CHANGES IN VERSION 1.5
----------------------

USER VISIBLE CHANGES

    o added estimation of completion time for calculations via the 'estimateTime' argument

    o added progress reporting to the functions using parallel support

    o added qpUpdateCliquesRemoving() to update a clique list after an edge removal

    o added qpUnifRndAssociation() to generate correlations between -1 and +1 uniformly at random

    o added network reporting through qpPlotNetwork

    o added network reporting through qpTopPairs

    o added parallel computation of gene ontology enrichment calculations in qpFunctionalCoherence()

    o added the calculation of the generalized non-rejection rate through the function qpGenNrr()

    o updated the functions that work with covariance, correlations, adjacency and non-rejection rate matrices to employ more efficient matrix classes from the Matrix package

    o added a new function qpCov() and its man page to calculate sample covariance matrices returning them as 'dspMatrix' objects. Fixed some NAMESPACE and dependence issues

    o handling of covariance matrices as 'dspMatrix' objects via the recommended 'Matrix' package

    o added parallel computation of average non-rejection rates in qpAvgNrr() via snow and rlecuyer

    o added parallel computation of non-rejection rates in qpNrr() via snow and rlecuyer

    o qpFunctionalCoherence() now takes an input list of transcriptional regulator modules

BUG FIXES

    o removed unnecessary calls to INTEGER() and REAL() within long loops in the C code in order to speed it up

    o binary adjacency matrices (and not only logical ones) are now also handled by qpFunctionalCoherence()

CHANGES IN VERSION 1.3
----------------------

USER VISIBLE CHANGES

    o added a NEWS file

	  o fixed help page of qpCliqueNumber

	  o implemented the C code of the clique number lower bound.

	  o fixed the handling of user interruption during long calculations

	  o updated some help pages

	  o re-organization of the functions to sample synthetic data from
	  multivariate normal distributions

BUG FIXES

    o added ifnotfound=NA in mget call within .qpFilterByGO to avoid
    errors when Entrez Gene IDs are given that do not exist as keys

    o fixes on the documentation

    o added R_CheckUserInterrupt() to the C code of the IPF algorithm


CHANGES IN VERSION 1.1
----------------------

USER VISIBLE CHANGES

    o updated few details on the main package help page

    o added R_CheckUserInterrupt() to the heavy computations in C

    o changed default value of identicalQs parameters to TRUE

    o documentation mismatches fixed on some function arguments

NEW FEATURES

    o added the new calculation of NRR with identical Q subsets

BUG FIXES
    o fixed a minor bug on reporting progress of calculations

    o fixed a minor bug on identifying variable names on matrices


CHANGES IN VERSION 0.99
-----------------------

USER VISIBLE CHANGES

    o fixed package name in the CITATION file

    o the qpTxRegNet vignette has been modified in order to reduce memory
    requirements

    o add an import line to the DESCRIPTION file

    o remove quotes from the import calls in the NAMESPACE file

    o add a zzz.R file with a GOenv function to load variables GOTERM and
    GOBPPARENTS

    o modify qpFunctionalCoherence to properly load variables GOTERM and
    GOBPPARENTS in order to sort out their notes of "no visible binding"

    o remove braces from references in EcoliOxygen.Rd

    o changed LaTeX package mathptm to mathptmx in the qpTxRegNet vignette

    o turn the first letter of the package title into a capital letter

    o replace 'qp' by 'qpgraph' in the main package help file

    o name of the package changed from 'qp' to 'qpgraph'

    o the corresponding manual pages for these generic methods have been
    modified to comply with the S4 methods documentation guidelines.

    o added the possibility of passing an ExpressionSet, a data frame or a
    matrix of observations to the qpEdgeNrr function using S4 generics
    and qpEdgeNrr

    o added the possibility of passing an ExpressionSet, a data frame or a
    matrix of observations to the qpCItest function using S4 generics

    o introduction of S4 generics for qpNrr, qpAvgNrr, qpPAC, qpPCC, qpCItest

    o qpDscale is now exported to the user and a manual page has been created

    o malloc calls in C code have turned into R_malloc and the corresponding
    free calls have been removed

NEW FEATURES

    o functions qpNrr, qpAvgNrr and qpGraph admit now parameters 'pairup.i' and
    'pairup.j' that allow to restrict the pairs of variables on which we
    estimate the non-rejection rate (qpNrr and qpAvgNrr) or from which we derive
    a qp-graph given a threshold

    o a new function qpAnyGraph has been added in order to obtain an undirected
    graph by thresholding any matrix of pairwise measurements in an analogous
    way to the functionality of the function qpGraph

    o a new function qpFunctionalCoherence has been added to estimate
    functional coherence of the qpgraphs with respect to available GO
    annotations. This includes also a new private function .qpFilterbyGO

    o seeds for random number generations have been specified in a couple of
    places within the vignette qpTxRegNet in order to enforce reproducing exactly
    the same numbers under the random sampling schemes used in the estimation of
    non-rejection rates and when drawing random correlations for the random
    method

BUG FIXES

    o calloc and realloc calls in C code have turned into Calloc and Realloc
    and the corresponding free calls have been turned into Free calls

(start date: 20 October, 2008)
