Note: as of 2009/03/10, changes that lead to different calculational results are marked as DIFF.

2010/12/17: 0.99

	. Functions [bi]cor gain the ability to calculate cosine [bi]correlations, 
	  invoked using the argument cosine = TRUE. Similar functionality added 
	  to blockwise[Consensus]Modules and TOMsimilarityFromExpr. 
	  For most other functions using correlations, the argument corOptions can be 
	  used to request cosine correlations.
	. Corrected error message in function adjacency
	. Functions [bi]corAndPvalue now also return the number of
	  observations for each p-value

2010/11/12: 0.98

	. Bugfix in functions [bi]corAndPvalue that gave incorrect p-values
	  when input y = NULL
	. Functions [bi]corAndPvalue now also return the Student t statistic
	  from which the p-values are calculated. 
	. Function standardScreeningNumericTrait now accepts arguments corFnc
	  and corOptions

2010/10/29: 0.97

	. Functions [bi]corAndPvalue now also return the Fisher Z statistics.
	. Function adjacency can now calculate distance-based networks as well, 
	  via type="distance". Various distance functions and options can be used.
	. Functions signedKME and networkScreening now accept arguments cor
	  and corOptions that can be used to specify the correlation function
	  to be used in the calculations.
	. Argument 'y' in [bi]corAndPvalue now has a default value NULL
	. DIFF: displayed value of correlation p-value in function
	  verboseScatterplot is now based on Student distribution instead of
	  Fisher normal approximation. This change only affects plots.

2010/09/23: 0.96

	. New functions pquantile, pmean, pmedian for calculation of
	  "parallel" quantiles, means, and medians.
	. Functions cor and bicor now give a more descriptive error description when 
	  an argument with one dimension equal zero is passed to the functions.

2010/09/16: 0.95

	. More changes to function collapseRows: renamed arguments, changed defaults, 
	  code cleaned up and bugs fixed. The function collapseRows should still be
	  considered experimental.

2010/09/05: 0.94

	. DIFF: big fixed in modulePreservation that put incorrect input into
	  Zconnectivity.preservation which also affected Zsummary. We apologize
	  for this error.
	. Bug fixes in function collapseRows

2010/08/25: 0.93

	. modulePreservation now also calculates density and connectivity
	  statistics based on clustering coefficient and maximum adjacency
	  ratio.
	. New functions mutualInfoAdjacency and AUV2predicted provide basic
	  interfacing between mutual information methods and weighted networks
	. Minor cleanup of help files

2010/07/26: 0.92-3

	. Package file cleanup, nothing changed from user perspective

2010/07/14: 0.92-1

	. Bug in compiled calculation of adjacency fixed. This may have
	  affected calculations of TOM when TOMType = "signed". Apologies if
	  important results were affected.

2010/06/24: 0.92

	. DIFF: in modulePreservation, by default Zsummary is only calculated
	  from meanAdj, cor.kIM and cor.Adj.
	. DIFF: in modulePreservation, a new option includekMEallInSummary (default FALSE)
	  controls whether cor.kMEall should be included in summary statistis
	. output of modulePreservation now has names in permutationDetails to facilitate 
	  detailed studies of permutation results

2010/06/10: 0.91

	. DIFF: in modulePreservation, values of cor.kME, cor.kMEall and
	  meanSignAwarekME are now stripped of their sign, both in observed
	  values and in permutations. This is done because the eigengene may
	  flip sign between data sets, leading to artificially low
	  preservation scores. 
	. DIFF: p-values calculated by modulePreservation are now returned as logarithms in base 10
	  (previously they were returned as natural logarithms). Names of the returned components also
	  changed slightly to emphasize that the p-values are returned as logarithms.
	. Additional summarycolumns added to the output of modulePreservation 
	  for observed and permutation preservation statistics
	. Function collapseRows now selects a single probe to represent each gene

2010/06/05: 0.90

	. modulePreservation now also returns p-values and optionally the q-values corresponding to the
	  permutation Z scores
	. simulateDatExpr now sets (artificial) gene and sample names, for easier integration with some	
	  analysis functions (notably modulePreservation)
	. incompatibilities with new versions of R in exportNetworkTo[Visant,Cytoscape] fixed 
	. new function subsetTOM to efficiently calculate TOM among a subset
	  of network nodes 
	. bugs in vectorTOM fixed
	. DIFF: modulePreservation now limits the size of the gold module to
	  at most half the total number of genes in the comparison, to make
	  sampling and permutation calculations meaningful. This may slightly affect
	  calculated results for the gold module, but will not affect results of
	  any other modules.


