24 October 2026. English source documentation; summaries on the main site are available in English and Indonesian. Original audit files are unchanged.
# CFF–longevity: applied corrections and working methods Documentation reviewed 24 October 2026. Prepared for Gilang Senja Kharisma. ## Start here: current status and files Pass 4 is the latest measurement audit. This documentation review adds no source decisions, numerical corrections or eligibility approvals. Read this README for current methods and PASS4_PROGRESS.md for the latest source-check findings. Earlier pass notes are historical snapshots. | Purpose | Current file | Meaning | | --- | --- | --- | | Measurement audit | `measurement_audit_pass4.csv` | 280 rows; 237 raw taxon/tree labels | | Identity and longevity crosswalk | `crosswalk_pass2.csv` | 237 labels; use audited pass-2 identity/quality fields | | Review queue | `candidate_source_check_queue_pass4.csv` | 117 measurements across 91 labels; not an approved sample | | Latest pass summary | `audit_summary_pass4.json` | Four records revisited; no numeric replacements in pass 4 | | Source decision history | `applied_decisions.csv`, `source_decisions_pass2.csv`, `source_decisions_pass3.csv`, `source_decisions_pass4.csv` | Pass-specific decisions; rows can recur across passes | | Tree-check history | `tree_checks.csv`, `audit_summary.json` | Earlier derived checks; raw trees absent from this ZIP | | Data gaps | `PLATYPUS_DATA_GAP.md`, `data_gap_register.csv`, `data_gap_register.json` | Separate register; not part of measurement counts | | Documentation changes | `DOCUMENTATION_REVIEW.md` | Review scope, changes and validation limits | There are **94 longevity-quality candidate labels**, recalculated from the bundled crosswalk, down from the historical 95 after domestic-cat reclassification. This is a different denominator from the 91 labels in the measurement review queue. Neither is the final analysis sample. All 280 measurement rows retain `final_analysis_eligible = not_finalized`. In `audit_summary_pass2.json`, `quality_candidates_not_final = 95` is inherited pass-1 metadata; use `quality_candidates_after_domestic_cat_reclassification = 94` for the updated count. In the crosswalk, original name, longevity and quality fields remain historical; audited `*_pass2` fields take precedence. Its measurement-status summaries are pass-2 snapshots: consult the pass-4 measurement table for current screening decisions. ## Evidence limits of this package This ZIP contains derived tables, decisions and scripts, not the raw CFF archive, raw AnAge snapshot, original crosswalk archive or raw trees. The documentation review checks internal consistency and incremental reproducibility; it does not independently reverify published sources, raw-input hashes or phylogenetic validity. Source links below preserve earlier audit provenance, not a claim of new source access on this review date. ## What has actually been completed The earlier raw-input audit reports that the supplied October 2025 Haarlem CSV contains 280 measurements and 237 taxon labels. The supplied AnAge file contains 4,645 entries and is byte-identical to the input documented in the previous crosswalk audit. These source files were previously supplied, but are not bundled here; full regeneration requires access to them. Four measurement decisions are implemented in `measurement_audit.csv` and propagated to `crosswalk_with_corrections.csv`: 1. Ficedula albicollis: compiled 138.2 Hz corrected to 128.1 Hz. 2. Ficedula hypoleuca: compiled 128.1 Hz corrected to 138.2 Hz. These are species means at peak temporal resolution, not the largest individual values (141 and 146 Hz). Primary source: Boström et al. (2016), Results, https://doi.org/10.1371/journal.pone.0151099 . Both means were measured at 1,500 cd/m². Retaining means avoids silently changing the measurement statistic. 3. Melanophila acuminata: the compiled 400 Hz value remains visible, but its endpoint is classified as nonvisual infrared pit-organ response and excluded from visual-CFF analyses. The source's abstract establishes sensory modality; the exact derivation of the compiled 400 is not verified from full text. No replacement visual value is invented. Source: Hammer et al. (2001), https://pubmed.ncbi.nlm.nih.gov/11282323/ . It had no AnAge match, so this exclusion does not reduce the previous 95 quality-rated overlap candidates. 