D/Delta full-run raw audit and post-processing recovery
Run integrity
The original benchmark runner exited 1 after timing completed: its final pair-order aggregate referenced first_implementation, which was absent from the pair projection. Raw timed rows were saved and left unchanged. The previous pairs CSV was snapshotted before repair. No benchmark calls were repeated. Executed runner SHA-256, from the matching immediately preceding smoke run: 440cb42d4c18ebc35863cc65e0ba771afb1cc9e918e4f9888333c4e1ab31349f Corrected runner SHA-256, adding the omitted pair field: a70fd6c4ab980f5d00838e3587ef48f04f661bdcae6d6a95037bb03ad6ee7831 Postprocessor SHA-256: 552e4f44064c48f028d7048ea0584f58fa98636392dfc85a759ab96ac45a7af6 Raw runs SHA-256, verified unchanged: e46a67a58f3e8519b1f50ae8ed31e88005053e947949517ec647e6fe99400318 Pre-repair pair snapshot SHA-256: 96164c7e9e26ed0b720f7ca402c9b1997ba7a153a14c2e92daa803fb7c94bda9 The metadata records the original process exit code; it does not claim the benchmark runner exited 0.
Design and provenance
Package fastphylosig 0.3.0 ; tarball SHA-256 909b7ad27485dcc2d96a7bb1fc70b65b54e93245d75761aca406b9c52f06cbff ; DLL SHA-256 1bd40080f1ea537b3c73c838dc98ff84940f1064f4e1c4dbfb2dd5063d999bdb D: fast_d(test=TRUE, nsim=199) versus caper::phylo.d(permut=199); all fast calls report 199/199 random and 199/199 Brownian simulations. Delta reference source SHA-256: 0dc1e987c13f0e972b0e7c3b4829b4d0fdc41ff0de3856bae4803f9ce0115175 ; source uses ape::ace(model=ARD), nentropy() and two emcmc chains. Fast Delta actual controls and requested/successful total iterations were audited from returned fields: 10000, thin 10, burn 100, lambda0 0.1, proposal_sd 0.5, LSE, ARD, two-chain contract, total 20000. Each timed interval measured one public call with Sys.time. Tree/trait generation, prepare_tree, comparative.data, matching, seeding and gc were excluded; Delta ACE/reconstruction and MCMC remained inside the call. The four panels compare runtime for different configured analyses: D uses a permutation test, Delta uses two-chain MCMC, and K/lambda use test=FALSE point estimates. They do not imply equal statistical work.
Raw audit
Raw calls: 480 (240 fast, 240 reference); pairs: 240 ; cells: 24; paired replicates/cell: 10. Finite successful calls: 480 / 480 ; errors: 0 Observed actual species match: 240 / 240 ; all counts equal n_tip; NA removals: 0. Tree, trait and reference-input hash matches: 240 / 240 ; 240 / 240 ; 240 / 240 First-call order balance by cell:
method scenario n_tip first_implementation comparison_id
D moderate 50 fastphylosig 5
D moderate 50 reference 5
D moderate 100 fastphylosig 5
D moderate 100 reference 5
D moderate 500 fastphylosig 5
D moderate 500 reference 5
D moderate 2000 fastphylosig 5
D moderate 2000 reference 5
D none 50 fastphylosig 5
D none 50 reference 5
D none 100 fastphylosig 5
D none 100 reference 5
D none 500 fastphylosig 5
D none 500 reference 5
D none 2000 fastphylosig 5
D none 2000 reference 5
D strong 50 fastphylosig 5
D strong 50 reference 5
D strong 100 fastphylosig 5
D strong 100 reference 5
D strong 500 fastphylosig 5
D strong 500 reference 5
D strong 2000 fastphylosig 5
D strong 2000 reference 5
Delta moderate 50 fastphylosig 5
Delta moderate 50 reference 5
Delta moderate 100 fastphylosig 5
Delta moderate 100 reference 5
Delta moderate 500 fastphylosig 5
Delta moderate 500 reference 5
Delta moderate 2000 fastphylosig 5
Delta moderate 2000 reference 5
Delta none 50 fastphylosig 5
Delta none 50 reference 5
Delta none 100 fastphylosig 5
Delta none 100 reference 5
Delta none 500 fastphylosig 5
Delta none 500 reference 5
Delta none 2000 fastphylosig 5
Delta none 2000 reference 5
Delta strong 50 fastphylosig 5
Delta strong 50 reference 5
Delta strong 100 fastphylosig 5
Delta strong 100 reference 5
Delta strong 500 fastphylosig 5
Delta strong 500 reference 5
Delta strong 2000 fastphylosig 5
Delta strong 2000 reference 5
Statuses (reference APIs do not expose a status field):
, , reported_status = not_reported_by_reference, success = TRUE
implementation
method fastphylosig reference
D 0 120
Delta 0 120
, , reported_status = ok, success = TRUE
implementation
method fastphylosig reference
D 120 0
Delta 120 0
Warning and Delta diagnostic audit
