NEWS.md

In parafac4microbiome: Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

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

parafac4microbiome documentation built on June 8, 2025, 11:40 a.m.