4. Ovis aries, Ezra-Elia et al. (2014): the compiled 80 Hz is a lower bound; the source reports CFF >80 Hz. Retain 80 as the bound and exclude this row from models requiring an exact threshold. The separate 60 Hz row remains pending source verification, not automatically excluded or accepted. Source: https://pubmed.ncbi.nlm.nih.gov/25204753/ . Raw source columns and original CFF values are retained. `CFF_corrected` is the numeric field for subsequent processing; it must be used together with endpoint status. A number in that field does not imply eligibility. ## AnAge provenance decision Use the uploaded, hashed 4,645-entry snapshot as the fixed input. The official Build 15 release notes list 4,671 entries (3 July 2023): https://genomics.senescence.info/species/release.html . HAGR explains that downloaded stable-build data and online data may differ: https://www.genomics.senescence.info/download.html . This does not specifically identify the 26-entry discrepancy. Do not claim the file is corrupt, outdated, or an exact verified Build 15 release based solely on counts. Record its hash and user-provided provenance; the exact upstream revision remains unverified. This is a provenance qualification, not a demand for another user upload or a reason to stop all checking. ## Supplied phylogeny checked The earlier tree audit, recorded in `tree_checks.csv` and `audit_summary.json`, reports that `Haarlem_et_al_tree.tre` contains 100 trees, each with 237 unique tips. Every compiled CFF label appears in every tree. All 95 previous quality-rated longevity candidates have label-level tree coverage. Across all trees there are no negative, zero or nonfinite non-root edge lengths. Each has 12 multifurcations. Root-to-tip spread is approximately 0.000005 in the file's branch units; this is consistent with rounding, rather than substantive non-ultrametricity. The accompanying CFF_phylo_2025.Rmd describes a composite distribution built with an Open Tree of Life backbone and clade-specific sources. Do not describe it as a newly downloaded TimeTree database product. Label coverage was reported verified in that audit; source-species identity, dating assumptions and suitability for the final model still need assessment. Preserve multifurcations; do not randomly resolve them merely to force binary trees. Check covariance positive definiteness after pruning to the final sample. ## Working inclusion and analysis rules These are proposed methodological decisions made after earlier exploratory work. They are not yet preregistered. Finalize after source checks, then register the remaining analyses with explicit disclosure of prior results. ### Measurement eligibility - Study endpoint: association between visual temporal resolution and maximum recorded longevity. Neither is a direct measure of subjective time or intrinsic ageing rate. - Primary measurement stratum: source-verified behavioural visual flicker-fusion thresholds in healthy, normally developed animals. Analyse source-verified retinal ERG thresholds separately as a secondary stratum. Central-neuron, single-cell, blood-flow and thermal-response endpoints must not be pooled with behavioural CFF merely because the compilation calls them electrophysiology. - Extract population, age/developmental stage, sensory site, method, stimulus luminance, spectrum, modulation/contrast, adaptation, temperature and threshold criterion from each included study when reported. Missing means unknown, never zero. AnAge temperature is not CFF experimental temperature; ecological light category is not stimulus luminance. - A maximum tested frequency with continuing response is a censored bound, not an exact CFF. Exclude bounds from the planned exact-response PGLS. Keep a separate inventory; any later censored model requires its own specified likelihood. - Following the pass-3 clarification, the working estimand is a measured behavioural uniform-flicker threshold under documented test conditions, not automatically a species maximum. The earlier default of selecting peak thresholds is superseded. Retain luminance-series results, individual-peak means and protocol-specific maxima with their statistic and conditions identified. A consistent condition/statistic-selection rule remains to be specified before freezing the sample; no automatic highest-value fallback is approved. - Within each species and measurement stratum, deduplicate shared experiments. Only after compatible endpoints, statistics and test conditions have been established, consider a geometric mean across independent eligible study-level estimates, with equal study weights when comparable uncertainty estimates are unavailable. This is a working summarization choice, not a claimed optimum. Report sensitivity to the maximum eligible study estimate and to restriction to directly reported species means. Never pick the highest value across incompatible methods. - Missing luminance or temperature does not automatically make a published genuine threshold invalid. Flag it, assess method and clade imbalance, and compare with a subset having