Warning-bearing calls: 113 /480; D=0; Delta reference=112/120; fast Delta=1/120. All warnings remain in raw rows; no retries or row removals. Warning-call counts by method and implementation:
method implementation warning_calls
Delta fastphylosig 1
Delta reference 112
All warning-component frequencies (components may co-occur):
NaNs produced
96
Inf replaced by maximum positive value
70
imaginary parts discarded in coercion
38
model fit suspicious: gradients apparently non-finite
11
transition-rate optimization did not converge: iteration limit reached without convergence (10)
1
Reference Delta warning-component frequencies:
NaNs produced
96
Inf replaced by maximum positive value
70
imaginary parts discarded in coercion
38
model fit suspicious: gradients apparently non-finite
11
Reference Delta warning components by species count and scenario:
, , scenario = moderate
n_tip
warning_component 50 100 500 2000
Inf replaced by maximum positive value 6 8 9 7
NaNs produced 7 8 9 7
imaginary parts discarded in coercion 1 2 0 0
model fit suspicious: gradients apparently non-finite 0 1 0 0
, , scenario = none
n_tip
warning_component 50 100 500 2000
Inf replaced by maximum positive value 1 0 0 0
NaNs produced 6 6 6 8
imaginary parts discarded in coercion 6 9 9 10
model fit suspicious: gradients apparently non-finite 2 4 2 1
, , scenario = strong
n_tip
warning_component 50 100 500 2000
Inf replaced by maximum positive value 9 10 10 10
NaNs produced 9 10 10 10
imaginary parts discarded in coercion 1 0 0 0
model fit suspicious: gradients apparently non-finite 1 0 0 0
The pinned reference delta() returns only a numeric scalar and discards the ACE convergence object; result_fields are
calls diagnostics_available ESS_alpha_min ESS_beta_min Rhat_alpha_max
120 120 52.40738 52.37619 1.060496
Rhat_beta_max MCSE_Delta_max
1.057219 0.06444899
One fast Delta warning row:
scenario n_tip replicate
none 2000 6
warning
transition-rate optimization did not converge: iteration limit reached without convergence (10)
estimate ESS_alpha ESS_beta Rhat_alpha Rhat_beta MCSE_Delta
0.1296409 601.6414 458.0392 0.9993196 1.000341 0.0001259713
Delta elapsed times describe calls returning finite values only. They do not validate equal accuracy, effective chains, or final-fit convergence.
Observed runtime
Ratio is median(reference seconds) / median(fast seconds), descriptive only:
method scenario n_tip n_pairs fast_median_seconds reference_median_seconds
D moderate 50 10 0.007730126 0.04118252
D moderate 100 10 0.010280013 0.06031001
D moderate 500 10 0.032377005 0.68169451
D moderate 2000 10 0.121750474 26.56591403
D none 50 10 0.007972479 0.04201508
D none 100 10 0.010466576 0.06171238
D none 500 10 0.033290982 0.66942251
D none 2000 10 0.122554421 26.77241051
D strong 50 10 0.007849932 0.04141653
D strong 100 10 0.010539055 0.06103456
D strong 500 10 0.032403469 0.68839347
D strong 2000 10 0.118285060 26.50673604
Delta moderate 50 10 0.029536963 0.89077008
Delta moderate 100 10 0.035795927 1.15015960
Delta moderate 500 10 0.115482330 3.70165396
Delta moderate 2000 10 0.594941020 14.21268451
Delta none 50 10 0.034136534 0.96909451
Delta none 100 10 0.042075992 1.37401056
Delta none 500 10 0.179730535 4.74966455
Delta none 2000 10 0.755549550 18.43380415
Delta strong 50 10 0.028530002 0.87821698
Delta strong 100 10 0.035148501 1.15239549
Delta strong 500 10 0.088249087 3.32639503
Delta strong 2000 10 0.335479021 11.26666796
reference_over_fast_ratio_of_medians paired_ratio_median warning_calls_fast
5.327535 5.350725 0
5.866725 5.885837 0
21.054897 20.977776 0
218.199676 218.990880 0
5.270014 5.274250 0
5.896139 5.896300 0
20.108223 20.109586 0
218.453241 218.616245 0
5.276036 5.260622 0
5.791275 5.786766 0
21.244437 20.432458 0
224.092003 231.485745 0
30.157809 30.057670 0
32.131019 32.925588 0
32.053856 33.093828 0
23.889233 24.180337 0
28.388779 28.468340 0
32.655453 30.216100 0
26.426587 25.928093 0
24.397876 22.608851 1
30.782227 30.400661 0
32.786476 32.758031 0
37.693251 38.642811 0
33.583823 33.445713 0
warning_calls_reference
0
0
0
0
0
0
0
0
0
0
0
0
8
9
9
7
9
10
10
10
10
10
10
10
D ratio range: 5.27 to 224.1 x. Delta ratio range: 23.89 to 37.69 x. The Delta figure panel must disclose reference warnings and the absence of a convergence certification.