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--- provenance:statistics:pvalue_corrections [2026/09/04 17:30] – Citekey consolidation 2026-09-04: repoint duplicate bibliography keys to the kept key and add a dated amendment; no prose or figure changed. Authored by Claude karel.kubicek.claude
+++ provenance:statistics:pvalue_corrections [2026/09/21 13:34] (current) – Quote-check refresh 2026-09-21: re-ran quote_check.mjs --statistics multiple-comparison-correction with the pypdf fallback; 62 below threshold -> 40 rescued + 22 below in both, plus a cross-map showing 10 (not 22) unread. Authored by Claude karel.kubicek.claude
@@ Line 9: / Line 9: @@
 | Report script | ''scripts/report_pvalue_corrections.mjs'' |
 | Free-text fold it depends on | ''scripts/mcc_fold.mjs'' — 11 procedure families plus two non-correction buckets, with a self-test |
-| Quote verification | ''scripts/quote_check.mjs --statistics multiple-comparison-correction'' (the ''--statistics'' filter was added for this page) |
+| Quote verification | ''scripts/quote_check.mjs %%--statistics%% multiple-comparison-correction'' (the ''%%--statistics%%'' filter was added for this page) |
-| Stale-number guard | ''scripts/check_page_numbers.mjs'', whole-page, with ''--code'' |
+| Stale-number guard | ''scripts/check_page_numbers.mjs'', whole-page, with ''%%--code%%'' |
 | Non-corpus number ledger | ''out/pvalue-external-facts.txt'' |
 | Runnable code published on the page | ''out/adjust_pvalues.py'' |
@@ Line 16: / Line 16: @@
 | Written | 2026-08-13, against the corpus as extended on 2026-08-11 (commit ''8a6b843'') |
-**Creating, not extending, and not overlapping.** ''statistics:pvalue_corrections'' was a red link promised from [[start]]. The only neighbouring page that existed when this was written is [[statistics:study_preregistration]], which touches multiplicity in one subsection ("For scale: the rest of the inference-hygiene stack is thin too") and cites this page forward. That subsection's figures (15.3% of ''inferential'', 24.5% of hypothesis-test papers) agree with this page's; this page keeps the ''hypothesisTest'' denominator throughout and adds the corrected-vs-tuple distinction the preregistration page did not need. **Nothing was overwritten and no neighbouring figure was contradicted.**
+**Creating, not extending, and not overlapping.** ''statistics:pvalue_corrections'' was a red link promised from [[:start]]. The only neighbouring page that existed when this was written is [[statistics:study_preregistration]], which touches multiplicity in one subsection ("For scale: the rest of the inference-hygiene stack is thin too") and cites this page forward. That subsection's figures (15.3% of ''inferential'', 24.5% of hypothesis-test papers) agree with this page's; this page keeps the ''hypothesisTest'' denominator throughout and adds the corrected-vs-tuple distinction the preregistration page did not need. **Nothing was overwritten and no neighbouring figure was contradicted.**
-**Reachability** needed no work: [[start]] already lists ''[[Statistics:Pvalue corrections|P-value corrections]]'' in its outline, and [[statistics:study_preregistration]] links it twice.
+**Reachability** needed no work: [[:start]] already lists ''[[Statistics:Pvalue corrections|P-value corrections]]'' in its outline, and [[statistics:study_preregistration]] links it twice.
