Add Satterthwaite and Kenward-Roger fixed-effect tests
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@@ -25,6 +25,8 @@ The engine diagonalizes the GRM once, rotates the common design and every unique
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- Signed standard-deviation parameterization with a separate one-sided KKT check for the \(\sigma_g^2=0\) boundary.
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- No explicit dense \(P\) matrix.
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- Variable numbers of extra fixed-effect covariates per task through a CSR index.
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- Satterthwaite t/F fixed-effect inference by default, with optional
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Kenward-Roger F tests and a joint test of task-specific covariates.
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- Atomic block output and safe resume/force semantics.
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- Generic Python CLI for manifest creation, validation, execution, provenance signatures, status, and result export.
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@@ -139,6 +141,12 @@ python python/spectra_reml.py finalize \
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`results.tsv.gz` retains the complete per-task summary and stores the fixed-effect vector and row-wise packed lower covariance as JSON arrays.
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Fixed-effect inference defaults to Satterthwaite. Select Kenward-Roger or turn
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inference off with `--fixed-effect-test kenward-roger` or
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`--fixed-effect-test none`. Coefficient-wise standard errors, statistics,
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denominator degrees of freedom, and p-values are exported as JSON arrays; tasks
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with extra covariates also report their joint F test in the summary columns.
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## Recovery and provenance
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Each block is written as four files, with `.complete` renamed last. The Python layer adds `run.signature.json`, which binds the canonical manifest, engine SHA-256, numerical options, thread settings, and block size.
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