refactor(imputation): Update AFT imputation method to linear time complexity - #222

Merged

tonywu1999 merged 30 commits into

develfrom

Sep 27, 2026

Commits on Sep 8, 2026

refactor(imputation): Initial attempt to refactor AFT imputation modeling with conjugate gradient instead of cholesky factorization for the Newton step
tonywu1999
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494e3e4
add adjustments w.r.t. logging and pcg option
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b54f256

Commits on Sep 9, 2026

fix imputation funneling of parameters into multicore
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93aa0c6

Commits on Sep 11, 2026

add divergence in residual warning
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0f177bf

Commits on Sep 12, 2026

add verbose logging options for running survreg imputation
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85d93ec
Get rid of divergence breakpoint in CG
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1194b96

Commits on Sep 13, 2026

Remove the artificial number_of_halvings > 30 hard-abort. Instead, let halving consume the shared iteration budget (aft_iterations), and when that budget runs out, fall back to the last accepted c…
tonywu1999
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0566a9f

Commits on Sep 17, 2026

set number of threads to 1 per core for blas operations for pcg
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8b180ab

Commits on Sep 26, 2026

remove dot documentation files, remove test comments
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7bf9309
fix unit tests for test_dataProcess to be easier to read and understand
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b689cb5
remove unnecessary parameters for cgsolve
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27e5581
make unit tests of utils_cgsolve more comprehensible
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ace892c
remove tests_utils_imputation_cg.R
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d1822a6
consolidate imputation tests to be simpler and lack redundancy
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12955ff
make utils imputation test file easier to read w.r.t plain english
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6a9e0ce
make utils_imputation tests more comprehensible
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9749a9e
adjust coderabbit comments
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e148a8f
update cgsolve docs
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a987222
deal with convergence warning problem
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988e74e
adjust tests for warning messages aft imputation
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78f37c3
remove unnecessary comments
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f1c2f14
fix unit test on convergence
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2cd10ad
move internal functions outside of .fitSurvivalCG
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89f07ee
update documentation on the math claims
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7225f78
update docs around n being number of entries in matrix
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560a755

Commits on Sep 27, 2026

update documentation for CG-solve
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e62c4ee
remove some unnecessary documentation
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8c1119a
fix docs w.r.t. negative hessian
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77d7e15
update docs
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bb30fa3
update imputation comments
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a1ab418