Changes in version 1.3.2 (2024-12-10)                  

Major changes

Minor improvements and bugfixes

  - Added harmonize = FALSE option to nipals_multiblock() to allow
    disabling (slow) sample harmonization for large datasets.
  - Fixed a bug in nipals_multiblock() to allow the numPCs =1 argument
    (i.e. ability to compute a single global score).

                 Changes in version 1.2.1 (2024-08-31)                  

Major changes

Minor improvements and bugfixes

  - Updated 'Single-Cell-Analysis' vignette to remove potential issue
    with BiocFileCache having two copies of data.
  - Updated author list and citation.
  - Updated references in readme.

                 Changes in version 1.2.0 (2024-04-26)                  

Major changes

Minor improvements and bugfixes

  - Clarified the dataset used in the single-cell vignette and
    reformatted the workflow diagram
  - Removed the final log transformation in the single-cell vignette
    when saving for MCIA
  - Minor plotting improvements (removed redundancies in legend names,
    consistency of axis text, etc.)

                 Changes in version 1.1.0 (2024-03-21)                  

Major changes

  - Added BiocFileCache to replace previous method of downloading large
    SC datasets.

Minor improvements and bugfixes

  - Updated nipals_iter to only use var(gs) to compute the significance
    of global scores.
  - Added to documentation for predict_gs() warning against use with
    CPCA deflation.

                 Changes in version 0.99.7 (2023-10-07)                 

Minor improvements and bug fixes

  - Updated README to reflect MAE changes.
  - Updated the citation.
  - Fixed bug in documentation for nipals_multiblock.
  - Stopped downloading one of the files for the single cell analysis
    vignette.

                 Changes in version 0.99.6 (2023-09-09)                 

Major changes

  - Switched primary input to nipals_multiblock() to a
    MultiAssayExperiment object.
  - nipals_multiblock() now outputs an object of the NipalsResult class.
  - Converted all downstream analysis functions to work with the
    NipalsResult class.

Minor improvements and bug fixes

  - Added simple_mae() function to convert a list of dataframes to a
    MultiAssayExperiment object.
  - Fixed missing \value fields in man page for NipalsResult class.

                 Changes in version 0.99.5 (2023-06-22)                 

Major changes

  - Bumping version number to trigger re-build following bug in
    BiocCheck.

                 Changes in version 0.99.4 (2023-06-01)                 

Major changes

  - Fixed data corruption issues from v0.99.3.

                 Changes in version 0.99.3 (2023-06-01)                 

Major changes

  - Changed the eigenvalue calculation in nipals_iter() to compute the
    variance of the global score at each deflation step. Prior versions
    used an SVD method to compute the singular values of the deflated
    data matrix directly.
  - Fixed bug in projection_plot() where there was a mismatch between
    color labels and plotting order.
  - Added parameter to nipals_multiblock that specifies whether the
    samples are in the rows or the columns.

Minor improvements and bug fixes

  - Changed vignette styling from rmdformats to BiocStyle and added
    installation sections to all of the vignettes.
  - Removed empty helper.R file.
  - Added significantly more unit testing.
  - Fixed bug in projection_plot() when metadata was provided but no
    color_col was selected.
  - Renamed the associated output of col_preproc_method in
    nipals_multiblock. The metadata field is also now available in the
    output independent of whether metadata is provided in the input.
  - Added checks for consistency in sample names across data blocks and
    metadata.

                 Changes in version 0.99.2 (2023-03-25)                 

Major changes

  - Shrank the vignettes sizes (especially the single cell analysis
    vignette).

Minor improvements and bug fixes

  - Restructured the single cell analysis vignette to be more
    streamlined and have more explanations.
  - Add an additional single cell data file to the repository using
    piggyback.

                 Changes in version 0.99.1 (2023-02-26)                 

Major changes

  - Included support for MultiAssayExperiment in nipals_multiblock.
  - Improved access to existing data objects.

Minor improvements and bug fixes

  - Made get_colors() more flexible for different color palette options.

                 Changes in version 0.99.0 (2022-10-21)                 

  - Added single cell data to the repository using piggyback.