Produced alongside the img/ chart refresh via scripts/univariate_analysis.py:
per-protocol and per-gradient averages tables, summary plots, and
univariate_summary.txt (mean 5.44, median 5.48, normalized midpoint
deviation 0.11).
Full pipeline per README command flow (steps 2-6): univariate averages and
distributions, multivariate analysis (2-cluster k-means: 209 relational vs
199 institutional; PCA/t-SNE/UMAP/factor/correlation/network/importance),
LDA separation and overlaid cluster plots, and LDA classifications (trained
on the 1.2.6 run via version-matched auto-selection). Cross-version summary
is on the console report: avg Euclidean distance 9.06 vs 1.2.6 (r=0.79).
Verified: bicorder-app has no classifier implementation and reads
bicorder_model.json nowhere (src, build config); ascii_bicorder.py doesn't
use it either. Corrected the stale 'read by bicorder-app at build time'
claims in README, WORKFLOW, and the export script docstring.
- README: new 'Command flow' section — dependency-ordered pipeline (setup →
batch generation → univariate → multivariate → LDA/cluster visualizations →
classify → cross-version compare → JSON/model export) with actual output
paths per step, using data/synthetic_1.4.0/ as the example
- README: document chart production — univariate_analysis --img publishes the
img/ summary charts; visualize_clusters added to the flow
- README: fix -b path in 'Adding a new run' (bicorder.json lives at repo root)
- WORKFLOW: script list and any-readings-CSV command block updated to match
411 protocols × 23 gradients scored against bicorder.json v1.4.0 with
gpt-oss:20b-cloud (same analyst standpoint as the 1.2.6 run); the
bicorder_version column makes the run self-describing. Analysis outputs to
follow in data/synthetic_1.4.0/analysis/.
- scripts/bicorder_common.py (new): single source of truth for historical
gradient renames (COLUMN_RENAMES), version detection (bicorder_version col
→ version col → data/<type>_<version>/ dir convention), and training-CSV
auto-selection (find_training_csv)
- classify_readings.py: auto-select training run by recorded bicorder version
(excludes the input itself to avoid circular training), canonicalize old
column names, version-mismatch warnings
- bicorder_classifier.py / export_model_for_js.py: share renames + dimension
loader; instructive error when clustering results are missing;
bicorder_version recorded in exported models
- compare_analyses.py: CLI (reference + comparison CSVs), rename
canonicalization so runs of different versions align on shared gradients,
Descriptor dedup (was silently skewing merges); legacy no-arg audit intact
- scripts/univariate_analysis.py (new): per-protocol/per-gradient averages,
distributions, summary stats; --img publishes the three README summary
charts to img/
- sync_readings.sh: defer classifier training to auto-matching; gitignore
analysis/.venv and __pycache__
Introduce a simple, show-don't-tell entry screen that lowers the "what
counts as a protocol" barrier and frames the activity as a short journey:
- Lead line "Examine the protocols around you" over a rotating, cross-fading
list of deliberately diverse examples (traffic, code, kitchens, ritual,
governance, play)
- Prominent "Begin" CTA above a three-step path: Describe / Understand / Share
- "About the Bicorder" link opens the existing help modal
Shown on first arrival; returning users with a reading in progress skip
straight to the diagnostic (computed synchronously, no flash). Remove the
now-redundant inline description from the focused flow.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The model (analysis/bicorder_model.json) maps a positive LDA score to
cluster 2 = Institutional/Bureaucratic = "formal", but ldaScoreToScale
added the score (5 + score*4/3), sending formal/institutional protocols
toward 9 (informal) and vice versa. bicorder.json defines this gradient
as 1 = formal, 9 = informal, so the score must be subtracted.
- Flip the sign: value = 5 - (ldaScore * 4/3); correct the doc comment to
state the model's actual sign convention
- Rename calculateBureaucratic -> calculateFormalInformal and update the
stale analysisOrder comment, matching bicorder.json's formal/informal terms
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Replace the click-anywhere ASCII bar (whose hit-mapping was offset from
the displayed marker, so taps registered the wrong value) with a track of
nine discrete, exact tap targets that fill from the center outward to the
selection: [----==#--]. Direction and distance from center read at a glance.
- Exact per-position selection on touch and desktop; no more position math
- Keyboard support (arrows/Home/End), scoped so it doesn't trigger
the app-level screen navigation
- Center the bar and slim mobile padding so the full track fits narrow
viewports
- Apply the same control to the manual analysis gradient; render the
automated ones as a matching read-only, dimmed display
- Add a subtle gray "Value: #" indicator below the buttons on the
diagnostic gradients, matching the analysis screens
- Move the "auto-calculated" note under the ANALYSIS header instead of
after the value
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Remove the intermediate readings/ subdirectory level — dataset naming
(synthetic_YYYYMMDD, manual_YYYYMMDD) already encodes what the data is.
Update all path references across scripts and docs accordingly.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The web/ directory (bicorder-classifier.js, .d.ts, test-classifier.mjs)
was a prototype superseded by bicorder-app/src/bicorder-classifier.ts.
The only integration point between this analysis directory and the app is
bicorder_model.json, which Vite reads at build time.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Move all scripts to scripts/, web assets to web/, analysis results
into self-contained data/readings/<type>_<YYYYMMDD>/ directories
- Add data/readings/manual_20260320/ with 32 JSON readings from
git.medlab.host/ntnsndr/protocol-bicorder-data
- Add scripts/json_to_csv.py to convert bicorder JSON files to CSV
- Add scripts/sync_readings.sh for one-command sync + re-analysis of
any dataset backed by a .sync_source config file
- Add scripts/classify_readings.py to apply the LDA classifier to all
readings and save per-reading cluster assignments
- Add --min-coverage flag to multivariate_analysis.py for sparse/shortform
datasets; also applies in lda_visualization.py
- Fix lda_visualization.py NaN handling and 0-d array annotation bug
- Update README.md and WORKFLOW.md to document datasets, sync workflow,
shortform handling, and new scripts
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Prevent horizontal overflow with overflow-x: hidden on body. Make the
gradient bar fill its container in focused mode (width: 100%;
min-width: 0) rather than holding a fixed minimum width.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Raise responsive layout breakpoints from 768px to 900px across all
components. This ensures narrow desktop browser windows (769–900px)
get the stacked, single-column layout rather than the three-column
grid that was too wide for those widths. The 768px breakpoint in
app.css is kept as-is since it only adjusts font sizes for iOS.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Both export_model_for_js.py and bicorder_classifier.py now read
DIMENSIONS and KEY_DIMENSIONS directly from bicorder.json at runtime,
so the model stays in sync whenever gradient terms are renamed or
added. A COLUMN_RENAMES dict handles historical CSV column name
changes. The model now includes bicorder_version so the app's version
check works correctly.
Regenerated bicorder_model.json against bicorder.json v1.2.6 with
correct dimension names, 9 key dimensions from shortform flags, and
updated thresholds.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Remove user-select: none from body, keeping it only on interactive
elements (buttons, sliders, tooltips) where it prevents accidental
selection during interaction.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Move the upload confirmation dialog above the action buttons so it's
immediately visible, and add overflow-safe CSS to prevent text from
spilling outside the dialog box on mobile.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Nathan Schneider