Wire up kootenay-lake.Rmd citations from 3-split lit reviews

planning/active/citation_audit.md

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+# Citation Audit — kootenay-lake.Rmd wire-up (#65)
+
+One row per `[@key]` insertion proposed for `kootenay-lake.Rmd`.
+This is the "what is where by who said what where" trail.
+
+For each row:
+- **Vignette excerpt** — the prose where the cite lands (with line ref)
+- **Source quote / paraphrase** — the load-bearing quote from the cited paper
+- **Rag store / topic** — where the quote was retrieved during lit-review mining
+- **Paraphrase as written** — how the cite appears in the vignette
+- **Why warranted** — what visible-in-vignette finding supports this cite
+
+The independent review agent (Phase 3) reads this audit + verifies
+each paraphrase against the source.
+
+---
+
+## 1. Hansen 2012 — 1951–1980 baseline (Trends section, L184)
+
+**Vignette excerpt (current):** "Anomalies are computed against a
+pre-warming reference period — 1951–1980, the three decades before
+climate change accelerated. Saying a year is '+1.5 °C' means it was
+1.5 °C warmer than the average year between 1951 and 1980."
+
+**Source quote (from #63 archive findings.md, topic
+`cumulative_impact_loaded_dice`):**
+> "3-sigma extreme outliers, which covered much less than 1% of
+> Earth's surface during the 1951–1980 base period, now typically
+> cover about 10% of the land area." — Hansen et al. 2012, PNAS
+
+**Rag store / topic:** `data/rag/interpretation_framing.duckdb` /
+`cumulative_impact_loaded_dice`
+
+**Paraphrase as written (proposed):** "Anomalies are computed against
+a pre-warming reference period — 1951–1980, the three decades before
+climate change accelerated. This is the same base period
+@hansen_etal2012Perceptionclimate use to detect the emergence of
+3-sigma summer-temperature outliers globally..."
+
+**Why warranted:** vignette explicitly justifies the 1951–1980
+choice; Hansen et al. 2012 is the strongest direct precedent (same
+window, cumulative-impact framing). Visible in **all anomaly plots**
+(every figure relative to the 1951–1980 baseline). Non-decorative —
+load-bearing for the methodology choice.
+
+---
+
+## 2. Arguez & Vose 2011 — WMO climate normal definition (Trends, L195–199)
+
+**Vignette excerpt:** "1981–present (45 years) — starts at the
+beginning of the World Meteorological Organization's most recent
+30-year 'climate normal' (1981–2010). This is the reference period
+used in most published climate products, so it makes results easy
+to compare against Intergovernmental Panel on Climate Change
+reports and government climate summaries."
+
+**Source quote (from #63 archive findings.md, topic
+`baseline_window_methodology`):**
+> "We propose that any potential alternative climate normal is the
+> result of changing one or more of these five attributes...
+> [WMO normals are] more useful as a comparison metric than as a
+> predictor of expected future conditions in a changing climate."
+> — Arguez & Vose 2011, BAMS
+
+**Rag store / topic:** `data/rag/interpretation_framing.duckdb` /
+`baseline_window_methodology`
+
+**Paraphrase as written (proposed):** "1981–present (45 years) —
+starts at the beginning of the World Meteorological Organization's
+most recent 30-year 'climate normal' (1981–2010)
+[@arguez_vose2011DefinitionStandard]."
+
+**Why warranted:** vignette explicitly references the WMO standard;
+Arguez & Vose 2011 is the canonical citation for that definition.
+Visible in **the second slope row of the Trends table** (1981-start
+trend window). One-cite, one-claim — minimal decoration.
+
+---
+
+## 3. Karl 1993 — DTR asymmetry (Daytime/Overnight Lows, L246)
+
+**Vignette excerpt (current):** "Overnight minimums warming faster
+than daytime maximums — the 'day-night asymmetry' — is one of the
+textbook fingerprints of greenhouse warming (Karl et al. 1993)."
+
+**Source quote (from #58 archive findings.md, topic
+`dtr_asymmetry`):**
+> "the rise of the minimum temperature has occurred at a rate three
+> times that of the maximum temperature during the period 1951-90
+> (0.84°C versus 0.28°C). The decrease of the diurnal temperature
+> range is approximately equal to the increase of mean temperature.
