itchyshin

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• Remaining #485 class: fitters that trust Optim.converged after a zero-length step (per-family verdicts)

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  bot-test-preexisting

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  itchyshin/GLLVM.jl#505 · Opened Sep 26, 2026

• `confint_family.jl`'s bootstrap and profile-refit helpers accept a non-converged replicate as valid

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  Difficulty 4/5 3-5 days Newbie friendliness 52/100

  itchyshin/GLLVM.jl#504 · Opened Sep 26, 2026

• Truncated-NB2 per-trait fitter stalls at an inferior interior optimum while reporting converged (mirror of #477)

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#499 · Opened Sep 26, 2026

• Binomial quasi-separation: engines flag it differently; Julia has no runaway-loading diagnostic

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  bot-test-preexisting

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  itchyshin/GLLVM.jl#498 · Opened Sep 26, 2026

• Beta grouped inner mode search can oscillate silently, leaving cliffs in the objective

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  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  itchyshin/GLLVM.jl#482 · Opened Sep 25, 2026

• NB2 per-trait dispersion: the Laplace likelihood has several maxima on small data (residual after #478)

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  bot-test-preexisting

  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  itchyshin/GLLVM.jl#477 · 2 comments · Opened Sep 24, 2026

• NATIVE-06 NB2 parity fixture: 2 of 5 traits sit at the Poisson boundary on both engines, so the cell cannot pass

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  bot-test-preexisting

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  itchyshin/GLLVM.jl#476 · Opened Sep 24, 2026

• perf(deferred): sparse assembly / MME Factor build profiling (next real perf track)

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  benchmarks engine enhancement

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  itchyshin/GLLVM.jl#468 · 1 comment · Opened Sep 24, 2026

• research(deferred): non-Gaussian phylo Laplace / selected-inverse path

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  engine enhancement experiment

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  itchyshin/GLLVM.jl#467 · 1 comment · Opened Sep 24, 2026

• docs(deferred): structure-dependent selected-inverse winner table (KEEP-OURS vs SI)

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  benchmarks documentation enhancement

  Difficulty 2/5 1-3 hours Newbie friendliness 68/100

  itchyshin/GLLVM.jl#466 · Opened Sep 24, 2026

• evaluate Latte.jl (INLA / TMB-style Laplace / HMC-Laplace on one model) and GaussianMarkovRandomFields.jl as borrow source or backend

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  itchyshin/GLLVM.jl#427 · 1 comment · Opened Sep 18, 2026

• [roadmap] Track inference evidence, Julia compatibility, and the R-to-Julia reader journey

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  cross-pollination documentation infrastructure roadmap

  Difficulty 5/5 Over a week Newbie friendliness 30/100

  itchyshin/GLLVM.jl#302 · Opened Sep 6, 2026

• Add comparator_targets.toml fixture handoff index (pattern from HSquared.jl)

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  Difficulty 3/5 1-2 days Newbie friendliness 68/100

  itchyshin/GLLVM.jl#276 · Opened Sep 1, 2026

• Seeded RNG in CI is not stable across Julia versions (cross-repo finding from HSquared.jl)

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#182 · Opened Aug 4, 2026

• Plotting: ship a prepare-data + Makie-extension plotting layer (adopt the HSquared.jl pattern)

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  itchyshin/GLLVM.jl#168 · 1 comment · Opened Jul 4, 2026

• Feasibility idea: matrix-free + Hutchinson stochastic-trace REML for very large datasets

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  itchyshin/GLLVM.jl#167 · Opened Jul 3, 2026

• [cleanup] Edge wrapper builds dense O(p^2) Σ_phy before validating loadings

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  Difficulty 1/5 Under an hour Newbie friendliness 85/100

  itchyshin/GLLVM.jl#162 · Opened Jul 2, 2026

• [cleanup] em_fa init comment claims it breaks rotational symmetry, but the unconstrained M-step immediately destroys the triangular structure

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  Difficulty 3/5 1-2 days Newbie friendliness 52/100

  itchyshin/GLLVM.jl#161 · Opened Jul 2, 2026

• [convention] size(F, i) throws BoundsError for i > 2 instead of returning 1

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  Difficulty 1/5 1-3 hours Newbie friendliness 85/100

  itchyshin/GLLVM.jl#159 · Opened Jul 2, 2026

• [convention] Homogeneous no-loadings branch diverges from dense path despite 'numerically identical' docstring

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#158 · Opened Jul 2, 2026

• [convention] Julia couples the two diagonal tiers under one has_diag flag; C++ toggles them independently

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#157 · Opened Jul 2, 2026

• [convention] bootstrap_ci reports SD parameters on the log scale under raw-scale term names

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  Difficulty 2/5 1-3 hours Newbie friendliness 76/100

  itchyshin/GLLVM.jl#156 · Opened Jul 2, 2026

• [robustness] GLLVM.jl binary-tree validation is a global node count that a non-binary topology can pass

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  Difficulty 3/5 1-2 days Newbie friendliness 72/100

  itchyshin/GLLVM.jl#153 · Opened Jul 2, 2026

• [robustness] _fitted_mean silently returns zeros when X is omitted for an X-trained fit

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  Difficulty 2/5 1-3 hours Newbie friendliness 75/100

  itchyshin/GLLVM.jl#152 · Opened Jul 2, 2026

• [robustness] low_rank_chol does not validate d > 0; zero/negative diagonal fails opaquely