2010/05/21: 0.89

	. DIFF: definition of cluster coefficient has been slightly changed,
	  which affects approximate conformity-based network concepts
	. new functions rankPvalue and metaZfunction
	. new function standardScreeningNumericTrait
	. bug in automatic labeling of axes in verboseBoxplot has been fixed
	. several help files added and updated
	. minor changes in standardScreeningBinaryTrait, standardScreeningCensoredTime
	. scaleFreeFitIndex now does not calculate a log(log(..)) based fit
	  that often led to errors
	. new function collapseRows by Jeremy Miller to convert probe-level
	  expression to gene-level expression

2010/05/07: 0.88-2

	. unnecessary dependence on package fields removed. 

2010/05/07: 0.88-1

	. DIFF: bug in cor(x) and bicor(x) fixed that produced incorrect results
	  when a column of x was all missing (NA). We aplogize for any incovenience
	  this error may have caused.

2010/03/17: 0.88

	. new functions corAndPvalue and bicorAndPvalue that calculate (bi)correlation p-values efficiently
	  for matrices of correlations


2010/02/19: 0.87

	. bicor gets a new argument pearsonFallback that lets the user specify 
	  the handling of cases with zero median absolute deviation that would
	  normally lead to NA values.
	. mergeCloseModules (and blockwise[Consensus]Modules) now more robust: 
	  works also in the case of a single module
	. DIFF: A bug was fixed that affected bicor(x) calculation with missing data on Windows
	  (calculations of 2-variable bicor, single-variable bicor without missing data, and any 
	   calculations where multi-threading is available [most platforms except Windows] were 
	   not affected by this bug). The bug caused some calculations to be a bit off. 
	   We apologize for any problems this may have caused.

2010/02/10: 0.86

	. bug in colQuantileC fixed.
	. EXPERIMENTAL: a major addition to modulePreservation now allows
	  module preservation calculations based on general adjacency matrices. 
	. bugfix in labelPoints fixes a warning message

2009/12/26: 0.85

	. DIFF: in modulePreservation, separability now correctly works for
	signed and signed hybrid networks.
	. modulePreservation gains argument to specify correlation function

2009/12/05: 0.84

	. new function spaste
	. addtions and corrections to help files
	. bugfix in standardScreeningCensoredTime
	. bugfix in blockwiseModules: module colors are now not scrambled when
	  some genes are excluded because they don't pass goodSamplesGenes
	. improved labelPoints: more consistent label offsets and fixed
	  meaning of 'offs' in help file

2009/11/24: 0.83-1

	. help cleaned up
	. Windows package now compatible with R-2.10

2009/11/22: 0.83

	. new function modulePreservation calculates module preservation
	  statistics between independent data sets
	. new dependence on package splines
	. new function labelPoints to semi-inteligently label points in a
	  scatterplot.
	. extended functions pickSoftThreshold, pickHardThreshold
	. minor bugfix in scaleFreePlot
	. new function standardScreeningCensoredTime
	. new function scaleFreeFitIndex

2009/11/17: 0.82-1

	. bugfix in plotEigengeneNetworks (thanks to Ronnie Alves for pointing it out)
	. bugfix in heatmapWithLegend when used with mixed color and text labels

2009/11/10: 0.82

	. new function standardScreeningBinaryTrait
	. bugfix in verboseBarplot: the function now passes the ... arguments to barplot
	. verboseScatterplot gets argument sample for better handling of large vectors
	. labeledHeatmap gets arguments xColorWidth and yColorWidth that control the witdth 
	  of the color labels

2009/10/29: 0.81-2

	. bugfix in blockwise[Consensus]Modules: function now works when number of modules 
	  exceeds number of available colors
	. bugfix in exportNetworkToCytoscape: all nodes are now included in
	  the node file (thanks to Tim Gernat for pointing it out and suggesting
	  the fix)

2009/10/22: 0.81-1

	. addTraitToMEs now works with colnames instead of names
	. bugfix in bicor(x): when x has missing data, bicor now does not crash
	. minor bugfix in plotEigengeneNetworks: printAdjacency is now respected

2009/10/19: 0.81

	. several functions from the now defunct package sma were added, mainly
	  to allow our users to run all tutorials smoothly. Note that if 
	  sma package is used concurrently, identical copies of the duplicated 
	  functions will be available. Warning messages about this fact can be 
	  disregarded safely.
	. labeledHeatmap re-written to use an internal heatmapWithLegend
	  function. This means labeledHeatmap now works also in complicated
	  sectionings using layout(), which was not the case before.

