Early Air Connectivity & Excess Mortality

Exploratory correlation study for a BSc thesis (University of Salzburg)

Research question

Among continental EUROCONTROL states, did higher volumes of direct inbound flights from China/Hong Kong (Dec 2019 & Mar 2020) associate with higher excess mortality on 5 May 2020?

We join EUROCONTROL IFR snapshots with OWID/WMD, then:

• build country-level exposure metrics (Dec-2019, Mar-2020, Dec+Mar; also flights-per-million),
• compute Spearman ρ for 2020–2023 with bootstrap CIs,
• run sensitivity checks (population scaling; complete 4-year mortality series; partial ρ by %≥65).

Everything is reproducible with R ≥ 4.4, Quarto ≥ 1.6, and a LaTeX engine.

Requirements

• R ≥ 4.4
• Quarto CLI ≥ 1.6 (quarto --version)
• LaTeX (TinyTeX recommended)

This repo vendors the Elsevier Quarto template in _extensions/ (MIT). No manual install needed. If you clone without _extensions/, run: quarto add quarto-journals/elsevier.

Data (bring your own)

EUROCONTROL IFR monthly CSV drops are not distributed here.

data/raw/
├── flight_data/
│   ├── 201912/          # all Dec 2019 *.csv.gz
│   └── 202003/          # all Mar 2020 *.csv.gz
├── OurAirports/         # reference airport list
│   └── airports.csv
└── owid/
    └── owid-covid-data.csv

Keep EUROCONTROL files compressed (*.csv.gz) and original filenames.

Quick start

# Optional: install TinyTeX if you don’t have LaTeX
INSTALL_TINYTEX=1 ./build.sh

# Build site + PDF (default)
./build.sh

# Or individual targets
./build.sh html      # Elsevier HTML
./build.sh pdf       # Elsevier PDF
./build.sh clean     # clear caches and outputs

What the script does:

1. checks data dependencies,
2. restores exact packages via renv (from renv.lock),
3. runs preprocessing scripts in R/,
4. renders Elsevier outputs (HTML + PDF).

Render manually (optional)

quarto render thesis.qmd --to elsevier-html
quarto render thesis.qmd --to elsevier-pdf

Repository map

bachelor-thesis/
├─ data/
│  ├─ raw/            # (you provide)
│  ├─ processed/      # created by scripts
│  ├─ derived/        # tables used in the paper
│  └─ figures/        # PNG/PDF figures
├─ R/
│  ├─ 00_load_libs.R
│  ├─ 01_excess_snapshots.R
│  ├─ 01b_vax_snap.R
│  ├─ 02_flight_filter.R
│  ├─ 02b_flight_opensky.R
│  ├─ 03_merge_exposure.R
│  ├─ 04_population_qc.R
│  ├─ 05_descriptive_plots.R
│  └─ 06_correlation.R
├─ thesis.qmd
├─ thesis_ref.bib
├─ _quarto.yml
├─ _extensions/       # vendored Elsevier template (MIT)
└─ build.sh

Outputs

• HTML site: _manuscript/index.html
• PDF: _manuscript/thesis.pdf
• Logs: _manuscript/logs/

Tip: avoid RStudio’s “Render” button. Use ./build.sh so checks and renv::restore() run.

Reproducibility

• Package versions are pinned in renv.lock.
• Quarto caching (freeze: auto) speeds re-runs but the lockfile is the source of truth.
• Scripts are idempotent; delete data/processed/data/derived to rebuild.

Data sources

Dataset	Licence	Link
EUROCONTROL ATM flight records (research release)	© EUROCONTROL¹	https://www.eurocontrol.int
OpenSky crowdsourced air-traffic data (2020)	Research only²	https://zenodo.org/records/7923702
Excess mortality (HMD-STMF + WMD via OWID)	CC-BY-4.0	https://ourworldindata.org/excess-mortality-covid
UN World Population Prospects 2024 (mid-2020 snapshot)	CC-BY-3.0 IGO	https://population.un.org/wpp/ (R pkg: https://github.com/PPgp/wpp2024)
OurAirports reference	CC0	https://ourairports.com

¹ Not redistributed; copy monthly drops to data/raw/flight_data/YYYYMM/. ² Redistribution of raw OpenSky files is not permitted.

License

• Code: MIT
• Text & figures: CC-BY 4.0
• Processed data: inherit upstream licences; attribute sources when reusing.

Maintainer: Maximilian Elixhauser — [email protected] Last updated: 2025-10-10