Changes in version 2.1.7                        

  - Fixed a bug when deleting a TreatmentResponseExperiment assay via
    NULL assignment
  - Added a names S4 method fo TreatmentResponseExperiment to enable tab
    autocomplete with $ access in interative sessions
  - Added additional methods for drug combination modelling; these
    changes will be documented in a new vignette once we have thoroughly
    tested the new functions
      - For now these are experimental and should not be considered a
        stable API

                        Changes in version 2.1.6                        

  - Changed default parallelization strategy inside aggregate2 (and
    therefore inside aggregate,TreatmentResponseExperiment-method and
    endoaggregate) to split the table into nthread tables instead of
    using by
      - Result should be (1) parallelization is now always faster than
        serial computations, which was not true previously
      - Memory usage of parallelization should be much smaller, since we
        aren't splitting into a very long list of tables
  - Optimized the internal representation of the
    TreatmentResponseExperiment assay index to remove storage of NA for
    rowKey-colKey combinations with no observations in any assay
      - This was causing memory usage to baloon if both rowKey and
        colKey were a large sequence
  - Prepended a "." to the internal assay index column names for each
    assay
      - This should reduce name clashes between internal TRE metadata
        and the column names of an assay (specifically, you can now have
        a column with the same name as the assay)

                        Changes in version 2.1.5                        

  - Add error message to CoreSet,show-method which lets users know to
    use updateObject if the slot names are not valid

                        Changes in version 2.1.4                        

  - Add endoaggregate method to compute TreatmentResponseExperiment
    assay aggregations within the object
  - Add mergeAssays method to allow joining assaying within a
    TreatmentResponseExperiment

                        Changes in version 2.1.3                        

  - Updated CoreSet vignette to reflect recent changes to the object
    structure
  - Renamed the LongTable vignette to TreatmentResponseExperiment and
    updated the content to reflect the changes in class structure
    from 2.1.1
  - Generated new TreatmentResponseExperiment class and structure
    diagrams and inlcuded them in the TreamentResponseExperiment
    vignette
  - Added new example TreatmentResponseExperiment object to package data
  - Added various unit tests for the LongTable (and therefore also the
    TreatmentResponseExperiment)
  - Added proper documentation object for the TREDataMapper-accessors
  - Added aggregate methods for data.table and LongTable
  - Added endoaggregate method for LongTable, which uses aggregate
    internally but assigns the result back to the object and returns the
    updated object. Thus this method is an endomorphic version of
    aggregate.
  - Added new argument summarize to assay,LongTable-method which only
    attaches columns which have been summarized over if FALSE
  - Added assayCols and assayKeys helper methods to retrive valid assay
    column names or the key columns for an assay, respectively.

                        Changes in version 2.1.2                        

  - Fix bug in logLogisticRegression causing tests to fail in
    Bioconductor 3.16 daily builds

                        Changes in version 2.1.1                        

  - First update since Bioconductor 3.15 release
  - Merged rework of the LongTable class back into main branch
  - The object has now been updated to

                        Changes in version 2.0.0                        

  - The @cell slot has become the @sample slot. Associated generics and
    accessor methods have been renamed, then aliased to their old names.
    As such, old code should still work as expected, but will in fact be
    calling different S4 methods.
  - Added the @treatment slot to the CoreSet-class
  - Renamed @sensitivity slot to @treatmentResponse

                        Changes in version 1.5.8                        

  - Fixed imports for the CoreSet2 constructor to resolve errors in
    downstream package PharmacoGx

                        Changes in version 1.5.7                        

  - Add TreatmentResponseExperiment class, a simple wrapper around
    LongTable to make the class syntax more domain specific
  - Add CoreSet2 structure to support creation of CoreSets with the
    modified class structure introducted in BioC 3.13
  - CoreSets can now be made with treatment combination experiments via
    the TreatmentResponseExperiment class!

                        Changes in version 1.5.6                        

  - Fix bug in LongTable -> data.table coerce method that was causing
    rows of some assays to be dropped (closes issue #)

                        Changes in version 1.5.5                        

  - Fix bug in .distancePointLine where function fails with no intercept
    specified (Issue #120)
  - Added support for aggregating an assay inside of a LongTable class
    object
  - Some in-progress updates to the CoreSet constructor which will be
    completed for the Fall release
  - Fixed an error in treatmentNames example
  - Fixed roxygen2 documentation warnings about S4 method documentation
  - Overhauled LongTable coerce methods to use the LongTableDataMapper
    class instead of the deprecated 'LongTable.config' attribute

                        Changes in version 1.5.4                        

  - Fix bug in $<- and [[<- methods where value was returned instead of
    updated object
  - Fix bug in .sanitize input caused by length > 1 coercing to logical
    vector

                        Changes in version 1.5.3                        

  - Fix bug in connectivityScore caused by length > 1 coercing to
    logical vector; this should fix errors in RadioGx and PharmacoGx
    vignettes that were caused by failed R CMD build

                        Changes in version 1.5.2                        

  - Add subsetBySample method for CoreSet object; this is the first step
    in modularizing the subset methods for reuse in dependent packages
  - Added a CoreSet-utils documentation section to document subset,
    intersect, combine and other set operations for a CoreSet object.

                        Changes in version 1.5.1                        

  - Fixed some spelling errors and incorrect code chunk configurations
    in the LongTable vignette
  - Fix bug in .rebuildProfiles where the function fails if replicate_id
    is assigned as a rowID column in the LongTable in @sensitivity

                        Changes in version 1.5.0                        

  - Bioconductor spring 2021 release
  - Added the DataMapper abstract class
  - Added the LongTableDataMapper concrete class
  - Added the metaConstruct method, for making an S4 object from a
    sub-class of DataMapper
  - Updated LongTable vignette with documentation for the DataMapper and
    LongTableDataMapper
  - Refactored various methods to work with a LongTable in @sensititivty
  - Refactored various methods to work with a MultiAssayExperiment in
    @molecularProfiles

                        Changes in version 1.1.5                        

  - Implemented a new class, the LongTable, to store the results of a
    treatment response experiment. This class provides a flexible and
    fast data storage object which can be subclassed for use in other R
    packages.
  - Added vignette documenting LongTable accessors and usage of the new
    object.

                        Changes in version 1.0.2                        

  - Bug fix: suppress warnings thrown by piano::runGSA inside the
    connectivitScore function

                        Changes in version 1.0.1                        

  - Updated the CoreGx vignette to include more information on extending
    the CoreSet class for use in other treatment-response experiments.

                        Changes in version 1.0.0                        

  - Implemented molecularProfiles as SummarizedExperiments instead of
    ExpressionSets
  - Modifying generic implementation to add ...; allows for additional
    arguments in setMethods() for CoreGx generics
  - Removing package from CRAN
  - Submitting package to Bioconductor