+> The asymmetry is detectable in all seasons and in most of the
+> regions studied." — Karl et al. 1993, BAMS
+
+**Rag store / topic:** `data/rag/temp_methodology.duckdb` /
+`dtr_asymmetry`
+
+**Paraphrase as written (proposed):** convert prose-style "(Karl et
+al. 1993)" → "[@karl_etal1993NewPerspective]"
+
+**Why warranted:** vignette already names Karl et al. 1993 in prose
+— this just promotes it to a proper citation. DTR figure
+(`plot-dtr` chunk, Fig caption mentions "the textbook day-night
+asymmetry shows up here") visualizes the exact effect Karl 1993
+documented. Direct match.
+
+---
+
+## 4. Pepin 2015 + Rangwala & Miller 2012 — elevation-dependent warming (Spatial Pattern, L581–587)
+
+**Vignette excerpt (current):** "Warming is not spatially uniform
+across the region. Total departures range from about +1.2 °C at
+the lowest-warming pixels to +2.2 °C at the highest, with a
+regional mean near +1.7 °C. Higher-elevation pixels tend to show
+stronger warming — the high-elevation amplification signal that
+shows up consistently at mid-latitude mountain sites — but the
+gradient is mixed enough that no single axis (north-south or
+east-west) carries the full pattern."
+
+**Source quotes (from #58 archive findings.md, topic
+`elevation_dependent_warming`):**
+> "growing evidence that the rate of warming is amplified with
+> elevation, such that high-mountain environments experience more
+> rapid changes in temperature than environments at lower
+> elevations. Elevation-dependent warming (EDW) can accelerate the
+> rate of change in mountain ecosystems, cryospheric systems,
+> hydrological regimes and biodiversity." — Pepin et al. 2015,
+> Nature Climate Change
+
+> "it is still uncertain whether mountainous regions generally are
+> warming at a different rate than the rest of the global land
+> surface, or whether elevation-based sensitivities in warming
+> rates are prevalent within mountains." — Rangwala & Miller 2012,
+> Climatic Change
+
+**Rag store / topic:** `data/rag/temp_methodology.duckdb` /
+`elevation_dependent_warming`
+
+**Paraphrase as written (proposed):** "Higher-elevation pixels tend
+to show stronger warming — consistent with the elevation-dependent
+warming (EDW) signal documented at mid-latitude mountain sites
+[@pepin_etal2015Elevationdependentwarming], though the regional
+evidence base is heterogeneous and not every mountain region shows
+the same pattern [@rangwala_miller2012Climatechange]..."
+
+**Why warranted:** spatial-pattern map (Figure under L597-625)
+visibly shows elevation-correlated departure values. Vignette's
+existing prose introduces "high-elevation amplification" — needs
+the EDW reference. Pepin 2015 = primary, Rangwala & Miller 2012 =
+caveat (the heterogeneity acknowledgment matters because the
+vignette itself notes "the gradient is mixed enough"). Two cites,
+one for the affirmation + one for the caveat — non-decorative.
+
+---
+
+## 5. Ficklin & Novick 2017 — VPD continental drying (Interpretation, L984–994)
+
+**Vignette excerpt (current):** "The atmosphere is drying. Vapour
+pressure deficit — the gap between how much water the air could
+hold and how much it actually does — is up significantly across
+the region. Combined with declining precipitation, this is a
+'double-dipping' signal: less water arriving as precipitation,
+*and* warmer air pulling more water out of soil and vegetation
+through evapotranspiration."
+
+**Source quote (from #61 archive findings.md, topic
+`vpd_drying_continental`):**
+> "spring, summer, and fall seasons exhibited the largest areal
+> extent of significant increases in VPD, which was largely
+> concentrated in the western and southern portions of the U.S.
+> Significant increases in VPD have been caused by air temperature
+> increases and relative humidity changes, especially during the
+> summer season in the southern portion of the U.S., over the
+> historical time period." — Ficklin & Novick 2017, JGR
+
+**Rag store / topic:** `data/rag/precip_drying_methodology.duckdb` /
+`vpd_drying_continental`
+
+**Paraphrase as written (proposed):** "Vapour pressure deficit —
+the gap between how much water the air could hold and how much it
+actually does — is up significantly across the region, mirroring
+the continental-scale drying that @ficklin_novick2017Historicprojected
+documented across the western United States, driven by combined
+air-temperature increases and relative-humidity declines."
