From e8825b471da7c64a73aa900cc4d75874600c85be Mon Sep 17 00:00:00 2001 From: Lukas Wallrich Date: Tue, 21 Jul 2026 12:11:28 +0100 Subject: [PATCH] Add per-effect focal-effect flags derived from abstract-coding Flags, for each of the 2164 FReD effects, whether it is the focal effect of its replication pair (the single effect the replication targeted). Focal effects resolved per pair by a tiered rule (single_effect -> abstract match -> outcome_quote match -> replication-report reading; LLM tiers use gemini-flash-lite-latest two-pass semantic matching, report tier is human-directed agent reading with cited evidence). Pairs with no single identifiable focal claim are classified as constituent_set, target_absent, focal_in_sibling (FReD-fragment pairs whose focal effect lives in a sibling fred_id), or not_applicable (association-matrix bundles); no pair remains needs_review. Effects outside the coded universe are uncoded. Exactly one is_focal=TRUE per resolved pair (957). Co-Authored-By: Claude Fable 5 --- cache/focal_effect_flags.csv | 2165 ++++++++++++++++++++++++++++++++++ cache/focal_effect_flags.md | 185 +++ 2 files changed, 2350 insertions(+) create mode 100644 cache/focal_effect_flags.csv create mode 100644 cache/focal_effect_flags.md diff --git a/cache/focal_effect_flags.csv b/cache/focal_effect_flags.csv new file mode 100644 index 0000000..2396822 --- /dev/null +++ b/cache/focal_effect_flags.csv @@ -0,0 +1,2165 @@ +effect_id,fred_id,doi_o,is_focal,focal_role,focal_source,confidence,needs_review,coverage,proposed_row +1,add_ai57,10.1037/0003-066x.54.6.408,TRUE,focal,abstract,high,FALSE,resolved, +2,CORE_160,10.1006/cogp.1998.0708,FALSE,constituent,report,low,FALSE,constituent_set, +3,CORE_146,10.3758/bf03197186,FALSE,constituent,report,low,FALSE,constituent_set, +4,add_ai57,10.1037/0003-066x.54.6.408,FALSE,none,abstract,high,FALSE,resolved, +5,CORE_160,10.1006/cogp.1998.0708,FALSE,constituent,report,low,FALSE,constituent_set, 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+2148,yAPR_single-trace,10.1007/s13524-018-0725-0,,,,,,uncoded, +2149,YpZZ_single-trace,10.1016/j.jenvp.2014.10.008,,,,,,uncoded, +2150,YWep_single-trace,10.1016/j.compedu.2014.04.009,,,,,,uncoded, +2151,yypJ_single-trace,10.1016/j.evolhumbehav.2016.06.001,,,,,,uncoded, +2152,zK2_single-trace,10.1016/j.jesp.2018.08.007,,,,,,uncoded, +2153,zNEm_single-trace,10.1016/j.cognition.2010.11.011,,,,,,uncoded, +2154,5Kgq_single-trace,10.1007/s13524-011-0026-3,,,,,,uncoded, +2155,kXp8_single-trace,10.1287/orsc.1080.0377,,,,,,uncoded, +2156,RrOb_single-trace,10.1016/j.jfineco.2014.05.008,,,,,,uncoded, +2157,jLr_single-trace,10.1016/j.jesp.2012.08.013,,,,,,uncoded, +2158,AvOr_single-trace,10.1177/0956797618756862,,,,,,uncoded, +2159,LyLd_single-trace,10.1086/597428,,,,,,uncoded, +2160,zlm2_single-trace,10.1016/j.evolhumbehav.2014.02.004,,,,,,uncoded, +2161,plLK_single-trace,10.1016/j.obhdp.2009.06.003,,,,,,uncoded, +2162,EQxa_single-trace,10.1016/j.cognition.2012.11.003,,,,,,uncoded, +2163,8wZ0_single-trace,10.1016/j.cognition.2012.05.011,,,,,,uncoded, +2164,AgO1_single-trace,10.1007/s10683-011-9295-3,,,,,,uncoded, diff --git a/cache/focal_effect_flags.md b/cache/focal_effect_flags.md new file mode 100644 index 0000000..6849bb1 --- /dev/null +++ b/cache/focal_effect_flags.md @@ -0,0 +1,185 @@ +# Focal-effect flags (`focal_effect_flags.csv`) + +Per-effect flag marking, for each FReD effect, whether it is the **focal effect** of its +replication pair — the single effect the replication study actually targeted as its primary +replication object. One row per FReD `effect_id` (2164 rows, keyed to `output/FReD.xlsx`). + +## Columns + +| column | meaning | +|---|---| +| `effect_id` | FReD effect id (join key to `output/FReD.xlsx`) | +| `fred_id` | FReD pair id (original study ↔ replication) | +| `doi_o` | original-study DOI (from FReD; not a unique key — see caveats) | +| `is_focal` | `TRUE` **only** for a pair's single focal effect (`focal_role == focal`); `FALSE` for every other coded effect (non-focal, constituent, target-absent, or a base fragment's effects); empty (NA) for `not_applicable`/`uncoded` effects | +| `focal_role` | the effect's role in its pair: `focal` \| `constituent` \| `none` \| empty (NA). See below | +| `focal_source` | how the focal effect / verdict was identified for that pair (see tiered rule); empty for `not_applicable`/`uncoded` | +| `confidence` | high/medium/low confidence of the determination; empty for `not_applicable`/`uncoded` | +| `needs_review` | `FALSE` for every coded pair (no pair is now open for review); empty for uncoded effects | +| `coverage` | `resolved` \| `constituent_set` \| `target_absent` \| `focal_in_sibling` \| `not_applicable` \| `uncoded` (see below) | +| `proposed_row` | `TRUE` for effects of a `target_absent` pair whose focal effect is a **not-yet-in-FReD row that should be added** (see below); empty otherwise | + +`focal_role` values: +- **focal** — this effect is the single focal effect of a focal-resolved pair (`is_focal = TRUE`). +- **constituent** — this effect is one member of an **aggregate replication's constituent set**: the replication targeted a whole set of co-equal effects, and this effect is one of them (no single focal). See "Constituent sets" below. +- **none** — a coded effect that is neither focal nor a constituent: a non-focal effect of a focal-resolved pair, a non-constituent candidate of a constituent-set pair, any candidate of a `target_absent` pair, or any effect of a `focal_in_sibling` base fragment. +- **empty (NA)** — effects of `not_applicable` pairs (Soto) and all `uncoded` effects. + +`coverage` classes (one per pair, broadcast to its effects): +- **resolved** — the pair has a single identified focal effect (exactly one `focal_role = focal`, `is_focal = TRUE`). +- **constituent_set** — an aggregate replication with no single focal effect; the verdict is about a set of co-equal constituent effects, flagged `focal_role = constituent`. +- **target_absent** — the effect the replication targeted is **not present among FReD's candidate rows** for the pair; the coded replication verdict exists but attaches to no candidate, so no effect is focal or constituent. 3 pairs; two carry `proposed_row = TRUE` (their focal effect is a specific row that should be added to FReD, staged in `proposed_fred_rows_final.csv`). +- **focal_in_sibling** — the pair is a **fragment**: FReD split one original↔replication pair across several `fred_id`s, and the effect the replication actually targeted lives under a *sibling* `fred_id` (same `doi_o` + `doi_r`) that is itself `resolved`. This base fragment holds only non-targeted effects, so none of its own effects is focal. See "fred_id fragmentation" below. +- **not_applicable** — the "focal effect" concept does not apply: the replication is an **association-matrix bundle** (`Soto`, the LOOPR project — a matrix of personality–outcome associations, not a focal-claim replication). +- **uncoded** — the effect's `fred_id` is outside the 987-pair coded universe (never assessed); all flag fields empty. + +Invariant: **exactly one `is_focal=TRUE` per focal-resolved pair** (957 resolved pairs → 957 TRUE rows). Each pair is exactly one of: focal-resolved, a constituent set, target-absent, focal-in-sibling, or not-applicable — and **no pair is `needs_review` any more**. + +## Derivation + +The coding unit is the **pair** (`fred_id`), not the individual effect, so the focal effect is +determined once per pair and then broadcast to that pair's effects here. A pair's focal effect was +resolved by a tiered rule, cheapest evidence first: + +1. **single_effect** — the pair has exactly one effect; it is trivially focal. +2. **abstract match** — LLM semantic match of the coder's abstract-level replication finding to + one candidate effect's original claim. +3. **outcome_quote match** — same, using the finding-level `outcome_quote` when the abstract was + too coarse. +4. **replication-report reading** — for pairs the abstract/quote could not disambiguate + (project-level/bundle abstracts, whole-model aggregate verdicts, or an abstract finding that + matched no candidate), a human-directed agent read the actual replication report to identify + the targeted effect, citing the report section/table/statistic as evidence. + +The LLM tiers (2–3) used **gemini-flash-lite-latest** in a two-pass semantic-matching setup, +validated against the pooled tier logic and spot-checked. The report tier (4) is human-directed +agent reading of the replication reports with cited evidence. When no single focal claim could be +identified, the focal effect was left empty (**never guessed**) and