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parafac4microbiome

INFRA · APIS
Velocity0.0

Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

github.com/grvanderploeg/parafac4microbiome ↗

A PARAFAC toolkit for microbiome time series, spending every release on packaging

microbiomeparafacbioconductorcran-policydependencies
◆Current state
parafac4microbiome fits parallel factor analysis models to longitudinal microbiome data, built on the Bioconductor data structures that field uses. All three releases in its recorded history concern the packaging boundary rather than the modelling: an R 4.5 compatibility release that pinned minimum versions of TreeSummarizedExperiment, MicrobiotaProcess and SummarizedExperiment, a README URL fix, and the removal of importMicrobiotaProcess for not meeting CRAN requirements.
◆Where it's heading
The visible arc is a CRAN package caught between two ecosystems: its scientific dependencies live on Bioconductor and move on Bioconductor's schedule, while its distribution channel enforces CRAN's rules. Both consequences are already on the record — compatibility with older Ubuntu was broken when versions had to be pinned, and a data import path was lost outright. Nothing in these entries describes a change to the PARAFAC modelling itself.
◆Prediction
Expect further releases driven by Bioconductor dependency changes rather than by the method; whether the removed MicrobiotaProcess import returns depends on a packaging problem the notes do not describe.

◆Recent moves

  1. 1y ago

    importMicrobiotaProcess removed over CRAN requirements

    Drops the importMicrobiotaProcess function because it did not meet CRAN requirements. This is a contraction rather than a gain — anyone loading data through that path loses it — and it is the third consecutive release in which the packaging boundary, not the modelling, is the whole story.

    View source ↗
  2. 1y ago

    R 4.5 compatibility with pinned Bioconductor versions

    Restores compatibility with R 4.5 after breaking changes in TreeSummarizedExperiment, at the cost of minimum version pins on three Bioconductor packages and a stated temporary break with older Ubuntu. Reactive dependency work with a real installation cost for some users.

    View source ↗
  3. 1y ago

    README URL correction

    Fixes a README link so it points to the correct website. The smallest possible release, and the only one not caused by a dependency.

    View source ↗