+
+**Why warranted:** Recent-vs-Pre-warming table (L533-572,
+`cmp_combined`) shows VPD with positive Δ absolute and a
+significant trend p — directly visible. The vignette's
+"double-dipping" framing is the same air-T-up + RH-down combination
+Ficklin & Novick 2017 attribute the western-US VPD rise to. Direct
+methodological match for the vignette's load-bearing claim.
+
+---
+
+## 6. Mantua 2010 + Eaton & Scheller 1996 — climate→stream-temp→fish bridge (Interpretation, L1012–1018)
+
+**Vignette excerpt (current):** "For the cold-water resident
+salmonids the Kootenay Lake region supports — bull trout, Gerrard
+rainbow trout, mountain whitefish, kokanee — these signals
+compound. Stream temperatures are likely rising in step with
+warmer ambient air temperatures; the evapotranspiration imbalance
+means low-flow conditions in late summer are not being relieved
+(precipitation is falling, not rising as in the Peace); the
+cold-water input that high-elevation snowpack provides to streams
+during the warmest, most thermally stressful weeks of summer is
+dropping in parallel with summer SWE..."
+
+**Source quotes (from #58 archive findings.md, topic
+`climate_stream_temp_bridge`):**
+> "Simulations predict rising water temperatures will thermally
+> stress salmon throughout Washington's watersheds, becoming
+> increasingly severe later in the twenty-first century... combined
+> effects of warming summertime stream temperatures and altered
+> streamflows will likely reduce the reproductive success for many
+> Washington salmon populations." — Mantua et al. 2010, Climatic
+> Change
+
+> "The effects of climate warming on the thermal habitat of 57
+> species of fish of the U.S. were estimated... cold-water and
+> cool-water species are predicted to lose substantially more
+> thermal habitat than warm-water species." — Eaton & Scheller
+> 1996, L&O
+
+**Rag store / topic:** `data/rag/temp_methodology.duckdb` /
+`climate_stream_temp_bridge`
+
+**Paraphrase as written (proposed):** "Stream temperatures are
+likely rising in step with warmer ambient air temperatures, with
+the combined effects of warming summer stream temperatures and
+altered low flows likely reducing thermally-suitable habitat for
+cold-water species
+[@mantua_etal2010Climatechange; @eaton_scheller1996Effectsclimate]..."
+
+**Why warranted:** this is the load-bearing climate→fish bridge
+for the FWCP fish-passage-planner audience. Visible in **summer
+Tmax warming** (Trends section, table) + **summer SWE collapse**
+(Snowpack section). Without this cite, the assertion that "stream
+temps rise → cold-water species lose habitat" is unsupported.
+Mantua 2010 = PNW regional anchor, Eaton & Scheller 1996 = the
+foundational cold/cool/warm-water-species thermal-habitat
+methodology.
+
+---
+
+## 7. Kang 2016 — Fraser freshet advance (Interpretation, L1024–1025)
+
+**Vignette excerpt (current):** "The neighbouring Fraser Basin
+documents the same kind of freshet advance (Kang et al. 2016) at
+comparable magnitude."
+
+**Source quote (already cited in vignette at L311 as
+`@kang_etal2016ImpactsRapidly`; from snow rag, archive #54
+findings.md):**
+> "10-day advances of the onset of the spring freshets for the
+> Fraser River at Hope... declines persist during the recession
+> to lower flows in autumn just when the salmon are migrating up
+> the Fraser River." — Kang et al. 2016, Sci Rep
+
+**Rag store / topic:** `data/rag/snow_methodology.duckdb` /
+`bc_specific`
+
+**Paraphrase as written (proposed):** convert prose "(Kang et al.
+2016)" → "[@kang_etal2016ImpactsRapidly]" or
+"[-@kang_etal2016ImpactsRapidly]" depending on narrative form
+
+**Why warranted:** existing prose-style author ref — just convert
+to consistent `[@key]` format. Kang 2016 is already cited
+elsewhere in the vignette in the same format we're targeting. This
+is consistency cleanup, not new attribution.
+
+---
+
+## Out-of-audit observations
+
+- **3 FWCP Peace cross-references** at L528, L973, L996 should
+  not be in this stand-alone vignette per
+  `feedback_thorough_cross_reference_removal.md` memory. Out of
+  scope for #65 (citation wire-up only); flagged in progress.md
+  as a separate follow-up issue worth filing.
+- The existing 14 Snowpack-section `[@key]` markers from #54 are
+  intact and well-grounded — not re-audited here.