the pair was classified into +one of the non-focal coverage classes: `constituent_set` (aggregate/whole-model, co-equal +multi-outcome), `target_absent` (candidate set missing the actually-targeted effect), or +`unresolved` (still undetermined). + +## Source of the coding + +Focal determinations derive from FORRT's abstract-level replication-success coding (the +*"Validating FReD replication success"* sheet), joined to FReD. + +The sheet is **double-coded**: each replication was coded independently by more than one coder, +and a `validation` column records which coding was adjudicated authoritative. Only rows marked +`validation == "validated - chosen"` are used here; discarded, on-hold, and unvalidated rows are +excluded. + +## Identity-keyed verdict attribution + +Coded verdicts (outcomes and their supporting quotes) are attached to each pair by matching +**replication identity**, not original DOI alone. A pair's replication identity is the coalesce of +its DOI and URL on *both* the original and replication side, plus **preprint/deposit-duplicate +equivalences** from `cache/confirmed_preprint_duplicates.csv` (so a preprint, its published +version, and a separate data deposit of the same replication are treated as one replication). A +provenance column records how each pair's verdict was matched — `outcome_match` in the analysis +file, mirrored by the tiers below: + +- **exact_key** — matched on the exact (original identity, replication identity) key; +- **url_key** — matched once URLs are coalesced with DOIs; +- **dedup_equiv** — matched via a confirmed preprint/deposit-duplicate equivalence; +- **fred_id_bind** — matched by binding to the pair's own FReD `fred_id` when the sheet's DOI/URL + were incomplete; +- **doi_o_fallback** — no verdict for this exact replication; the outcome is **pooled from other + replications of the same original** (3 single-trace pairs, flagged in their rationale); +- **none** — no validated verdict is keyed to this replication at all (2 pairs; outcome blank). + +This identity keying supersedes the earlier original-DOI-only keying, which had mis-attributed +verdicts across different replications sharing an original DOI and missed verdicts recorded under a +duplicate deposit. + +## DOI join / normalisation + +DOIs and URLs were normalised before joining (lowercased, trimmed, `https?://(dx.)?doi.org/` prefix +stripped, `na`/`null`/`n/a`/empty → missing). The pair-level assignment joins to FReD on `fred_id`; +the `doi_o` column is carried for reference. + +## Constituent sets (aggregate replications) + +Many replications are **aggregate**: they target a whole set of co-equal effects (e.g. a full set +of problems, a path model, a battery of trait–outcome correlations, a multi-ROI confirmatory +replication) with no single primary effect. These pairs get `coverage = constituent_set`, +`is_focal = FALSE` for all their effects, and `focal_role = constituent` on the member effects +(non-member candidates stay `none`). The pair's coded verdict describes the set as a whole. 23 pairs +are constituent sets; 3 are `target_absent` (the targeted effect is not among FReD's candidates), +3 are `focal_in_sibling` fragments, and one (`Soto`) is `not_applicable`. This replaces the previous +`needs_review` bucket — the coding is now positive rather than merely "no single focal", and **no +pair remains open for review**. + +## fred_id fragmentation (focal_in_sibling) + +FReD sometimes splits **one** original↔replication study pair across several `fred_id`s that share +the *same* `doi_o` **and** `doi_r` (a base id plus `_1`/`_2` siblings). When that happens, the +effect the replication actually targeted can live under a **sibling** `fred_id` while the base +`fred_id` holds only the pair's other, non-targeted effects. Three base fragments are affected — +`OpenMKT7` (target lives in `OpenMKT7_1`, effect 927), `Boyce_etal202319` (`Boyce_etal202319_1`, +effect 520), `Boyce_etal202325` (`Boyce_etal202325_1`, effect 533). They are coded +`coverage = focal_in_sibling`; their sibling's focal effect keeps `is_focal = TRUE` (unchanged), +and the base fragment's own effects stay `focal_role = none`. In `focal_effects.csv` the base rows +carry `sibling_fred_id` / `sibling_focal_effect_id`. + +**Consequence for downstream de-duplication:** a replication study is