more documentation

Author: ttuff

CHANGELOG_CLIMATE_REVISION.md

@@ -1,6 +1,6 @@
 # Climate Revision Changelog
 
-Generated: 2026-07-23T00:33:06.820919+00:00
+Generated: 2026-07-23T01:49:47.909965+00:00
 
 ## Added or elevated
 

PROMPT_LOG.md

@@ -1795,3 +1795,62 @@ secrets, credentials, private tokens, or unrelated transcript text.
   to 13 page PNGs plus an internal QA PDF with the document renderer, and
   visually checked the title page, back matter, dense Figure 3 page, caption
   continuation page, and final figure page.
+
+## 2026-07-22 - Morphospace figure story refinement
+
+- User goal: restore the visual story where VASE shapes are laid over the
+  morphospace and the morphospace itself is colored by climate variables to
+  show which climate dimensions align with which developmental forms.
+- Updated `scripts/fire_vase_climate_revision.py` so Figure 2 overlays
+  representative VASE glyphs within the population morphospace with
+  non-overlapping callouts, making shape transitions across VASE axes visible.
+- Updated Figure 3 so panels A-D show the same VASE morphospace colored by
+  event-mean maximum temperature, VPD, 1000-hour fuel moisture, and wind speed,
+  with simplified facet labeling and tighter colorbar spacing.
+- Regenerated `figures/climate_revision_main/Figure_2_climate_revision.png`,
+  `figures/climate_revision_main/Figure_3_climate_revision.png`,
+  `output/pdf/fire_vase_climate_revision_science_style_manuscript.pdf`, and
+  `output/docx/fire_vase_climate_revision_google_docs_sanitized.docx`.
+- Validation: compiled `scripts/fire_vase_climate_revision.py`, rebuilt the
+  full climate-revision figure/manuscript package, ran the Google Docs title
+  sanitizer/check, rendered the DOCX to 13 page PNGs plus an internal QA PDF,
+  and visually checked Figure 2 on page 9 and Figure 3/caption continuation on
+  pages 10-11.
+
+## 2026-07-22 - Science-style figure legends and numbering
+
+- User goal: revise the figure and figure legends so figure numbers/titles are
+  not part of the image artwork and the legends tell the full scientific story
+  of each figure.
+- Updated `scripts/fire_vase_climate_revision.py` so panel labels use
+  lowercase `(a)`, `(b)`, etc., and rewrote all five generated main figure
+  legends to begin with `Fig. N. Title.` followed by self-contained guidance on
+  what is plotted, how to read it, and the science message.
+- Updated both manuscript builders so the figure number/title is emitted as
+  the first sentence of the figure legend rather than as a separate heading
+  above the figure image.
+- Regenerated `figures/climate_revision_main/figure_legends.md`,
+  `output/pdf/fire_vase_climate_revision_science_style_manuscript.pdf`, and
+  `output/docx/fire_vase_climate_revision_google_docs_sanitized.docx`.
+- Validation: compiled the figure/PDF and DOCX builder scripts, rebuilt the
+  figure/manuscript package, sanitized and rendered the DOCX, rendered the PDF
+  with Poppler, visually checked the Figure 2 and Figure 3 pages in both DOCX
+  and PDF outputs, and confirmed by `pdftotext` that the PDF legends begin with
+  `Fig. 2.` and `Fig. 3.` rather than standalone figure headings.
+
+## 2026-07-23 - Final Citation Check
+
+- User goal: perform one last citation check, verify current references and
+  uses, and add any missing citations only if needed.
+- Audited
+  `docs/manuscripts/fire_vase_developmental_morphology/manuscript_climate_revision_science_style.md`;
+  all 16 references are cited, no cited number is missing, no reference is
+  uncited, and the abstract has no citations.
+- Verified the current references against external DOI, publisher, and
+  bibliographic records, then checked claim fit by citation group.
+- Added
+  `docs/manuscripts/fire_vase_developmental_morphology/final_citation_check_2026-07-23.md`.
+- No new main-text citations were added; the remaining pre-submission citation
+  item is the final code/data archival DOI or accession, with optional
+  supplementary-method citations for ridge regression, blocked validation, or
+  software if those details are expanded.

analysis/climate_data_inventory.md

@@ -1,6 +1,6 @@
 # Climate Data Inventory
 
-Generated: 2026-07-23T00:32:52.648770+00:00
+Generated: 2026-07-23T01:49:24.448582+00:00
 
 ## Population-wide daily centroid climate
 

analysis/climate_revision_stats/climate_revision_artifact_manifest.json

@@ -1,5 +1,5 @@
 {
-  "generated_at": "2026-07-23T00:33:08.920870+00:00",
+  "generated_at": "2026-07-23T01:49:49.927609+00:00",
   "figures": {
     "Figure_1": {
       "png": "/Users/tuff/Library/CloudStorage/OneDrive-UCB-O365/Documents/github/cubedynamics/figures/climate_revision_main/Figure_1_climate_revision.png",

docs/manuscripts/fire_vase_developmental_morphology/final_citation_check_2026-07-23.md