2009/09/18: 0.80-1

	. crash in blockwise[Consensus]Modules and TOM calculations when using
	  bicor fixed; blockwise[Consensus]Modules and TOM calculations using
	  compiled code get a new argument maxPOutliers corresponding to the
	  bicor argument of the same name (see news in 0.80).

2009/09/13: 0.80

	. new functions conformityBasedNetworkConcepts and fundamentalNetworkConcepts
	  calculate network concepts (indices)
	. bicor gains the argument maxPOutliers specifying the maximum
	  fraction of data that can be considered outliers
	. new function verboseBarplot to produce annotated barplots
	. verboseBarplot, verboseBoxplot and verboseScatterplot now have
	  complete help files

2009/09/01: 0.79-4

	. bug in networkConcepts fixed
	. goodGenesMS and goodSamplesMS now a bit more robust
	. new function vectorizeMatrix to turn a matrix into a vector of non-redundant components
	. orderMEs now works also on the single set output of moduleEigengenes.
	. plotColorUnderTree, plotDendroAndColors, and plotClusterTreeSamples
	  are now capable of displaying text labels that identify the
	  displayed colors by name.
	. overlapTable now works when the arguments are 1xn or nx1 matrices.

2009/08/07: 0.79-3

	. GOenrichmentAnalysis now works for yeast data as well. Yeast GO
	  mappings are given in a slightly different database (ORF identifiers
	  instead of Entrez) and previous versions of the function did not
	  handle this difference (thanks to Maryam Anwar for pointing this out).

2009/08/05: 0.79-2

	. Default color in addGuideLines now darker ((grey30 instead of grey70).
	. Default color in addGrid now darker (grey30 instead of grey70).
	. Error in bicor help file corrected.
	. moduleEigengenes gets the option to turn off scaling expression data
	  before calculating the singular value decomposition. This should only
	  be used to speed up calculation if the data has been scaled
	  previously.
	. Bugfix in simulateMultiExpr: the function now works when leaveOut=NULL
	. Minor changes to diagnostic messages in TOM calculations
	. Minor changes to printed values in verboseBoxplot
	. GOenrichmentAnalysis a bit more stable
	. GOenrichmentAnalysis can now analyze several sets of labels at the same time;
	  the idea is to give the user the option to quickly calculate enrichments
	  for a collection of competing module assignments. 
	. Enrichment calculations can optionally be restricted to a subset of modules

2009/06/05: 0.79-1

	. GOenrichmentAnalysis now faster and a bug in returned genePositions fixed.
	. function plotEigengeneNetworks gained two additional arguments controling the printing of
	  numerical values into the adjacency heatmaps.

2009/06/01: 0.79

	. Added (experimental) function GOenrichmentAnalysis for automatic GO enrichment
	  analysis 

2009/05/26: 0.78

	. Package qvalue becomes optional. If it is not installed, q values
	  will not be calculated in the network screening functions.

2009/05/18: 0.77-1

	. Hubgene calculation in moduleEigengenes now works even if only
	  one gene has valid data.
	. Bug in labeledBarplot fixed that crashed the function if no error bars were given.

2009/05/05: 0.77

	. DIFF: reverting to default TOM denominator method "min"
	. Bug fix in .clustOrder affecting consensusOrderMEs and
	  mergeCloseModules when there is only one proper module present.

2009/04/02: 0.76

	. Display of p-value in verboseScatterplot improved: small p values now shown more accurately
	. Spurious warning message in matchLabels is now suppressed
	. additional TOM option added: use mean denominator instead of minimum	
	. DIFF: default TOM denominator method is mean. Use TOMDenom = "min" where necessary to reproduce
	  older results
	. help files for [unsigned]adjacency corrected