documented conditions. Do not pool unlike photometric units or fabricate conversions. If comparability remains poor, restrict scope and report descriptive results. ### Longevity and identity eligibility - Require a documented same-organism match, positive maximum longevity, and AnAge quality acceptable/high for the primary analysis. Keep questionable values for a separately labelled sensitivity analysis. Exclude missing longevity; never impute it from a related species. - Verify synonyms, spelling corrections and specimen suffixes. Keep the raw dataset/tree label, accepted biological name and AnAge identifier as separate fields. An exact text match does not settle domestic/wild or experimental-species conflicts. - Withhold unresolved cat/wildcat, dog/wolf, lionfish species, neonatal pig and caste-mismatch records from the primary sample pending adequate source evidence. Pass 2 already records domestic-dog and domestic-cat candidate joins; this does not resolve experimental population or tree placement. Do not silently rename tree tips. The current quality-rated candidate count is 94. - Retain wild/captive/unknown origin and ordinal longevity sample-size category for sensitivity analyses; these are not individual counts or precision weights. Maximum recorded longevity depends on observation effort and husbandry. ### Planned statistical approach, after the dataset is frozen - Primary working model within the behavioural stratum: log10(CFF in Hz) as response, log10(maximum longevity in years) and log10(adult body mass in grams) as predictors, using phylogenetic generalized least squares with Pagel's lambda estimated by maximum likelihood. This direction defines the coefficient and must be stated consistently. It does not establish causation. Use a fixed documented mass-source hierarchy, preferably the same AnAge adult-mass field throughout; do not substitute the metabolic-assay body mass without explicit review. - Fit an unadjusted longevity model on the same complete-case sample for comparison. Report exclusions due to missing mass. Do not build an over-parameterized model if the eligible sample is small or clade coverage is inadequate; report that the planned model is not supportable rather than choose a smaller model by its p-value. - Run the same frozen sample and formula over all 100 supplied trees. Report tree-specific estimates and confidence intervals, the distribution of estimates and the range of interval endpoints. Quantiles across trees reflect tree sensitivity, not a replacement sampling-confidence interval. Do not average p-values or select the tree producing significance. - Secondary ERG analysis follows the same rules and stays separately labelled. Any combined-method exploratory model must include method and explicitly discuss remaining confounding; a method indicator does not make distinct endpoints equivalent. - Diagnostics: residual patterns, heteroscedasticity, collinearity, influential species, likelihood/convergence, lambda boundaries and pruned covariance validity. Sensitivities: humans omitted, influential species left out one at a time, sufficiently represented clades analysed separately, wild/captive origin, questionable AnAge records, measurement-condition completeness, study aggregation choice, and lambda fixed at 0/1. - Report beta, 95% confidence interval, sample counts, clade/method coverage, uncertainty across trees and limitations. Avoid claims about a species experiencing more lifetime or about physical time. - R packages ape and caper are suitable standard implementations; caper documents PGLS and likelihood-estimated lambda: https://search.r-project.org/CRAN/refmans/caper/html/pgls.html . These are scientific software packages, not ChatGPT plugins. No extra plugin is needed for the present audit. The earlier audit recorded Rscript as unavailable at that time; this is not a current environment check. This package contains no final PGLS results. Installation or an available equivalent environment must be checked before the modelling stage, with version logging and validation. ## Still pending, precisely This package resolves the two Ficedula numeric assignments, the Melanophila modality exclusion and the 80 Hz sheep bound. It does not claim all 280 measurements have been verified. Other priority records and the remaining candidate sources require primary-source extraction. The current 94 quality-rated candidates are not a final analysis sample. Human review remains pending; it is not replaced by this computational audit. Preregistration, final models, manuscript changes and public release updates are deferred as requested. ## Reproduce and inspect Python 3 standard library is sufficient for these audit scripts. Run from the extracted