NEWS

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PACE 0.99.18

• Condition signals build their messages without paste(), and the ridge check handles empty input directly rather than suppressing the warning it would raise.

PACE 0.99.17

• New compactFit() drops the per-cell matrices before saving a fit, which the vignette previously did by assigning into a slot.
• The vignettes read fits through accessors rather than @, which clears BiocCheck's note about slot access in examples and vignettes.

PACE 0.99.16

• New stashPACE() copies a fit's readouts into metadata(spe), so results can travel with the data they came from. The solver state is not copied.

PACE 0.99.15

• Records the Australian Government Research Training Program as funder in Authors@R.

PACE 0.99.14

• PACEFit gains a validity method. Replacing a slot wholesale used to pass silently and break every readout downstream; fit@fit <- list() is now refused.
• New accessors cellTypes(), paceParams() and fitState(), and validated replacement methods for neighbourSlopes(), varianceDecomposition() and topDrivers().

PACE 0.99.13

• verbose = FALSE is now silent. The shrinkage step reported its progress regardless, because it never received the flag, and mashr printed its own on top of that.
• Installation instructions use BiocManager::install().
• The vignette evaluates every chunk.
• Minimum R version is 4.6.0.

PACE 0.99.12

• plotDecomposition() draws the zoom panel's percentage labels upright, so that neighbouring bars of similar height no longer overlap each other's text.

PACE 0.99.11

• Added a canonical multivariate adaptive shrinkage implementation to the compiled core, alongside the existing mashr path. It reproduces mashr's calls exactly on both reference cohorts.

PACE 0.99.10

• The driver score columns are named for what the method calls them: driver_score and driver_score_spec4, previously MCSD and MCSD4. plotDrivers() takes panels = "score" in place of "mcsd".

PACE 0.99.9

• topDrivers() documents which model term each column holds. On a fit with a condition the table carries two different slopes, and they are not a raw and shrunken pair of the same quantity.
• The condition vignette shows the responder decomposition and driver figures, and prints the driver table.

PACE 0.99.6

• The per-pair gene score is called the driver score throughout the documentation and plot labels, matching the method description.

PACE 0.99.4

• Fixed portability defects found by the Bioconductor build matrix: bit identity on arm64, a crash on Windows from static thread_local destructors, an unsupported system2(env=) on Windows, and missing -pthread on compile flags for Wasm.

PACE 0.99.0

• Initial Bioconductor submission.