added options for read.network
CHANGES IN VERSION 1.5.11 (2011-06-28)
o compiler added
o corrected weight estimation from vdp.mixt
CHANGES IN VERSION 1.5.09 (2011-06-13)
o updated toydata
o compute.weights: now operating in log-domain to avoid occasional
floating point errors
CHANGES IN VERSION 1.5.08 (2011-05-27)
o added plot.pca function to visualize subnets in 2D with ellipsoid
confidence intervals and annotation colors
CHANGES IN VERSION 1.5.04 (2011-05-27)
BUG FIXES
o fixed discretization NAMESPACE issues
CHANGES IN VERSION 1.5.02 (2011-05-18)
SIGNIFICANT USER-VISIBLE CHANGES
o 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
o changed AIC to default information criterion (previously
BIC). Both remain to be available through information.criterion
argument
CHANGES IN VERSION 1.3.43 (2011-04-13)
o updated vignette
CHANGES IN VERSION 1.3.41 (2011-04-08)
o updated documentation for ICMg functions
CHANGES IN VERSION 1.3.39 (2011-04-07)
o optimized the code (vdp.mixt, compute.weight,
detect.responses:subgraph)
CHANGES IN VERSION 1.3.37 (2011-04-06)
o read.sif function improved
CHANGES IN VERSION 1.3.36 (2011-04-04)
SIGNIFICANT USER-VISIBLE CHANGES
o added default speedups (speedup, speedup.max.edges options in
detect.responses)
CHANGES IN VERSION 1.3.35 (2011-04-04)
o added functions for the ICMg (Interaction Component Model for finding
Gene modules) package by Juuso Parkkinen
CHANGES IN VERSION 1.1.34 (2011-04-03)
o 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)
CHANGES IN VERSION 1.1.33 (2011-03-30)
o added various information criteria for model selection to
detect.responses and find.similar.features (AIC, AICc, BIC)
o added vignette PDF windows buildcheck seems to require it
CHANGES IN VERSION 1.1.31 (2011-03-26)
o polished vignette
o optimized memory usage
CHANGES IN VERSION 1.1.29 (2011-03-23)
SIGNIFICANT USER-VISIBLE CHANGES
o package: xadded support for reading in SIF network files through read.sif function
o 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
o within detect.responses now handling the network through edge
list; this is considerably more memory-efficient than previous
implementation
o added dependencies to graph and igraph packages
CHANGES IN VERSION 1.1.28 (2011-03-23)
o 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.
CHANGES IN VERSION 1.1.27 (2011-03-22)
o removed nodes and samples from NetResponseModel output
CHANGES IN VERSION 1.1.26 (2011-03-22)
o moved NetResponseModel functions in AllGenerics.R
o removed intermediate matrices from detect.responses.R (costs,
Nparams, bic.ind, bic.joint)
o added two fields in pick.model.parameters: free.energy and Nparams
o added internal function bic for bic calculations
o removed costs from NetResponseModel output
CHANGES IN VERSION 1.1.22 (2011-03-13)
USER-VISIBLE CHANGES
o added support for sparse matrices with the Matrix package (from
CRAN)
CHANGES IN VERSION 1.1.19 (2011-01-25)
BUG FIXES
o now providing names for the elements in model@params list
USER-VISIBLE CHANGES
o renamed result.stats into model.stats
o 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
o 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
CHANGES IN VERSION 1.1.18 (2011-01-25)
USER-VISIBLE CHANGES
o in get.subnets function now using default min.responses=2
and subnet.size=2 (at least 2 genes in a subnetwork)
o added 'subnets' field to the NetResponseModel class. This lists
the subnetworks by feature names.
BUG FIXES
o NetResponseModel class now returns the original network used in
the experiment (diagonal set to zero, however), previous version
returned the agglomerated network
NEW FEATURES
o added functions order.responses and order.samples
BUG FIXES
o in result.stats function corrected the minimum responses filtering
part
CHANGES IN VERSION 1.1.17 (2011-01-19)
o 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.
CHANGES IN VERSION 1.1.16 (2011-01-16)
BUG FIXES
o 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
CHANGES IN VERSION 1.1.15 (2011-01-15)
BUG FIXES
o in split.qofz minimum cluster size check added. clusters smaller
than min.size cannot be splitted any more; this caused problems
CHANGES IN VERSION 1.1.13 (2011-01-07)
BUG FIXES
o in split.qofz speedup function added the line 'indices <-
indices[rinds]'. Without this, an erroneous subset is selected and
the program will eventually fail.
CHANGES IN VERSION 1.1.12 (2011-01-02)
BUG FIXES
o 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
CHANGES IN VERSION 0.99.3 (2010-10-03)
o 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.
o Added project URL address to DESCRIPTION file
o Added 'speedup' option to vdp.mixt
CHANGES IN VERSION 0.99.2 (2010-09-28)
o 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
o changed the output format of function vdp.mixt to focus on variables
relevant for the end user.
o updated toydata and man pages according to the change to vdp.mixt output
o added test/demo.R testing and demonstrating vdp.mixt
CHANGES IN VERSION 0.99.0 (2010-09-23)
o Improved man pages and examples
o Removed greedy and find.best.splitting from user-visible function
space
o Added pre-calculated NetResponseModel object to toydata
CHANGES IN VERSION 0.4.4 (2010-09-17)
o Initial release.