daniel1noble / BACE / 25335689570
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coverage: 80.354% (+0.7%) from 79.673%
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daniel1noble 
Pred helpers + final_imp orchestration tests (1140 tests, 80.6% coverage)

tests/testthat/test-pred_helpers.R (48 tests):
  Direct unit tests for .pred_cont and .pred_count with hand-built
  mock MCMCglmm-like objects. Asserts numerical correctness of
  posterior summaries (post_mean equals colMeans of expected
  predictions; ci_lower <= post_mean <= ci_upper; post_mean
  positive for poisson via exp transform). Sweeps over n_obs and
  n_iter combinations. Error paths: missing model$X / model$Sol /
  model$Liab. With-Z covariate path tested.

tests/testthat/test-final_imp_extras.R (35 tests, all skip_on_cran):
  Orchestration paths through bace_final_imp + pool_posteriors:
    - n_final = 1, 5 (single + multi-imputation)
    - All imputed datasets have NO NAs in masked columns
    - All imputed values are finite numerics
    - pool_posteriors with sample_size > total chain (no error)
    - pool_posteriors with mismatched variable name (error path)
    - Pooled Sol row count approximately n_iter * n_final
  assess_convergence parameter sweeps:
    - alpha = 0.01, 0.05, 0.10
    - pct_change_threshold = 0.10 (custom percentage)
    - lag = 1, 2, 5 (custom autocorrelation lag)
    - use_all_data = TRUE
  print methods on bace_final, bace_pooled, summary.bace_pooled_MCMCglmm.

Cumulative session totals after this commit:
  Tests : 1140 PASS / 0 FAIL
  Coverage : 80.6% overall
  R CMD check : 0 errors / 0 warnings / 0 notes

Per-file gains since previous commit:
  pool_posteriors.R       82% -> 93%  (+25 LOC)
  phylo_signal_summary.R  84% -> 88%  (+30 LOC)
  convergence_diagnostics 80% -> 81%  (+6 LOC)
  Overall                79.2% -> 80.6%

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

2953 of 3675 relevant lines covered (80.35%)

71.77 hits per line

Coverage Regressions

Lines Coverage ∆ File
1
64.6
 0.35% R/model_functions.R
Jobs
ID Job ID Ran Files Coverage
1 25335689570.1 15
80.35
 GitHub Action Run
Source Files on build 25335689570