 ===== 2. The number the task started from, and what happened to it =====
@@ Line 52: / Line 52: @@
 node scripts/report_pvalue_corrections.mjs                  # every figure on the page
 node scripts/report_pvalue_corrections.mjs --wiki           # DokuWiki tables
-node scripts/quote_check.mjs --statistics multiple-comparison-correction --show 62
+node scripts/quote_check.mjs --statistics multiple-comparison-correction --show 400
 python3 out/adjust_pvalues.py --demo                        # the published code's output
 cat out/pvalue-report.txt out/adjust_pvalues_demo.txt \
@@ Line 154: / Line 154: @@
 ===== 6. Quotes checked against source =====
-Bulk pass over every correction quote, with the ''--statistics'' filter added to ''quote_check.mjs'' for this page:
+Bulk pass over every correction quote, with the ''%%--statistics%%'' filter added to ''quote_check.mjs'' for this page. **Re-run 2026-09-21** with the PDF fallback — see //Quote-check refresh, 2026-09-21// at the foot of this page:
 <code>
-$ node scripts/quote_check.mjs --statistics multiple-comparison-correction
+$ node scripts/quote_check.mjs --statistics multiple-comparison-correction --show 400
-quotes checked: 167 exact, 63 partial (>=60% of 5-word windows), 62 below threshold, 0 with no full text on disk.
+quotes checked: 167 exact, 63 partial (>=60% of 5-word windows), 40 rescued from the PDF, 22 below threshold in both renderings, 0 with no full text on disk.
 </code>
-below threshold is 21% and higher than this tool usually reports. **The first 40 of the 62 were read** (the tool's ''--show 40'' default output, kept in ''out/pvalue-quotecheck.txt''); the remaining 22 were **not** read. In all 40 read, the cause is not fabrication: correction quotes are short (median well under 20 words), so one dropped citation marker or one extractor ellipsis destroys a large fraction of the five-word windows. ''"Fisher's binomial proportion test ... with a Bonferroni correction."'' scores 0% and is real. **The 22 unread ones are an open item** — nothing on the content page depends on them, since every quote the page uses was checked by hand (below), but they are not evidence for anything either.
+**The old figure was 62 below threshold, i.e. 21%, and it was higher than this tool usually reported because the tool was only reading one rendering.** 40 of the 62 are located in an independent ''pypdf'' rendering of the same ''paper.pdf'' and are a defect in the stored text, not in the extraction. **22** are below threshold in both, which is **7.5%** of 292. ''exact'' (167) and ''partial'' (63) did not move.
+**The 40/22 split is not the 40-read/22-unread split, and the coincidence is a trap.** The August run printed only the first 40 of the 62 (''%%--show%% 40'' was its default; that output is kept in ''out/pvalue-quotecheck.txt''), and those 40 were read by hand. Cross-mapping the two runs on paper/label/section:
+  * **28** of the 40 read by hand are now //rescued// — the hand read and the PDF fallback agree.
+  * **12** of the 40 read by hand are still below threshold in both renderings. All 12 were found present when read; the hand read remains the only evidence for them.
+  * **10** of the 22 now below threshold in both were never printed by the August run and have **not** been read. These are the open item, not 22.
+  * The remaining 12 //rescued// come from the 22 the August run never printed, so the fallback has closed 12 of those 22 without anyone reading them.
+In all 40 read, the cause was not fabrication: correction quotes are short (median well under 20 words), so one dropped citation marker or one extractor ellipsis destroys a large fraction of the five-word windows. ''"Fisher's binomial proportion test ... with a Bonferroni correction."'' scores 0% and is real. **The 10 unread ones are the open item** — nothing on the content page depends on them, since every quote the page uses was checked by hand (below), but they are not evidence for anything either.
 **Every quote used on the content page was then located by hand** in ''data/fulltext/<year>/<venue>/<slug>/paper.cols.txt''. All 18 checked out:
@@ Line 184: / Line 193: @@
 | {[ho2025_efficacy]} | "multiple comparison" | found verbatim, including "N = 2,693 per group" |
-<wrap todo>
+<WRAP todo>
 One thing found while checking and **not** put on the page. {[kablo2023_privacy]} writes //"we adjusted the standard threshold of 0.05 to a new threshold of 0.00047 (0.005 / 106)"//. 0.05/106 = 0.00047, so the printed threshold is right and the parenthetical divisor has a typo, or is a PDF-extraction artefact of "0.05". It is a one-character slip in an otherwise exemplary paper and calling it out on the page would be a gotcha, not a lesson. Recorded here instead.