identified by +`doi_o + doi_r`, **not** by `fred_id`. Any pooling or z-curve de-duplication over replications must +key on `doi_o + doi_r` (or the identity keys used for verdict attribution), or these fragment +siblings will be double-counted. + +## SCORE single-trace pairs (no local outcome) + +Three single-effect pairs (`88xa_single-trace`, `LmBx_single-trace`, `xYbO_single-trace`) originate +from the SCORE programme and **carry no outcome in this abstract-coding sheet**. Their focal effect +is structurally determined (single effect), so they stay `resolved` with `is_focal = TRUE`, but +their `abstract_outcome`/`outcome_quote` are blank and `outcome_match = score_no_local_verdict` (an +earlier `doi_o_fallback` value, pooled from *other* teams' replications of the same original, was +removed as not this replication's verdict). + +## Proposed FReD rows (proposed_row) + +Two `target_absent` pairs have `proposed_row = TRUE`: their focal effect is a specific +original↔replication result that is **genuinely not yet a row in FReD** and should be added. Both +have verified original coefficients staged in `proposed_fred_rows_final.csv`. +- `curatescience15` — the *ego-depletion* DV (prior self-regulation exertion → worse subsequent + self-control), Muraven 1998 Study 2; only effortfulness manipulation checks are currently coded. +- `resciencex_01` — three *teacher-credential* effect rows (Croninger 2007 Table 3, standardized + HLM), including a **sign correction** (school-avg advanced-degrees→math γ=−0.068* is adverse); + the 8 existing candidates are student/school control covariates, not the credential effects. +See `focal_validation_report.md` §8 for the full proposed original + replication statistics. + +## additional_studies94 — FReD claim_text defect (not a missing effect) + +`additional_studies94` was briefly `target_absent` but is now **`resolved`, focal = effect 323**. +Effects 323/324 already code the paper's Study-1 *God salience → AI-reliance* DV (323 the direct +replication, 324 the conceptual one), but their `claim_text` fields were **mis-pasted with the +manipulation-check wording** ("thinking about God…") while their statistics are the reliance DV. +This is a claim_text defect in FReD, not a missing row. **Fixed in the FReD source on 2026-07-23** +(the "FReD Validation — USE THIS" workbook, "COS coding" tab, rows 2412 and 2415): `claim_text_orig` +and `claim_text_orig_page` were corrected to the focal reliance-DV claim ("a one-way ANOVA on an +index score…F(1,319)=12.91…f=0.20"), recovered from the parallel discarded coding (rowid 664/665), +with a `notes_validation` entry recording the correction. Effect 323 → `is_focal = TRUE`, +`focal_role = focal`; effect 324 → `focal_role = none`. + +## Caveats + +- **Coded DOIs with no FReD match (10):** DOIs coded in the sheet but absent from FReD after + normalisation — never enter the pair universe. +- **Orphan effects (5):** FReD effects (`effect_id` 1834, 1847, 1848, 1939, 1968) whose DOI is + coded but whose `fred_id` is missing; cannot be assigned to a pair (fall in `uncoded`). +- **fred_ids spanning multiple DOIs:** `FORRT_187_1` (2 DOIs) and `Soto` (25 DOIs) — `doi_o` is + not a unique key for these; the join is on `fred_id`. +- **Aggregate / whole-model verdicts and bundle replications:** many report-tier pairs replicate + a whole model or a set of co-equal outcomes; where no single primary effect exists they are + `constituent_set` (member effects flagged `focal_role = constituent`). +- **Candidate sets missing the targeted effect:** some replications target an effect not present + among the pair's candidate rows → `target_absent`. +- **Duplicate candidate rows:** where duplicate effect rows encode one and the same finding and + that finding is focal, the resolution picks the **lowest / fullest `effect_id`** by rule. +- **Verdict/finding mismatches (av_199-style):** in a few report-tier pairs the coded replication + verdict refers to a different finding than the targeted focal effect; the focal effect is still + flagged, and under identity keying the replication-level verdict is attached (its rationale notes + the finding-level caveat). + +See `abstract_coding/focal_validation_report.md` (in the analysis repo) for the full coverage +tables, spot-check, the constituent/target-absent lists, and LLM spend.