@@ -0,0 +1,64 @@
+# Final Citation Check
+
+Date: 2026-07-23
+
+Object reviewed:
+`docs/manuscripts/fire_vase_developmental_morphology/manuscript_climate_revision_science_style.md`
+
+## Bottom Line
+
+No new main-text citations were added. The current 16-reference set is real,
+cited in the manuscript, and appropriately matched to the claims it supports.
+The manuscript remains intentionally lean: technical citations for ridge
+regression, blocked validation, and software packages can be added in a final
+supplementary methods section if those implementation details become more
+prominent, but they are not required for the current main-text argument.
+
+## Integrity Checks
+
+- In-text citation groups found: `(1-3)`, `(4)`, `(5-7)`, `(8)`,
+  `(9-11)`, `(1-3)`, `(12)`, `(13)`, and `(14-16)`.
+- References cited: 1 through 16.
+- Missing references for cited numbers: none.
+- Uncited references: none.
+- Abstract citations: none, consistent with the Science-style draft.
+- First-use order is correct for unique citations; repeated `(1-3)` later in
+  the Results section does not disturb citation order.
+
+## Claim Fit
+
+- References 1-3 correctly support the broad climate-fire motivation:
+  warming, earlier springs, anthropogenic climate effects, fuel aridity, VPD,
+  and warming-driven fuel drying.
+- Reference 4 correctly supports the shift from final burned area to daily fire
+  growth histories and the hazard relevance of fast daily growth.
+- References 5-7 correctly support the MODIS burned-area, FIRED event, and
+  FIREDpy/perimeter data provenance.
+- Reference 8 correctly supports gridMET as the high-resolution gridded
+  meteorological data source used for ecological applications in the
+  conterminous United States.
+- References 9-11 correctly support the conceptual method framing:
+  morphometrics/shape spaces, functional data analysis for histories or
+  curves, and PCA/dimension reduction.
+- Reference 12 correctly supports the statement that human ignitions reshape
+  the spatial and seasonal fire niche.
+- Reference 13 correctly supports the need for spatially explicit daily fire
+  progression tracking.
+- References 14-16 correctly support the role of environmental controls,
+  fuels, vegetation/topography, fire boundaries, spread constraints, and
+  scale-dependent topographic controls.
+
+## Verified Bibliographic Records
+
+External records checked included publisher, DOI, PubMed, USGS, NOAA, NASA,
+FRAMES, Nature, Springer, Wiley, MDPI, CSIRO, EPA HERO, and university
+bibliographic pages. The citation metadata in the manuscript matched the
+verified records for author lists, year, title, journal/book, volume, pages or
+article number, and DOI where applicable.
+
+## Remaining Pre-Submission Item
+
+The only citation-related item left is not a scholarly-source problem: before
+submission, replace the placeholder repository availability note with the final
+archival repository DOI/accession for the derived tables, figure-generation
+scripts, and manuscript-generation code.

docs/manuscripts/fire_vase_developmental_morphology/manuscript_climate_revision_science_style.md

@@ -32,7 +32,7 @@ Figure 2 shows that observed fires occupy recurring developmental neighborhoods,
 
 ### Climate shifts the probability of developmental forms
 
-Figure 3 projects climate onto Fire VASE space. Event-mean VPD varies across the developmental axes, and composite VASEs show that low-, middle-, and high-VPD fires differ in where normalized growth is allocated through developmental time. Developmental-neighborhood prevalence shifts across VPD groups, and effect-size summaries show that maximum temperature, VPD, relative humidity, fuel moisture, precipitation, and fire-danger indices relate to different developmental responses. These associations are coherent with the broader literature linking warming, aridity, and fuel dryness to fire activity (1-3), but the VASE analysis resolves the outcome as a developmental distribution rather than a single aggregate burned-area response.
+Figure 3 projects climate onto Fire VASE space. Climate-colored morphospace maps show that maximum temperature, VPD, fuel moisture, and wind emphasize different portions of the developmental space, while composite VASEs show that low-, middle-, and high-VPD fires differ in where normalized growth is allocated through developmental time. Developmental-neighborhood prevalence shifts across VPD groups, and effect-size summaries show that maximum temperature, VPD, relative humidity, fuel moisture, precipitation, and fire-danger indices relate to different developmental responses. These associations are coherent with the broader literature linking warming, aridity, and fuel dryness to fire activity (1-3), but the VASE analysis resolves the outcome as a developmental distribution rather than a single aggregate burned-area response.
 
 The predictive limit is equally important. In conservative blocked validation, which summarizes transfer across year, region, and region-year blocks rather than random-fire splits alone, the best transferable event-level representation is core event means, with median held-out R2 of 0.349 across developmental responses. Region-season anomaly diagnostics do not outperform core event means, comprehensive event means do not outperform core event means, and temporally resolved exposure summaries do not outperform core event means in the median blocked comparison. This does not mean that humidity, fuel moisture, precipitation, or fire danger are unimportant. It means that, in these correlated daily centroid summaries and linear blocked baselines, adding more climate descriptors did not improve transfer beyond the core atmospheric variables. Modest blocked R2 is therefore a bound on deterministic prediction, not a rejection of the distributional result. The claim is probabilistic: climate redistributes fires across developmental possibilities. It does not assign a unique developmental form.