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Manifest

This file gives a concise description of the main files and folders in the archive.

  • README.md: top-level reproduction instructions.
  • REQUIREMENTS.md: R, OS, and package versions used in the reference run.
  • MANIFEST.md: this file.
  • FIGURE_MAP.md: mapping from scripts and cached files to manuscript outputs.
  • run_quick.R: quick driver script using cached outputs whenever available.
  • run_all.R: fuller driver script that also renders the split notebooks.
  • PDfiltering_library.R: low-level implementation of the filtering, smoothing, and simulation methods.
  • R/pdhmm_setup.R: package checks, path helpers, and project-wide setup.
  • R/pdhmm_api.R: documented public API for reusable PD-HMM software.
  • R/pdhmm_reusable.R: reusable software entry point; sources the public API.
  • analysis/00_setup.R: shared setup for all manuscript-specific scripts.
  • analysis/01_infectious_analysis.R: empirical Infectious-data workflow.
  • analysis/02_simulation_study.R: simulation-study workflow.
  • analysis/03_benchmarks_and_supplement.R: supplementary coordinate plots and benchmark-oriented cached outputs.
  • notebooks/infectious_analysis.Rmd: shorter notebook for the empirical section.
  • notebooks/simulation_study.Rmd: shorter notebook for the simulation section.
  • notebooks/benchmarks.Rmd: shorter notebook for benchmark and supplementary plots.
  • data/raw/listcontacts_2009_06_28.txt: bundled SocioPatterns file used in the manuscript.
  • results/cached/*.csv: cached intermediate outputs used to regenerate expensive figures and supplementary plots.
  • results/figures/: figure files generated by the split scripts.
  • results/tables/: tables written by the split scripts.
  • results/logs/package_versions.csv: package-version log for the reference run.
  • results/logs/sessionInfo.txt: session information for the reference run.

Cached output files

The cached .csv files in results/cached/ are precomputed intermediate outputs for computationally expensive figures.

  • my_data_filter_bootstrap_graphs.csv, my_quantiles_filter_bootstrap_graphs.csv: cached bootstrap-filter outputs for the Infectious analysis.
  • my_data_filter_coord*.csv, my_quantiles_filter_coord*.csv: cached filtering outputs for the first three coordinates in the simulation supplement.
  • my_data_smoothing_coord*.csv, my_quantiles_smoothing_coord*.csv: cached smoothing outputs for the first three coordinates in the simulation supplement.
  • my_true_top_coord*.csv, my_true_top_and_Y_coord*.csv: true latent-coordinate summaries and observation overlays for the simulation supplement.
  • my_MLEs_filter3.csv, my_score_filter3.csv, my_score_smooth3.csv, my_score_boot3.csv, my_score_ind.csv, my_times.csv, my_scores.csv: cached benchmark and pruning outputs used in the supplementary comparison sections.
  • size_top_propagation.csv, size_top_update.csv, top_propagation_relative.csv, top_update_relative.csv: cached support-size summaries used in the supplementary timing/complexity discussion.