-</wrap>
+</WRAP>
 ===== 7. External sources, and how each was verified =====
@@ Line 242: / Line 251: @@
 ==== 7.4 The published code was run, and its Holm implementation cross-checked ====
-''numpy'' 2.4.6, ''scipy'' 1.17.1, ''statsmodels'' 0.14.6, installed into the sandbox with ''pip install --break-system-packages''. The page publishes the unedited ''--demo'' output.
+''numpy'' 2.4.6, ''scipy'' 1.17.1, ''statsmodels'' 0.14.6, installed into the sandbox with ''pip install %%--break-system-packages%%''. The page publishes the unedited ''%%--demo%%'' output.
 <code>
@@ Line 332: / Line 341: @@
 **36 of the 38 recruited human participants.** The two that did not are ''IEEE-SP/2020/are-anonymity-seekers-just-like-everybody-else'' and ''IEEE-SP/2024/a-picture-is-worth-500-labels''. **Exactly one of the 38 ran a crawl**: ''PETS/2024/what-does-it-mean-to-be-creepy'', whose ''studyTypes'' includes ''automated-web-crawl'' and which also recruited participants. So the population that sizes a study with a correction in the calculation is, with one partial exception, a user-study population.
-<wrap todo>
+<WRAP todo>
 An earlier version of this section said "37 of the 38" and named ''IMC/2022/what-factors-affect-targeting-and-bids-in-online-advertising'' as the exception and as a crawl. **All three parts of that were wrong** — the count is 36, that paper has ''participants'' tuples, and its ''studyTypes'' are ''['user-study', 'manual-audit']'' with ''crawlConfig === null'', so it is not a crawl by the definition in §3. It was caught by the figures-vs-script reviewer and is recorded here rather than silently corrected, because it is the clearest example on this page of a claim written from memory instead of from a query.
-</wrap>
+</WRAP>
 ===== 10. Judgement calls =====
@@ Line 352: / Line 361: @@
 Four reviewers, all told explicitly that the author's context may not be exhaustive, and all handed the page text, the report script, its unedited output, and these notes. The three focused passes ran in parallel first; the generic pass ran after their findings were applied.
-==== 11.1 ''sonnet'' — figures against the script ====
+==== 11.1 sonnet — figures against the script ====
 Re-ran all three scripts (byte-identical to the committed output), re-derived the 1,025 / 269 / 141 anchor counts from ''extractions.jsonl'' in an independent Python re-implementation of the fold, and cross-checked ''holm()''/''bonferroni()'' against ''statsmodels'' on 20 random families plus edge cases (all-ones, single value, ties): max abs diff 0.0.
@@ Line 366: / Line 375: @@
 One correction to the reviewer, recorded for the record: it reported that ''IMC/2022/what-factors-affect-targeting-and-bids'' //"has 286 participants (recruited via Prolific)"//. The ''participants'' array on that record has **2 tuples**, not 286 people; the reviewer conflated a tuple count with a headcount. Its substantive point — that the paper has participants and is not a crawl — is correct and was the basis for the fix.
-==== 11.2 ''sonnet'' — citations and quotes ====
+==== 11.2 sonnet — citations and quotes ====
 Verified all 27 citekeys resolve with no collisions, all 17 corpus entries against ''data/corpus2/.meta'' and the papers' own front matter, all 8 external DOIs through ''doi.org'', and all 18 quotations against ''paper.cols.txt''.
@@ Line 378: / Line 387: @@
 | Kablo & Cabarcos's //"(0.005 / 106)"// is confirmed as an error in the paper itself, not an extraction artefact | **no change needed** | Stays off the content page for the reason in §6 |
-==== 11.3 ''sonnet'' — external currency, as of 2026-08-13 ====
+==== 11.3 sonnet — external currency, as of 2026-08-13 ====
 ^ Finding ^ Accepted? ^ What was done ^
@@ Line 388: / Line 397: @@
 | All 17 corpus DOIs and all 3 USENIX URLs return HTTP 200; SciPy 1.18.0 and statsmodels 0.14.6 are current; ''false_discovery_control'' is unchanged between 1.17.1 and 1.18.0 | **no change needed** | — |
-==== 11.4 ''fable'' — generic ====
+==== 11.4 fable — generic ====
 No checklist; run after the three focused passes were applied. It returned fifteen findings and **fourteen were accepted**, which is the highest accept rate of the four reviewers and the reason this slot is worth keeping.