package directory, preferably in a disposable copy: scripts overwrite their generated outputs. **Self-contained pass-4 regeneration:** ```bash python continue_audit_pass4.py . ``` This reads the bundled pass-3 table and regenerates four pass-4 CSV/JSON files. It does not regenerate documentation, the gap register or checksums. During the documentation review, all four outputs matched the bundled files byte-for-byte in a temporary directory. **Full measurement pipeline, with external inputs available:** ```bash python apply_audit.py INPUT_DIRECTORY OUTPUT_DIRECTORY python continue_audit.py INPUT_DIRECTORY OUTPUT_DIRECTORY python continue_audit_pass3.py INPUT_DIRECTORY OUTPUT_DIRECTORY python continue_audit_pass4.py OUTPUT_DIRECTORY ``` INPUT_DIRECTORY must contain `anage_data.txt`, `30556475.zip` and `AnAge_Haarlem_2026_Final_Crosswalk_Audit_2026-10-23.zip`. Preserve their internal layouts. Pass 1 reads `Supplementary files/Haarlem_et_al_cff_dataset_21_10_2025.csv` from the first archive and `237_taxa_anage_crosswalk.csv` from the crosswalk archive. The raw tabular input hashes are asserted by the script. Pass 3 retains the two-argument interface but reads the existing output directory. The full pipeline was not rerun during this documentation-only review because its external inputs are absent from this package. Assertions and deterministic output checks test implementation consistency, not scientific truth or independent human review. `SHA256SUMS.txt` covers the packaged files except itself; regenerate it after intentional changes. Original third-party rights remain unchanged.
# Pass 4 — 24 October 2026 Current table: measurement_audit_pass4.csv. Four records received additional source checks; none is newly certified analysis-ready. Existing corrections and platypus gap entry remain intact. No CFF numeric replacements were made. ## Findings - H2025_064, pigeon, Delius et al. 2017: Table 1 reports 73 Hz (70–74) for green light, four birds. Compiled 70 matches the range low rather than the mean. Source mean is stored separately in source_supported_summary_Hz_pass4; retain the compilation value until the statistic-selection rule is applied consistently. Conditions and sample size now recorded. https://pmc.ncbi.nlm.nih.gov/articles/PMC5679541/ - H2025_005, goldfish, Behrend et al. 2007: abstract supports approximately 39 Hz, not exact 39.5. Behavioural and ERG experiments and drug manipulations require arm-specific extraction. https://doi.org/10.1017/S0952523807070691 - H2025_006, goldfish, Mora-Ferrer and Gangluff 2002: pre-injection range 33–39 Hz verified; exact 37.5 and summary type remain unverified. https://doi.org/10.1017/S0952523802196106 - H2025_008, goldfish, Bilotta et al. 1998: behavioural sinusoidal-flicker contrast-sensitivity procedure verified; 24 Hz and corresponding luminance/contrast still need full-text extraction. https://pubmed.ncbi.nlm.nih.gov/9474375/ Sources accessed 24 October 2026. Pigeon full text/table was available through PMC after the PLOS image endpoint failed. Goldfish evidence here is abstract-level; it is not a full-text audit. ## Working method clarification For a baseline comparative analysis, use demonstrably untreated measurements. Record drug, lesion and recovery arms separately. A paper containing treatment arms is not automatically excluded; its eligible baseline must be identified. Do not collapse sinusoidal contrast thresholds, square-wave flicker, wavelength-specific means, or training variants into a single species maximum. Missing conditions remain missing, not imputed from another experiment. Reported ranges are not confidence intervals. ## Status and remaining work 280 measurement rows remain. The screening queue remains 117 measurements across 91 tree labels; these are workload counts, not a final sample. The earlier longevity-quality candidate count is not re-audited in this pass. Human review, tree/population reconciliation and final sample freeze remain pending. No final model, preregistration or public-release changes. Next priorities: obtain exact goldfish baseline values and conditions; decide the pigeon statistic under a consistent estimand; continue remaining behavioural sources. The raw AnAge data and trees are not in this ZIP, so this pass does not claim to have rerun their checks. ## Reproduction and validation Run `python continue_audit_pass4.py` from the package, or pass its directory as the argument. It reads the bundled pass-3 table; no raw external files are required for this incremental pass. Validation checks unique IDs, unchanged CFF/identity/longevity fields, preservation of untouched rows, deterministic regeneration, and ZIP integrity. Earlier passes still require their original external inputs.
