Changes in version 1.3.2.9000                      

  - Temp

                 Changes in version 1.3.2 (2025-07-31)                  

  - Removal of importMicrobiotaProcess due to not meeting CRAN
    requirements.

                        Changes in version 1.3.1                        

  - Addition of age, gender and oral health data to vanderPloeg2024.
  - Addition of TIFN2, MAINHEALTH, GOHTRANS, and AP articles to package
    documentation. These are only rendered for the website due to
    computational requirements.

                        Changes in version 1.3.0                        

  - Removal of the all-at-once optimization for parafac() since the ALS
    scheme outperforms it under all circumstances.
  - Removal of deprecated verbose option for parafac().
  - Renaming of vignettes to be easier to visually parse (also in
    preparation of the addition of new vignettes).
  - Overhaul of the entire testing suite to be more robust and fast.

                 Changes in version 1.2.1 (2025-05-20)                  

  - The package is now fully compatible with R version 4.5.
  - Due to breaking changes to the TreeSummarizedExperiment package that
    came with R version 4.5, minimum version requirements for
    TreeSummarizedExperiment, MicrobiotaProcess, and
    SummarizedExperiment have temporarily been added to the
    dependencies. This breaks compatibility with older versions of
    Ubuntu temporarily.

                        Changes in version 1.2.0                        

  - Added the function reshapeData() which reshapes a long dataframe of
    counts into a data cube.
  - Added tests for reshapeData().
  - Fujita2023, Shao2019, and vanderPloeg2024 now utilize reshapeData
    when they are being generated.
  - Many bugfixes across all functions in the package.

                 Changes in version 1.1.2 (2025-03-21)                  

  - Fixed a URL in README.md to now point towards the correct website.

                        Changes in version 1.1.1                        

  - corcondia() is now fully based on the N-way toolbox implementation.
  - Fixed a URL in README.md to now point towards the correct website.

                        Changes in version 1.1.0                        

  - vanderPloeg2024 now contains all datasets from the original paper.
  - The contents in /data-raw/ are updated to better organize the
    studies.
  - The Frobenius norm of the tensor is now collapsed into the subject
    mode (was the O-norm).
  - Fixed an issue where flipLoadings() would not flip any of the modes
    if there was evidence that all three modes should be flipped.
  - Fixed an issue where flipLoadings() would not work when one model
    was provided.
  - All vignettes are updated to better reflect the updated functions
    for this version.

                 Changes in version 1.0.3 (2024-09-24)                  

  - Minor changes to tests for parafac_gradient to make them more robust
    towards various platforms checked by CRAN.

                 Changes in version 1.0.2 (2024-09-17)                  

  - Further rework of importPhyloseq, importTreeSummarizedExperiment and
    importMicrobiotaProcess to meet CRAN requirements.

                        Changes in version 1.0.1                        

  - Streamlined examples in importPhyloseq,
    importTreeSummarizedExperiment and importMicrobiotaProcess.

                        Changes in version 1.0.0                        

  - Edited DESCRIPTION to meet CRAN requirements.
  - importPhyloseq was modified to use rTensor-based cube folding
    instead of a for-loop.
  - importTreeSummarizedExperiment was modified to use rTensor-based
    cube folding instead of a for-loop.
  - importMicrobiotaProcess was modified to use rTensor-based cube
    folding instead of a for-loop.

                        Changes in version 0.2.0                        

  - 'parafac' is now capable of running an all-at-once optimization
    using the methods="opt" parameter. For now, the default remains
    methods="als" (i.e. the ALS algorithm) because it converges faster
    to a similar solution.
  - importPhyloseq allows the user to import a phyloseq object for
    parafac modelling.
  - importTreeSummarizedExperiment allows the user to import a
    TreeSummarizedExperiment object for parafac modelling.
  - importMicrobiotaProcess allows the user to import a
    MicrobiotaProcess object for parafac modelling.
  - The text in the vignettes were updated to better reflect the changes
    per version 0.1.0.
  - The readme and vignettes figures now use sign flipping to make
    comparison with the paper easier.
  - Some documentation and testing changes anticipating a CRAN release.

                        Changes in version 0.1.0                        

  - parafac is now a custom function based on an ALS algorithm allowing
    for much more output (see documentation).
  - initializePARAFAC initializes the input vectors either randomly on
    based on a best-guess SVD model of the unfolded array.
  - parafac_core_als contains this ALS algorithm.
  - parafac_fun calculates the loss of a parafac model in anticipation
    of an all-at-once optimization implementation.
  - assessNumComponents and checkModelStability have been renamed into
    assessModelQuality and assessModelStability respectively to clarify
    their use.
  - checkModelStability now works with a minimum and maximum number of
    components.
  - checkModelStability reports Factor Match Score in a plot.
  - calculateFMS calculates pairwise Factor Match Scores for a list of
    model objects.
  - parafac, multiwayCenter, multiwayScale and multiwayCLR are now based
    on the new rTensor dependency for tensor unfolding
  - plotOverallTCCs has been merged with plotModelTCCs.
  - Many bugfixes. PARAFAC model solutions should be more stable as a
    result.
  - Many documentation changes across the board. Overall, the use case
    per function should be much clearer.
  - Vignettes are updated to reflect and utilize the new changes.
  - Removed dependency: paramGUI

                        Changes in version 0.0.2                        

  - Added NEWS.md