parafac4microbiome - parafac4microbiome 1.3.2

• Removal of importMicrobiotaProcess due to not meeting CRAN requirements.

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Published by GRvanderPloeg 7 months ago

parafac4microbiome - 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.

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Published by GRvanderPloeg 9 months ago

parafac4microbiome - parafac4microbiome 1.1.2

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

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Published by GRvanderPloeg 11 months ago

parafac4microbiome - parafac4microbiome 1.0.3

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Published by GRvanderPloeg over 1 year ago

parafac4microbiome - parafac4microbiome 1.0.2

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Published by GRvanderPloeg over 1 year ago

parafac4microbiome - v0.2.0

• '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.

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Published by GRvanderPloeg over 1 year ago

parafac4microbiome - v0.1.0

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

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Published by GRvanderPloeg over 1 year ago

parafac4microbiome - Submission ready

Submission ready

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Published by GRvanderPloeg almost 2 years ago

parafac4microbiome - 0.0.2

Ready for submission

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Published by GRvanderPloeg almost 2 years ago