2009/03/18: 0.75

	. fixed a bug in matchLabels that caused unrelated modules to be
	  matched
	. faster correlation calculations are now implemented both for [bi]cor(x)
	  as wellas [bi]cor(x,y). On platforms where POSIX threads are
	  available, certain parts of the [bi]cor calculations are threaded
	. functions [bi]cor, blockwise[Consensus]Modules, TOMsimilarityFromExpr
	  now have additional parameters providing control over threading and
	  over the tradeoff between speed and precision in handling missing data
	  in the correlation calculations
	. fixed a bug in bicor(x,y) that was present when any of the columns
	  consisted of only missing data and that caused incorrect NAs and 0s
	  in the result.
	. DIFF: softConnectivity now subtracts 1 from the sum of adjacencies to remove 
	  the adjacency of a gene with itself.
	. DIFF: order of parameters in softConnectivity has changed.
	. DIFF: default number of centers in [consensus]projectiveKMeans is
	  now an attempt to fully utilize resources estimated from preferredSize.
	. softConnectivity now accepts parameter 'type' that can specify the
	  network type to be used;
	. fixed a bug in function adjacency that would crash the function in
	  certain circumstances.

2009/03/04: 0.73

	. default p value threshold in matchLables relaxed to 5e-2
	. DIFF: [consensus]ProjectiveKMeans now default to a much higher number
	  since that seems to lead to better results.
	. Faster versions of correlation and bicorrelation implemented. Fast correlation available 
	  for general use in function cor1.
	. bugfix in labeledHeatmap: xLabels and xSymbols do not overlap anymore
	. goodGenes, goodGenesMS, etc now resistant to whole gene profiles containing only NAs
	. minor changes in verbosity of [consensus]projectiveKMeans

2009/02/18: 0.72

	. corPvalueStudent now correctly returns small values instead of zero
	. minor changes in default sectioning in plotDendroAndColors
	. plotDendroAndColors and plotColorUnderTree now plot colors top to bottom
	  (previously was bottom to top)
	. faster median calculation in C implementation of bicor
	. added function overlapTable for computing significance of module overlaps
	. added function matchLabels for relabeling modules in a source partition 
	  to best approximate module labels in a given reference partition

2009/02/06: 0.71-1

	. minor changes in verbosity of TOM calculations
	. blockwise[Consensus]Modules: random seed is now set only if it is non-NULL; this allows the
	  user to force the functions to run without setting a seed, which was not possible before.

2009/02/05: 0.71

	. package flashClust that implements fast hierarchical clustering is now required and used
	  throughut.

2009/01/29: 0.70

	. adapted for dynamicTreeCut-1.20: PAM stage in the dynamic tree cut
	  used in blockwise module detection functions can now optionally
	  respect the dendrogram  in the sense an object can be PAM-assigned
	  only to clusters that lie below it on the branch that the object is
	  merged into. Note that this requires dynamicTreeCut 1.20 or higher.
	. TOM calculation: "Rough guide to max array..." now respects verbose parameter

2009/01/25: 0.67-2

	. bug in recutBlockwiseTrees fixed (only visible if some genes or samples were bad)
	. bug in clusterCoef fixed
	. typos in help files fixed (cutreeStatic[Color])
	. drawing of color label rectangles slightly modified in labeledHeatmap to
	prevent excessively large rectangles 

2008/12/23: 0.67-1

	. help file for intramodularConnectivity corrected
	. corPvalueFisher corrected when twoSided=TRUE: used to give p-values inflated by a factor of 2

2008/12/09: 0.67

	. addTraitToMEs now works also when the multiMEs only contain the eigengenes but no average 
	  expression
	. labeledBarplot now accepts xLabelsAngle
	. fixed interpretation of grey name in orderMEs, consensusOrderMEs
	. scaleTOMs in consensusBlockwiseModules now actually has an effect

2008/12/04: 0.66

	. new function exportNetworkToCytoscape

2008/12/04: 0.65-3

	. new function networkConcepts
	. Bug fix in plotEigengeneNetworks when only one set is given
	. Minor changes and cleanup in help files and printed diagnostics

2008/11/05: 0.65-2

	. Bugfix in exportNetworkToVisANT: no more spurious errors when probe to gene name translation
	  table is given.

2008/11/02: 0.65-1

	. Bugfix in reassigning genes between modules when KME difference too significant: 
	  an empty set of reassign candidates doesn't throw an error anymore.
	. Several help files added

2008/10/25: 0.65

	. added function preservationNetworkAdjacency 

2008/10/09: 0.64

	. different versions of package impute are now supported.
	. help files expanded
	. help files' syntax corrected so all item descriptions are now
	  displayed properly.