@@ Line 405: / Line 414: @@
 | //"The only mechanism that addresses it"// is contradicted twice on the same page (the "cheap version" paragraph, and the multiverse open question) | **yes** | Now "the standard mechanism", with the alternatives named |
 | Provenance §11.4 was published as an empty placeholder while §12 counted a ''fable'' pass among the reviewers | **yes** | This section. The placeholder should not have been saved; recording a review before it exists is the same defect as publishing a figure before checking it |
-| Provenance §6 says //"Reading them, the cause is not fabrication"// about the 62 below-threshold quotes without saying how many were read, on the one bucket where fabrication would hide | **yes** | §6 now states 40 read, 22 not, and says the 22 are evidence for nothing |
+| Provenance §6 says //"Reading them, the cause is not fabrication"// about the 62 below-threshold quotes without saying how many were read, on the one bucket where fabrication would hide | **yes** | §6 stated 40 read, 22 not, and said the 22 are evidence for nothing. **Superseded 2026-09-21:** the 62 is now 40 //rescued// + 22 below threshold in both, and §6 gives the cross-map — 10 quotes, not 22, are unread |
 | Provenance arithmetic drift: the content page said "nine DOIs" where §7.1 listed eight, and §12 said "26 entries" next to "27 keys" | **yes** | CONSORT's DOI added to §7.1; §12 corrected to 27 entries and 28 keys |
 | The headline box's three bullets omit the //both// cell (34.7%), which is the one that sharpens the story | **yes** | Fourth bullet added, and it is now the point the box makes: the two participant rows are the two high ones |
@@ Line 413: / Line 422: @@
 **Rejected: none outright.** The one partial is the ''gelman2014_statistical'' page range from §11.2, left at ''460'' because no primary source for an end page could be found.
-==== 11.5 Re-review, both ''sonnet'' passes, after the fixes ====
+==== 11.5 Re-review, both sonnet passes, after the fixes ====
 The two focused reviewers whose findings were acted on were re-run against the edited pages, as the workflow requires. Both found real defects in the **new** material, which is the argument for re-running them.
@@ Line 437: / Line 446: @@
 | Reviewers | three ''sonnet'' passes (figures-vs-script, citations-and-quotes, external currency) and one ''fable'' generic pass |
 | New scripts | ''scripts/mcc_fold.mjs'', ''scripts/report_pvalue_corrections.mjs'' (which carries its own two-sided Fisher exact test, checked against ''scipy.stats.fisher_exact'' to four significant figures) |
-| Modified scripts | ''scripts/quote_check.mjs'' — added a ''--statistics <kind>'' filter, which did not exist |
+| Modified scripts | ''scripts/quote_check.mjs'' — added a ''%%--statistics%% <kind>'' filter, which did not exist |
 | New artifacts | ''out/pvalue-report.txt'', ''out/pvalue-quotecheck.txt'', ''out/pvalue-external-facts.txt'', ''out/adjust_pvalues.py'', ''out/adjust_pvalues_demo.txt'', ''out/bib_additions_pvalue.bib'' |
 | Bibliography | **27 entries appended**: 17 corpus papers via ''bibgen.mjs'', 9 external statistics references, and ''hopewell2025_consort'' added after the currency review. No duplicate keys; all 28 keys used on the page resolve and the rendered page reports zero bibtex warnings |
@@ Line 459: / Line 468: @@
 <bibtex bibliography></bibtex>
+===== Markup sweep, 2026-09-17 =====
+Mechanical rendering repair only: a fresh live raw/XHTML export of 188 pages was checked with ''check_wrap.mjs'' and ''check_typography.mjs''. Affected plugin tags, CLI flags and heading markup were repaired; no figures or substantive prose were changed. The resulting source and rendered DOM were re-checked after saving.