# Platypus data-gap entry — 24 October 2026 Platypus (Ornithorhynchus anatinus) is documented separately from the measurement dataset. It is not added to the analysis sample or candidate count. ## Evidence and provenance - Confirmed in this update: no platypus/Ornithorhynchus entry in the 280 rows of measurement_audit_pass3.csv. - Carried forward from the earlier conversation audit: AnAge ID 02622; maximum recorded longevity 22.6 years (captivity); acceptable quality; small sample-size category; adult body mass 1,250 g. These are snapshot fields, not an average lifespan or newly verified current species records. - Earlier audit reported no platypus tip in the supplied trees. Raw AnAge and tree inputs are not in this ZIP, so those claims have not been independently rechecked in this update. - Earlier targeted literature searches did not locate a usable CFF measurement. This is not evidence that no such study exists; no new literature search was performed for this bookkeeping update. ## Missing-data rules CFF is null in JSON and blank in CSV, with an explicit not-available status. It must never be interpreted as zero or inferred from another species. No CFF value, tree tip, branch length, or regression result has been invented. ## Requirements for future inclusion Locate an original visual flicker-threshold study; verify species, endpoint, numerical threshold/bounds and experimental conditions; independently confirm the AnAge row; establish supported placement and branch lengths in an appropriate phylogeny; then apply the same eligibility rules used for other species. Any scope expansion must be recorded before remaining analyses are registered. ## Effect on the existing audit The 280 measurement rows, 237 compiled taxon labels, 117-row screening queue and previously reported 94 longevity-quality candidates remain unchanged. The final sample remains unfrozen. At the time this gap entry was added, existing files other than README.md and SHA256SUMS.txt were preserved byte-for-byte. Later documentation revisions are recorded in DOCUMENTATION_REVIEW.md.
# Source-checking progress: pass 2 > Historical pass snapshot. Current status and methods: README.md; current measurement audit: measurement_audit_pass4.csv. Counts and pending items below describe this pass at the time, not the latest state. 23 October 2026. Working audit; final sample not frozen. ## Current files Read this update alongside README.md. The original pass-1 outputs remain as provenance. For current working values use measurement_audit_pass2.csv, crosswalk_pass2.csv and audit_summary_pass2.json. The 19 additional row-level decisions, their evidence links and limits are in source_decisions_pass2.csv. The queue is an inventory of 118 candidate measurements across 92 taxon labels, not 92 approved species. It includes rows already checked in part but still requiring eligibility or provenance work. ## Changes applied - Dog: source confirms domestic beagles. The corrected candidate joins to AnAge Canis familiaris, 27 years, acceptable, instead of Canis lupus, 20.6 years. Exact 84 Hz extraction and a defensible domestic-dog tree placement remain pending. No tree tips were silently renamed. - Cat: the compilation labels all four rows House cat. The appropriate candidate is AnAge Felis catus, 30 years, questionable, not wildcat Felis silvestris, 19 years, acceptable. Full-text source population remains to be confirmed. This removes the cat from the acceptable/high candidate tier, reducing that tier from 95 to 94. Neither number is a final eligible sample. - Cat measurements: 75 Hz is from a blood-flow study, 70 Hz from intracellular horizontal-cell recording, and 40 Hz from cortical recording. The last was incorrectly labelled Behavioural. These three endpoints are excluded from the behavioural and whole-retina ERG strata. The 47.5 Hz behavioural study remains separately traceable. - Painted turtle: Graf 1972 is behavioural psychophysics. Corrected Electrophysiology to Behavioural. Species identity is supported; the compiled 31 Hz needs full-text extraction. Replaced reliance on the unrelated iNaturalist link with the original article DOI in the evidence field. - Slider turtle: the original study names Pseudemys scripta and the taxonomic source supports Trachemys scripta. The corrected biological name is supported; the raw misspelled tree label is retained for traceability. The exact 52.6 Hz endpoint remains unverified. - Blue tit: confirmed Parus caeruleus/Cyanistes caeruleus identity and 130.3 Hz source mean. - Chicken (Lisney 2012) and tree shrew (Tigges 1967): both are ERG studies incorrectly labelled Behavioural. Corrected their audited method. Exact numeric