Changes in version 0.99.3 (Release date:  2016-07-26)
==============

Changes:
* plot in mergeClusters now uses cluster names and colors from clusterLegend
* plotDendrogram now calls plot.phylo
* add 'clusterLabel' argument to `clusterSingle`
* add options 'mad' and 'cv' to the dimensionality reduction. Also made option to only use clustered samples for feature reduction for relevant functions (e.g. `makeDendrogram`).
* clusterSingle now always returns the D matrix to the slot coClustering (previously only did so if D was from subsampling).
* change so that clusterSingle takes dissimilarity matrix, and now clusterMany calculates dissimilarities up front (rather than recalculating each time)
* add RSEC function for wrapper that leads to RSEC algorithm.
* add test for clusterMany to make sure replicable with past results (not unit test because too long to run, so not part of R build)

Bug fixes:
* fix bug in .TypeIntoIndices so that handles mix of clusterType and clusterLabels in whichClusters
* fixed bug in plotCoClustering so handles clusterSamplesData
* D for clusterD is now distance, not similarity, for 0-1, meaning larger values are values that are less similar.
* fix bug in plotClusters that would give clusterLegend entries that were vectors, not matrices.

Changes in version 0.99.1 (Release date: 2016-05-24 )
==============

Changes:
* changes to pass development version of bioConductor checks.

Changes in version 0.99.0 (Release date: 2016-05-24 )
==============

Changes:
* changed number to indicate bioconductor submission

Changes in version 0.2.0 (Release date: 2016-05-10 )
==============

Changes:

* Allow 'whichCluster'/'whichClusters' arguments to match to clusterLabels, not just clusterTypes
* Added slot 'dendro_index' 
* Added 'whichCluster' argument to `makeDendrogram`
* Added 'hierarchicalK' clustering
* Added default distance for 0-1 clustering
* Added ability to define distance for clustering
* Added 'setToCurrent' and 'setToFinal' options to update status of a cluster.
* Added unit tests for workflow function (in test_constructor)
* 'getBestFeatures' now calls 'clusterContrasts' internally
* Output for 'clusterContrasts' changed
* Removed 'Index' output for getBestFeatures
* Changed tests for getBestFeatures to run on standard objects (which means now have -2 values to test against)
* User can now give clusterLabel for resulting cluster of combineMany and mergeClusters


Changes in version 0.1.0 (Release date: 2016-05-04)
==============

Changes:

* Conversion to S4 language for bioConductor submission
* All previous functions have been overhauled, renamed, etc.

Changes in version 0.0.0.9006
==============

Changes:

* fixed so that mergeClusters, clusterHclust, and getBestFeatures will appropriately convert if the input of clustering vector is a factor rather than numeric (with warning).
* fixed mergeClusters to have option to indicate that input matrix is a count matrix (in which case will create dendrogram with log(counts+1) and will do getBestFeatures with the voom correction) 
* added more tutoral-oriented vignette (old vignette is now the documentation vignette with more detail about the internal workings of package). Currently is just simulated data, but will be updated to real single-cell sequencing dataset.

Changes in version 0.0.0.9005
==============

Changes:

* Changed simulated data so load all with data(simData) rather than separate calls for simData and simCount. Also added 'trueCluster' vector to give true cluster assignments of simulated data
* added dendro example to getBestFeatures
* added example to clusterHclust
* added single function for converting to phylobase tree (used internally by package)
* added functionality to find proportion of significant null hypotheses for merging clusters (mergeClusters)

Changes in version 0.0.0.9004
==============

Changes:

* Changed clusterMany.R to only set k<-NA if sequential=FALSE (previously for all where findBestK=TRUE)
* Added to vignette
* fixed bug in plotClusters to correctly plot "-1"