+
+## Independent review agent — checklist
+
+The Phase 3 review agent should verify, for each row above:
+
+1. The source quote actually exists in the cited paper (not
+   hallucinated)
+2. The paraphrase as written in the vignette is faithful to the
+   source — no overreach, no claim the paper doesn't support
+3. The "why warranted" reasoning matches an actually-visible
+   feature in the vignette's plots/tables (not a feature claimed
+   but not shown)
+4. No BS — if a citation looks like decoration rather than
+   load-bearing, flag it for removal
+
+## Phase 3 — Review agent sign-off (2026-05-05)
+
+Spawned an Explore subagent to verify each row. **All 7 rows
+passed** scientific-integrity review: no hallucinated quotes,
+paraphrases faithful, warrants visible in plots/tables, all cites
+load-bearing. Agent flagged one minor scope concern:
+
+- **Row 5 (Ficklin & Novick 2017):** initial paraphrase said
+  "documented across the western United States" but the paper
+  covers the entire continental US (1979–2013), with the
+  strongest historical VPD increases concentrated in the
+  western/southern portions. **Fixed in vignette** —
+  "documented for the United States as a whole, with the
+  strongest historical VPD increases concentrated in the western
+  and southern portions, driven by combined air-temperature
+  increases and relative-humidity declines." Now accurate to the
+  paper's full scope.
+
+No other edits or removals required. Agent's overall
+recommendation: **keep all 7 cites as-is** (with the Ficklin
+fix applied).

planning/active/findings.md

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+# Findings — Wire up kootenay-lake.Rmd citations (#65)
+
+## Issue context (verbatim from #65)
+
+The `kootenay-lake.Rmd` vignette interpretation paragraphs make
+claims about temperature, precipitation, snowpack, and drying that
+currently land on zero peer-reviewed citations in the non-snow
+sections. The 3-split climate-departure lit reviews built the
+citation backbone specifically for this consumer; time to wire it
+up.
+
+## Pre-work read of `kootenay-lake.Rmd`
+
+1031-line vignette. Section structure:
+- L50 Area of Interest
+- L127 Connect to the Data Catalog
+- L154 Extract Climate Time Series
+- L182 Trends
+- L240 Daytime Highs and Overnight Lows
+- L296 Snowpack (heavily cited from #54 — 14 `[@key]` markers in
+  this + per-ecoregion + interp-snow paragraphs)
+- L512 Recent vs Pre-warming
+- L576 Spatial Pattern
+- L627 Per-Ecoregion Variation
+- L879 Watershed Groups Across Ecoregions
+- L959 Interpretation
+- L1031 References
+
+Existing `[@key]` markers (14): all in Snowpack section + Per-
+Ecoregion-Snow + Interpretation-snow. **Non-snow sections have
+zero cites.**
+
+## Pre-work concern flagged (out of scope, separate follow-up)
+
+3 FWCP Peace cross-references slipped back in despite the v0.2.1
+scrub:
+- L528: "and unlike the FWCP Peace just to the north..."
+- L973: "diverges sharpest from the FWCP Peace just north..."
+- L996: "diverge from the FWCP Peace pattern..."
+
+Per `feedback_thorough_cross_reference_removal.md` memory, these
+shouldn't be in a stand-alone vignette. **Out of scope for #65**
+(citation wire-up only) — flagged here for the user to call as a
+separate follow-up issue.
+
+(The Fraser Basin reference at L1024-1025 is fine — different
+region used as a literature anchor for freshet timing, not a
+cross-ref to the sibling Peace vignette.)
+
+## Source corpus
+
+Pulling `[@key]` markers from the 4 cite-this-for-that maps:
+- `planning/archive/2026-05-issue-53-snow-lit-review/findings.md`
+- `planning/archive/2026-05-issue-58-temperature-lit-review/findings.md`
+- `planning/archive/2026-05-issue-61-precip-drying-lit-review/findings.md`
+- `planning/archive/2026-05-issue-63-interpretation-framing-lit-review/findings.md`
+
+For each candidate insertion, the audit log
+(`planning/active/citation_audit.md`) tracks: vignette excerpt,
+source quote/paraphrase, rag store + topic, my paraphrase as
+written, why warranted.
+
+## Plan-mode insertion candidates
+
+7 high-value insertions identified in Phase 0 read (table in
+task_plan.md). Will refine/cull during Phase 1 audit-log build
+and Phase 3 review-agent feedback.
+
+## Citation audit log
+
+See `planning/active/citation_audit.md` (built during Phase 1).