HO-storms

This repository contains two related but distinct Florida tropical-cyclone health studies:

1. Mortality — daily mortality before, during, and after tropical-cyclone impacts. The manuscript is currently under review.
2. Birth outcomes — the newer pregnancy and preterm-birth analyses using corrected, residence-specific storm exposure and time-at-risk models.

Run scripts and render notebooks from the repository root so that relative paths resolve consistently.

Repository layout

HO-storms/
├── analysis/
│   ├── mortality/       # Mortality R Markdown analyses
│   └── births/          # Birth analyses; historical code is under legacy/
├── apps/
│   └── mortality/       # Mortality Shiny applications and deployment files
├── data/                # Local data; ignored by Git
│   ├── mortality/
│   │   ├── raw/
│   │   ├── derived/
│   │   ├── population/
│   │   └── processed/
│   ├── births/
│   │   ├── raw/
│   │   ├── derived/
│   │   └── processed/
│   └── shared/
│       ├── storm/       # IBTrACS and warning/advisory inputs
│       └── geography/   # Boundaries used across studies
├── figs/
│   ├── mortality/
│   └── births/
├── literature/          # References relevant to either study
├── manuscript/
│   ├── mortality/       # Submitted manuscript and reviewer material
│   └── births/          # Birth-outcomes manuscript drafts
├── models/
│   ├── mortality/
│   └── births/
├── outputs/
│   ├── mortality/       # Tables, summaries, and spatial products
│   └── births/
└── scripts/
    ├── mortality/
    └── births/

Main entry points

Mortality study

• analysis/mortality/ThreatDays.Rmd: principal threat-day analysis.
• analysis/mortality/All-Cause_Mortality.Rmd: all-cause mortality analysis.
• analysis/mortality/Figures.Rmd: manuscript figures.
• scripts/mortality/: reproducible count, model, table, and spatial scripts.
• manuscript/mortality/: submitted paper and review documents.

Birth-outcomes study

• analysis/births/HO-storms-exposure.Rmd: corrected storm-exposure build.
• analysis/births/HO-storms-models.Rmd: conventional trimester models.
• analysis/births/HO-storms-time-to-event.Rmd: gestational time-at-risk models.
• analysis/births/legacy/: original exploratory and collaborator notebooks; retained for provenance but not treated as the current workflow.
• scripts/births/draft_figure1_gestational_timeline.R: revised manuscript Figure 1.
• models/births/conventional-window7/: corrected symmetric seven-day model results.
• models/births/time-to-event/: time-to-event model results.
• manuscript/births/: current birth-outcomes manuscript drafts.

Naming convention

New work should be placed under the appropriate study subfolder. Inputs shared by both studies belong in data/shared; study-specific intermediate datasets belong in data/<study>/derived; model objects and model-estimate files belong in models/<study>; publication-ready figures and tables belong in figs/<study> and outputs/<study>.