feat(mu): save_mu_method storage policy + 6-grid prior benchmark + 0.16.1 compat - #12

Merged

gaow merged 28 commits into

StatFunGen:mainfrom

al4225:fix-mu-storage

Jun 10, 2026

Commits on May 4, 2026

chore(notes): add plan memo and baseline benchmark results

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fix(track): susieR 0.16.1 compact-snapshot compat

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feat(mu): save_mu_method storage policy + mf_thin helper

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chore(bench): driver scripts for the 2026-05-03 prior-grid benchmarks

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chore(notes): append heavy-tailed + null follow-up sections

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docs(notes): tone down per_scale_normal claims in results memo

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docs(vignette): show save_mu_method storage shapes via str()

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docs(notes): tighten plan memo to mu-storage scope, drop sbatch refs

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docs(notes): clarify CS-level vs PIP-threshold metric difference

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chore(bench): add CS-level + hybrid SNP-level metrics, retroactive shape

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docs(vignette): make save_mu_method MWE chunks evaluate at build

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fix(ci): vignette + smash test for susieR 0.16.1 compact trace
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Commits on May 11, 2026

docs(notes): full engineering comparison mfsusieR vs mvf after reading all sources

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docs(notes): correct posthoc section — mfsusieR uses susieR::susie_post_outcome_configuration + lbf_variable_outcome

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test(mwe): complete pipeline comparison mfsusieR vs mvf — fit, HMM, CS, LFSR, posthoc

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docs(notes): correct two errors in engineering comparison

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docs(notes): add §21 summary — right/wrong vs design-choice classification
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test(mwe): add observed-results summary comment at end of file
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Commits on May 17, 2026

refactor: move save_mu_method helpers to R/utils.R, internalize mf_thin

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refactor: move save_mu_method helpers to R/utils.R, internalize mf_thin

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fix(vignette): use mfsusieR:::mf_thin after internalization
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refactor: rename save_mu_method mode "alpha_collapsed" to "aggregated"

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Commits on May 19, 2026

docs: add design notebooks for na_idx and per-scale variance

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Commits on May 20, 2026

docs: add FDR inflation analysis notebook

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fix: preserve NA positions in mf_quantile_normalize; add cross_iter_prior param

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fix(cross_iter_prior): guard fitted_g_per_effect writes in M-step

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docs: add S3 dispatch design note

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docs: merge FDR investigation notes into fdr-code-scan.md

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