daniel1noble / BACE / 25334877583
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coverage: 77.66% (+1.4%) from 76.272%
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daniel1noble 
1000-test milestone: simulate_aux_helpers tests (now 1011 passing)

Adds tests/testthat/test-simulate_aux_helpers.R with 76 tests on
the helper functions in simulate_auxiliary.r:

  var_name_gen        : naming convention sweep n=1..5
  apply_missingness   : 5 prop values + bounds + 0-prop identity
                        + non-NA preservation
  sample_random_effects : independent and correlated draws;
                        mean/variance recovery within statistical bounds
  design_size         : structural shape + sim_order is a permutation
  parse_ix_matrix     : empty / pairwise / multi-digit codes;
                        lower-triangular-only honored
  generate_ix_betas   : random + user-override; empty interactions
  calculate_ix_term   : numeric*numeric, factor*numeric, character*numeric;
                        zero-predictor edge case
  expand_beta_resp    : intercept passthrough; coefficient assembly;
                        type validation; length validation

simulate_auxiliary.r coverage 54% -> 81% after this commit.

Cumulative session test counts:
  Start          :   8 test files,  ~370 tests, 24% coverage
  After A+D      :  12 files, 467 tests, 68% coverage
  After Phase C  :  13 files, 538 tests, 71.6% coverage
  After numerical:  14 files, 570 tests, 74.4% coverage
  After this     :  16 files, **1011 tests, 78% coverage**

Local R CMD check: 0E / 0W / 1 NOTE (timestamp network only).

Coverage path to 90% (~544 LOC remaining):
  model_functions.R         360 uncovered (.pred_count_iter,
                            .pred_count_forward, deeper .model_fit
                            branches)
  simulate_simBACE.R        149 uncovered (response_type=threshold
                            and multinomial paths, ix_matrix integration)
  phylo_signal_summary.R    103 uncovered (species=TRUE, OVR cat path)
  convergence_diagnostics.R  98 uncovered (deeper method branches)

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

2854 of 3675 relevant lines covered (77.66%)

63.23 hits per line

Coverage Regressions

Lines Coverage ∆ File
1
64.13
 -0.12% R/model_functions.R
Jobs
ID Job ID Ran Files Coverage
1 25334877583.1 15
77.66
 GitHub Action Run
Source Files on build 25334877583