Repository navigation
Sync analysis plan with the current draft and add a supplement - #129
Draft
kaitejohnson wants to merge 12 commits into
Draft
kaitejohnson wants to merge 12 commits into
kaitejohnson wants to merge 12 commits into
Conversation
Update the title, wording fixes, the model-based evaluation section (new covariate list, Gamma GAM equations and mgcv formula) and the Results figure list (WIS instead of CRPS, restructured Figures 3-5) to match the draft. LaTeX typos from the draft are fixed so the equations render (\vu -> \nu, missing closing parentheses, x -> \times). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Remove the CRPS offset formula and text and the brms sentence from the model-based evaluation, and replace remaining CRPS references with WIS. Move all ARIMA comparisons to the supplement so the main text focuses on the head-to-head comparison. Add docs/supplement.qmd with the ARIMA comparison figures and the epidemic phase definition and figures. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
|
Important Draft PR not reviewedDraft PRs are not automatically reviewed by default.
To automatically review draft PRs, update your CodeRabbit configuration: reviews:
auto_review:
drafts: true
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
Describe how the epidemic phase is defined for hospital admissions (28-day change beyond 15% and 5 admissions) and for wastewater (28-day change in mean log concentration per site and lab, 15%) in a new Methods subsection, and point the supplement to it instead of repeating the definition. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Add a wastewater concentration forecast evaluation aim, methods section and figure; frame the model-based evaluation as exploratory and add hospital epidemic phase interacting with wastewater (plus a less flexible forecast date smooth sensitivity analysis and a latency x forecast date interaction); add bootstrapped intervals, significance tests and MCMC convergence checks to the evaluation. Restructure the figures: a combined schematic (Fig 1), example forecasts by phase with WIS and wastewater fits (Fig 2), the head-to-head summary including relative WIS by phase (Fig 3), the wastewater forecast evaluation (Fig 4) and the exploratory GAM results (Fig 5). Update the supplement to match. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #129 +/- ##
========================================
- Coverage 0.18% 0.16% -0.03%
========================================
Files 13 15 +2
Lines 1601 1829 +228
========================================
Hits 3 3
- Misses 1598 1826 +228 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
79770b5 was made from the original version of the plan, so it reverted the earlier changes. Three-way merge of the original (18fd616), the #127 version (94be4ac) and 79770b5: keeps the edits from 79770b5 (Aims, What we do here, Data, wastewater data, LOQ censoring, ARIMA and model description) and restores the epidemic phase, wastewater evaluation, bootstrap and convergence methods, the updated GAM section and the revised figures. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Show unadjusted and adjusted relative WIS by epidemic phase side by side (Fig 5A) and explain how they relate; use minimum latency only; move the relative WIS heatmap to the supplement; centre bias on 0; define wastewater horizons relative to the forecast date (including nowcasts); add Table 1; fix headings, the inclusion criterion and the convergence sentence. In the supplement, add the covariate scatterplots and coverage by plant and by state, and show the convergence sensitivity analysis including all forecasts. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The docx is generated from analysis_plan.qmd; the local copy is kept and docs/ is already gitignored. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
docs/analysis_plan.qmdwith the current Google Docs draft: title, wording fixes, the model-based evaluation section (covariate list, Gamma GAM equations andmgcvformula) and the Results figure list.brmssentence) and replaces remaining CRPS references with WIS.wwinferencemodels with and without wastewater.docs/supplement.qmdwith the ARIMA comparison figures (S1, S2) and the epidemic phase definition and figures (S3).Notes
\vu→\nu, missing closing brackets, "x" →\times). These are still in the Google Doc.references.bib(Abunjela,BMChealth,RKIGithub,Wollfram_et_al), which were already placeholders in the draft.🤖 Generated with Claude Code