+===== Link-hygiene sweep, 2026-09-17 =====
+The fresh rendered-DOM sweep found this page's two bare ''start'' links resolved to ''provenance:statistics:start''. They are now root-anchored; the post-save DOM was re-checked for red links. No figures or citations changed.
+===== Quote-check refresh, 2026-09-21 =====
+The 2026-09-04 ''cols''-vs-PDF audit on [[:provenance:literature:corpus]] showed that 73.1% of evidence quotes that cannot be located in ''paper.cols.txt'' **are** present in an independent ''pypdf'' rendering of the same ''paper.pdf''. ''scripts/quote_check.mjs'' was patched the same day to re-check everything below threshold against that second rendering and report a fourth verdict, **RESCUED**. §6's figure predates the patch and overstated this page's quote-failure rate by nearly a factor of three. Re-run, unedited first line:
+<code>
+$ node scripts/quote_check.mjs --statistics multiple-comparison-correction --show 400
+quotes checked: 167 exact, 63 partial (>=60% of 5-word windows), 40 rescued from the PDF, 22 below threshold in both renderings, 0 with no full text on disk.
+</code>
+^ Figure ^ Was ^ Is ^ Why ^
+| quotes checked | 292 | 292 | population unchanged — the corpus has not moved |
+| exact | 167 | 167 | unchanged |
+| partial (≥60% of 5-word windows) | 63 | 63 | unchanged |
+| rescued from the PDF | — | **40** | new verdict; these were inside the old 62 |
+| below threshold | **62** | **22** (in both renderings) | 62 = 40 + 22 exactly; nothing else moved |
+| below-threshold rate | 21% | **7.5%** | 22 of 292 |
+| unread below-threshold quotes | 22 | **10** | cross-mapped against ''out/pvalue-quotecheck.txt'' — see §6 |
+**What this does and does not say.** It does not say 40 extractions were wrong and are now right — the quotes were always in the papers, and 28 of these 40 had already been read by hand and found present. It says the //stored text// could not locate them and a second rendering of the same PDF can, so counting them as quote failures measured ''decolumn.mjs'', not the extraction.
+**The one number that needed more than the script.** ''62 = 40 + 22'' and ''62 = 40 read + 22 unread'' are two different partitions of the same 62, and reading the new output alone would let a future editor merge them. §6 now carries the cross-map: 28 of the 40 hand-read are //rescued//, 12 are still below in both, and 10 of the 22 now-below have never been read.
+**Scope of this edit.** §6, the §3 command line (''%%--show 62%%'' → ''%%--show 400%%'', since 62 no longer sizes the output), the review-log row that quoted the old disposition, and the content page's quote bullet. ''report_pvalue_corrections.mjs'' and ''mcc_fold.mjs'' were **not** re-run in this pass; no fold, rate, Fisher //p//-value or citation was touched, and every other figure on [[:statistics:pvalue_corrections]] and this page stands as published.
+^ Item ^ Value ^
+| Date | 2026-09-21, unsupervised |
+| Command | ''%%node scripts/quote_check.mjs --statistics multiple-comparison-correction --show 400%%'' |
+| Artifacts | ''out/qc0921/stat_mcc.txt'' (full run, 40 RESCUED rows and 22 below-threshold rows listed); the August output ''out/pvalue-quotecheck.txt'' was kept and used for the cross-map |
+| Script changes | none — ''quote_check.mjs'' was already patched on 2026-09-04 |
+| Reviewers | one ''sonnet'' figures-vs-script pass over this page and [[:statistics:pvalue_corrections]] |
+| Pages saved | this page, [[:statistics:pvalue_corrections]] |