extraction remains open. - Lionfish: 88 Hz is explicitly a median at maximum stimulus intensity, not a species mean. The inspected study reports Pterois spp.; a P. volitans-only longevity pairing remains withheld. - Honeybee: primary source identifies approximately 200 Hz movement fusion with rotating patterns. Kept separate from uniform-field flicker thresholds. Caste compatibility remains unresolved; no queen/worker longevity substitution was made. - Loggerhead and leatherback: the primary abstract describes frequency-following responses extending to about 15 Hz and not above 10 Hz respectively, unlike the compiled 40 and 15 Hz. Both rows are held. These response limits were not converted into invented exact CFF means. Their hatchling life stage and isolated-retina preparation are recorded. - Piglet: neonatal treatment study confirmed. The compiled 60 Hz is not validated as a fusion threshold by the accessible abstract. Held pending control-group and endpoint extraction. - Cane toad: rod-photoreceptor endpoint separated from whole-retina ERG. Historical synonym is supported but source locality/species-complex identity still requires care. - Green frog: nomenclatural connection supported. Original experiment is still needed; the compilation points to a review and its human-effects table. - Pigeon (Delius 2017): genuine behavioural threshold experiment confirmed. The symmetry-focused title is not grounds for exclusion; numerical table extraction and protocol selection remain pending. ## Consequences for methods The original broad method column cannot be used without source checks. Four explicit method corrections in this pass are painted turtle to Behavioural; cat Rager 1998 to cortical electrophysiology; chicken Lisney 2012 and tree shrew Tigges 1967 to retinal ERG. Other electrophysiological rows have been assigned more specific endpoint classes where supported. The original quality-rated overlap contained 40 rows labelled Behavioural across 30 taxa. This was a compiled-method inventory, not verified sample size. Exact uniform-field flicker, patterned movement fusion, intracellular responses, blood flow and cortical entrainment should remain distinct. A loss of sample size is preferable to silently merging incompatible endpoints. Retain reported medians as medians. The lionfish result highlights that a field called CFF can mix means, medians, individual extremes and stimulus limits. The working study-aggregation rule in README.md applies only after identifying compatible summaries; unverified statistic type must not be treated as a mean by default. Developmental studies require a stated life-stage scope, not automatic substitution of hatchling or intervention measurements for normative adult values. ## What is and is not resolved 19 additional measurement rows now have explicit source-based decisions or documented holds. These are not 19 fully validated records. Source identity, numeric extraction, endpoint comparability, longevity population and phylogenetic mapping are separate checks. All 280 source rows remain in the audit; nothing was silently deleted. No new CFF numeric values were changed in pass 2. The earlier two Ficedula corrections remain. The 94 acceptable/high candidates include taxonomically or methodologically unresolved records. The queue contains 92 taxa because current endpoint exclusions remove the sole available records for the cane toad and honeybee. It still includes ERG-only taxa, unresolved identities, partial checks and uncertain developmental scope. The questionnaire-like phrase final_analysis_eligible remains not_finalized throughout. Full-text extraction remains necessary for several older studies. Graf 1972 exposes a publisher access barrier; multiple indexed abstracts verify method but cannot support exact numeric claims. Many other rows have not yet received source review. The next work is to extract the remaining primary-source values and conditions, beginning with behavioural candidates and shared sources, then audit ERG candidates separately. Do not move to preregistration or final regression on the basis of this queue. Human independent review remains pending. No emails, registration, final model, manuscript revision, Zenodo replacement or website deployment occurred. ## Reproduction 1. Run `python apply_audit.py INPUT_DIRECTORY OUTPUT_DIRECTORY`. 2. Run `python continue_audit.py INPUT_DIRECTORY OUTPUT_DIRECTORY`. The scripts preserve raw inputs and assert row counts, the dog join, corrected methods and candidate counts. Evidence URLs are recorded per decision. Biological interpretation remains subject to human review; assertions test consistency, not scientific truth.
