# parafac4microbiome 1.3.3

* Updated maintainer email.
* Temporary removal of some articles pending re-release of `CMTFtoolbox`.

# parafac4microbiome 1.3.2

* Removal of importMicrobiotaProcess due to not meeting CRAN requirements.

# parafac4microbiome 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.

# parafac4microbiome 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.

# parafac4microbiome 1.2.1

* 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.

# parafac4microbiome 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.

# parafac4microbiome 1.1.2

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

# parafac4microbiome 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.

# parafac4microbiome 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.

# parafac4microbiome 1.0.3

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

# parafac4microbiome 1.0.2

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

# parafac4microbiome 1.0.1

* Streamlined examples in `importPhyloseq`, `importTreeSummarizedExperiment` and `importMicrobiotaProcess`.

# parafac4microbiome 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.

# parafac4microbiome 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.

# parafac4microbiome 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

# parafac4microbiome 0.0.2

* Added `NEWS.md`