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  Difficulty 2/5 1-3 hours Newbie friendliness 84/100

  itchyshin/GLLVM.jl#151 · Opened Jul 2, 2026

• [robustness] Missing size(Λ_B,1)==p check enables @inbounds OOB write in phylo path

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  Difficulty 2/5 1-3 hours Newbie friendliness 76/100

  itchyshin/GLLVM.jl#150 · Opened Jul 2, 2026

• [robustness] Julia hard-requires n_sites >= p; C++ Laplace engine has no such restriction

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  Difficulty 4/5 3-5 days Newbie friendliness 42/100

  itchyshin/GLLVM.jl#149 · 1 comment · Opened Jul 2, 2026

• [robustness] Beta density has no boundary guard in Julia; R clamps y away from 0 and 1

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  Difficulty 3/5 1-2 days Newbie friendliness 68/100

  itchyshin/GLLVM.jl#147 · 1 comment · Opened Jul 2, 2026

• [robustness] Premature-stop fallback can return the known-suboptimal SQUAREM point

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  Difficulty 3/5 1-2 days Newbie friendliness 68/100

  itchyshin/GLLVM.jl#146 · Opened Jul 2, 2026

• [robustness] em_fa default initialisation uses the global RNG, so results are non-reproducible

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  Difficulty 2/5 1-3 hours Newbie friendliness 78/100

  itchyshin/GLLVM.jl#145 · Opened Jul 2, 2026

• [robustness] Transformed-Wald covariance treats any invertible Hessian as positive-definite

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  Difficulty 2/5 1-3 hours Newbie friendliness 74/100

  itchyshin/GLLVM.jl#143 · Opened Jul 2, 2026

• [robustness] R clamps derived-quantity CIs to natural boundaries; Julia returns NaN on a flat profile

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  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  itchyshin/GLLVM.jl#142 · 1 comment · Opened Jul 2, 2026

• [robustness] correlation() divides by zero for a degenerate-variance trait

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  Difficulty 3/5 1-2 days Newbie friendliness 68/100

  itchyshin/GLLVM.jl#141 · Opened Jul 2, 2026

• [robustness] Bootstrap percentile CIs include non-converged refits

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  Difficulty 3/5 1-2 days Newbie friendliness 68/100

  itchyshin/GLLVM.jl#140 · Opened Jul 2, 2026

• [robustness] bridge_fit `d::Integer` rejects R-side doubles despite defensive Int(d)

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  Difficulty 2/5 1-3 hours Newbie friendliness 76/100

  itchyshin/GLLVM.jl#139 · Opened Jul 2, 2026

• [robustness] _bridge_scores swallows all exceptions and reports success with empty scores

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#138 · Opened Jul 2, 2026

• [correctness] Julia derived-profile refit never verifies the constraint g(theta)=c was met; R rejects refits off by >0.05

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  Difficulty 4/5 3-5 days Newbie friendliness 62/100

  itchyshin/GLLVM.jl#137 · 1 comment · Opened Jul 2, 2026

• [correctness] phylo_unique SD uses a signed identity link in Julia vs a positive log link in C++

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  itchyshin/GLLVM.jl#136 · 1 comment · Opened Jul 2, 2026

• [correctness] W-tier reduced-rank term drops cross-trait covariance in Julia but not in C++

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#135 · 1 comment · Opened Jul 2, 2026

• [correctness] Dead guard: phylo loadings silently ignored when Σ_phy omitted

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  Difficulty 2/5 1-3 hours Newbie friendliness 78/100

  itchyshin/GLLVM.jl#134 · 1 comment · Opened Jul 2, 2026

• [correctness] Ordinal location parameterization differs: per-trait intercept + K-2 cutpoints (R) vs shared cutpoints + no intercept (Julia)

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  Difficulty 5/5 Over a week Newbie friendliness 38/100

  itchyshin/GLLVM.jl#133 · Opened Jul 2, 2026

• [correctness] Communality/correlation total-variance denominator differs: Julia full Sigma_y_site vs R tier-local shared+Psi

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  itchyshin/GLLVM.jl#131 · Opened Jul 2, 2026

• [bug] Julia Wald and profile CIs disagree on sigma_phy scale (identity vs log); R uses log-SD in both

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  Difficulty 4/5 3-5 days Newbie friendliness 42/100

  itchyshin/GLLVM.jl#129 · Opened Jul 2, 2026

• [speed] Structured Schur / structured Poisson prototype from #94 archive

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  benchmarks engine experiment

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  itchyshin/GLLVM.jl#110 · Opened Jun 20, 2026

• [diagnostics] Unified check_fit diagnostics, calibration, and plots

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  documentation engine enhancement

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  itchyshin/GLLVM.jl#109 · Opened Jun 20, 2026

• [inference] ANOVA/LRT model-comparison API with boundary-safe wording

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  documentation engine enhancement

  Difficulty 5/5 Over a week Newbie friendliness 30/100

  itchyshin/GLLVM.jl#108 · Opened Jun 20, 2026

• [coordination] Per-response-column family dispatch — companion to DRM.jl #280

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  itchyshin/GLLVM.jl#98 · 1 comment · Opened Jun 13, 2026

• [speed] Borrow DRM.jl REML restricted-objective term for the Gaussian path (gated on the maintainer hold)

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  itchyshin/GLLVM.jl#97 · 2 comments · Opened Jun 13, 2026