2008/10/01: 0.63-1

	. bug in [consensus]ProjectiveKMeans fixed that would cause a crash if
	  the center with highest index became empty
	. numbers2colors resistant to values out of range of the given min and max.
	. p-value in verboseScaterplot now corresponds to the actual correlation printed instead of
	  the Pearson correlation value. However, the p-values are always calculated assuming the
	  correlation value is actually Pearson. 

2008/09/18: 0.63

	. [automaticN|n]etworkScreening now accept option getQValue that can be used to turn off q value 
	  calculations; they also report counts of module eigengenes with gene
	  significances in specific intervals.

2008/09/17: 0.62-1

	. C implementation of column quantile (i.e., apply(data, 2, quantile)) giving immense speedup 
	  of consensus quantile calculations in new function colQuantileC

2008/09/17: 0.62

	. Fixed bugs in blockwiseConsensusModules when disk cache not in use, and when consensusQuantile>0
	. Added function exportNetworkToVisANT to export a network to VisANT.
	. Help files for several functions added

2008/09/13: 0.61

	. TOMdist function added, defined simply as 1-TOMsimilarity, for easier migration of older code.

2008/09/10: 0.60-3

	. [consensus]projectiveKMeans now resistant to an svd failure, using a weighted mean if svd
	  returns an error.

2008/09/05: 0.60-2

	. Bug fix in C implementation of bicor (bad bug!!)

2008/09/04: 0.60-1

	. Big fixes in blockwiseConsensusModules related to TOM sampling

2008/09/02: 0.60

	. minCoreKME default now 0.5 (was 0.7 for Consensus functions, which didn't make much sense)
	. blockwise functions now complete all blocks even if there is a block
	  with no modules detected or with an error during ME calculation.
	. consensusProjectiveKMeans can now optionally use mean as definition
	  of consensus distance, improving convergence in multiple set situations
	. several help files added
	. bicor now implemented consistently in R code and in compiled code:
	  both call the same set of C functions and treat NAs correctly and
	  consistently. Functions bicov and bicorNAy are removed. 
	. pickSoftThreshold now accepts networkType argument
	. blockwiseConsensusModules can now optionally save samples used for TOM scaling

2008/08/29: 0.55

	. Changes of input arguments and output for blockwise[Consenus]Modules
	. Errors in pre-clustering and calculation of signed networks fixed
	. New functions for re-cutting dendrograms produced in blockwise[Consenus]Modules
	. Bug in the return value of blockwise[Consensus]Modules fixed: blockGenes now correctly refer to
	  all genes instead of goodGenes; 
	. New function numbers2colors

2008/08/26: 0.50-2

	. Fixed bugs in blockwiseConsensusModules causing a crash when module eigengene calculation fails

2008/08/20: 0.50-1

	. fixed bug in compiled code bicor1 function that used quick calculation whenever at least one of
	  the x,y had the correct NAs instead of both.  
	. fixed crash in consensusBlockwiseModules when data not checked for missing entries
	. added info printing when merging clusters in consensusProjectiveKMeans

2008/08/15: 0.50

	. [consensus]projectiveKMeans improved: no crash when some clusters become empty, faster
	. blockwise[Consensus]Modules: additional parameter checkMissingData can optionally turn off
	  checking for missing data when it's not necessary.
	. a few help files added

2008/08/05

	. Added random seed setting to blockwise[Consensus]Modules and [consensus]ProjectiveKMeans 
	  for repeatability

	. Lowered reassignThreshold to 1e-6 to prevent too many reassigned genes.

2008/08/03: 0.42-2

	. Fixed bug causing a crash when no modules are detected.

2008/08/02: 0.42-1

	. More complete help pages, bug in blockwiseModules fixed (reported by Anatole Ghazalpour)

2008/07/23: 0.41

	. Many enhancements, improvements and bugfixes

2008/06/02: 

	. Changes to TOMplot to make the dendrograms on the side more informative

	. Changes to scaleFreePlot to pass more of ... to the plotting
	function (removed separate title() command).

2008/05/29: 0.12

	. Performance improvements, extra parameters in blockwiseConsensusModules

2008/05/16: 0.11-1

	. nearestNeighborConnectivity (and softConnectivity) now work even when there is 1 gene in the
	  last block
	. More bug fixes.

2008/05/15: 0.11-0

	. Numerous bug fixes
	. blockwise[Consensus]Modules fixed (ub-broken) from the change of batch to block.
	. blockwise[Consensus]Modules get an option to choose the TOM function.

0.1.0: Basic functions in place.
