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Sorting out assortativity: when can we assess the contributions of different population groups to epidemic transmission?

Structure

📦script
 ┣ 📂modelling
 ┃ ┣ 📜master.R
 ┃ ┗ 📜modelling_helpers.R
 ┣ 📂simulations
 ┃ ┣ 📜generate_scenarios.R
 ┃ ┣ 📜master.R
 ┃ ┣ 📜process_helpers.R
 ┃ ┗ 📜test.R
 ┗ 📂visualisations
 ┃ ┣ 📜1_AR_last_date.R
 ┃ ┣ 📜2_scenario_histograms.R
 ┃ ┣ 📜3_violin_ROC.R
 ┃ ┣ 📜4_hexbin.R
 ┃ ┣ 📜5_hexbin_all.R
 ┃ ┣ 📜7_delta_gamma_peak_coeff.R
 ┃ ┣ 📜8_delta_saturation.R
 ┃ ┣ 📜master.R
 ┃ ┗ 📜plot_helpers.R

Order of execution

The code was tested on R version 4.1.3 (2022-03-10).
Requires the o2groups R package.
The analysis was conducted using the pre-release version of the o2groups package (v0.0.0.9000), which is available on github and zenodo.
DOI

  1. Source master.R in simulations, it will store the results in a new data folder.
  2. Source master.R in visualisations, it will store the figures in a new plots folder.
  3. Source master.R in modelling, it will print the results in the console.

License

Creative Commons Attribution (CC BY) 4.0 International License