# Source audit pass 3 — 23 October 2026 > Historical pass snapshot. Current status and methods: README.md; current measurement audit: measurement_audit_pass4.csv. Counts and pending items below describe this pass at the time, not the latest state. Current measurement table: measurement_audit_pass3.csv. Seven additional records received source adjudication; none received a numerical CFF replacement. These are partial evidence decisions, not seven fully approved observations. Raw measurements, prior corrections and supplied trees remain preserved. Read source_decisions_pass3.csv for row-specific evidence, URLs and holds. The current screening queue contains 117 measurements from 91 tree labels. It is a review workload, not a final sample; excluded endpoints remain in the full table. Prior crosswalk_pass2.csv remains the current identity crosswalk; this pass changes measurement classification only. ## Method decision before pooling Define the estimand explicitly: a behavioural threshold under recorded test conditions, versus maximum temporal capacity over luminance. The working default is measured behavioural uniform-flicker thresholds with conditions retained. Analyse retinal ERG separately. Motion responses, reported maxima, means, medians and range midpoints must not be pooled as interchangeable estimates. No geometric averaging across incompatible statistics or protocols is authorised by this audit. A threshold measured at a particular luminance remains a measurement even if the species peak was not reached. This is different from a tested frequency ceiling that supplies only a lower bound. The new maximum_capacity_status field records that distinction. tested_lower_Hz and tested_upper_Hz are descriptive source ranges/brackets, not confidence limits or automatically valid individual censoring intervals. ## Remaining work Extract outstanding figures/tables and original reports, record light, temperature, age and threshold criteria, reconcile taxon/population and longevity quality, and document exclusions. Missing researcher replies remain open evidence requests; no response is assumed. Freeze the sample only after these gates are reviewed. No final models, preregistration or publication were performed. ## Reproduction Run apply_audit.py DATA OUT, then continue_audit.py DATA OUT, then continue_audit_pass3.py DATA OUT using Python 3. The input directory must contain the supplied datasets in their existing layout. Scripts use the standard library. All three passes were rerun in a fresh temporary directory and generated CSV/JSON outputs were compared byte-for-byte. ZIP integrity was checked.
# Documentation review — 24 October 2026 Scope: internal accuracy, consistency and clarity of the supplied pass-4 package. No new literature search, raw-source audit, statistical model or independent human review was performed. ## Changes - Replaced three competing start-here instructions with one current-file index. - Distinguished 280 measurements, 237 raw labels, 94 longevity-quality candidate labels and the 117-measurement/91-label screening queue. - Explained the inherited historical count of 95 in pass-2 JSON and the precedence of audited crosswalk fields. - Marked pass-2 and pass-3 progress notes as historical. Their pending items may have been addressed in later passes. - Reconciled the older peak-selection rule with pass 3: measured thresholds under recorded conditions are the working target. Selection across conditions remains unresolved; geometric aggregation is conditional on comparability. - Qualified raw AnAge, tree and software-environment claims as earlier findings rather than newly performed checks. - Added complete reproduction commands and distinguished self-contained pass 4 from the externally dependent full pipeline. - Made the platypus preservation statement explicitly historical. ## Validation Recounted the current measurement table, queue and crosswalk; confirmed all 280 eligibility fields remain not_finalized. Regenerated the four pass-4 outputs in a temporary directory and compared them byte-for-byte successfully. All pre-existing CSV, JSON and Python files, plus tree checks, remain byte-identical to the supplied ZIP. Only documentation and checksums changed; this review note was added. Refreshed package checksums and checked ZIP integrity. ## Still unresolved Primary-source exact values and conditions; consistent statistic/condition selection; organism and tree matching; final eligibility; human review; registration of remaining analyses; final modelling and public-release updates. No candidate count is presented as a finished analysis sample.