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EpiNow2-v1.2.0.zip

epiforecasts-EpiNow2-b400a5b
- .Rbuildignore 268 Bytes
- .github
  - workflows
    - build-docker.yaml 585 Bytes
    - check-full.yaml 3.1 kB
    - pkgdown.yaml 1.2 kB
    - pr-commands.yaml 1.8 kB
    - test-coverage.yaml 1.0 kB
- .gitignore 112 Bytes
- DESCRIPTION 3.1 kB
- Dockerfile 729 Bytes
- EpiNow2.Rproj 328 Bytes
- LICENSE 42 Bytes
- LICENSE.md 1.1 kB
- NAMESPACE 4.2 kB
- NEWS.md 3.4 kB
- R
  - adjust.R 6.0 kB
  - create.R 10.9 kB
  - data.R 693 Bytes
  - dist.R 21.1 kB
  - epinow.R 24.7 kB
  - estimate_infections.R 27.1 kB
  - extract.R 4.6 kB
  - forecast_infections.R 9.0 kB
  - get.R 7.8 kB
  - map.R 13.0 kB
  - plot.R 9.6 kB
  - report.R 14.0 kB
  - simulate.R 6.5 kB
  - stanmodels.R 1.2 kB
  - summarise.R 18.5 kB
  - utilities.R 11.0 kB
- README.Rmd 12.3 kB
- README.md 16.8 kB
- _pkgdown.yml 2.5 kB
- configure 117 Bytes
- configure.win 134 Bytes
- cran-comments.md 427 Bytes
- data
  - example_confirmed.rda 833 Bytes
  - generation_times.rda 433 Bytes
  - incubation_periods.rda 388 Bytes
- data-raw
  - generation-time.R 1.1 kB
  - gi.rds 159.2 kB
  - incubation-period.R 320 Bytes
- inst
  - CITATION 1.2 kB
  - WORDLIST 405 Bytes
  - include
    - stan_meta_header.hpp 48 Bytes
  - pkg-structure
    - generate-pkgstructure-report.R 317 Bytes
  - stan
    - estimate_infections.stan 11.1 kB
    - exp.stan 283 Bytes
    - functions
      - approximate_gp_functions.stan 612 Bytes
      - convolve.stan 368 Bytes
      - discretised_gamma_pmf.stan 608 Bytes
      - discretised_lognormal_pmf.stan 436 Bytes
    - gamma.stan 747 Bytes
    - include
      - license.stan 643 Bytes
    - lnorm.stan 331 Bytes
  - templates
    - _add-region-reports.Rmd 577 Bytes
    - _all-region-summary.Rmd 2.9 kB
    - _region-report.Rmd 2.6 kB
    - _regional-summary.Rmd 6.2 kB
- man
  - R_to_growth.Rd 645 Bytes
  - adjust_infection_to_report.Rd 4.2 kB
  - allocate_delays.Rd 419 Bytes
  - bootstrapped_dist_fit.Rd 1.6 kB
  - clean_nowcasts.Rd 528 Bytes
  - clean_regions.Rd 566 Bytes
  - country_map.Rd 4.3 kB
  - create_clean_reported_cases.Rd 587 Bytes
  - create_initial_conditions.Rd 1.4 kB
  - create_shifted_cases.Rd 848 Bytes
  - create_stan_args.Rd 2.2 kB
  - create_stan_data.Rd 3.9 kB
  - dist_fit.Rd 1.6 kB
  - dist_skel.Rd 2.3 kB
  - epinow.Rd 9.4 kB
  - estimate_infections.Rd 14.6 kB
  - example_confirmed.Rd 358 Bytes
  - extract_parameter.Rd 663 Bytes
  - extract_parameter_samples.Rd 742 Bytes
  - extract_static_parameter.Rd 571 Bytes
  - figures
    - unnamed-chunk-11-1.png 469.8 kB
    - unnamed-chunk-12-1.png 381.4 kB
    - unnamed-chunk-13-1.png 397.8 kB
    - unnamed-chunk-14-1.png 393.9 kB
    - unnamed-chunk-15-1.png 146.2 kB
    - unnamed-chunk-16-1.png 146.3 kB
    - unnamed-chunk-17-1.png 149.3 kB
    - unnamed-chunk-18-1.png 149.0 kB
  - fit_model_with_nuts.Rd 860 Bytes
  - fit_model_with_vb.Rd 623 Bytes
  - forecast_infections.Rd 3.4 kB
  - format_fit.Rd 692 Bytes
  - gamma_dist_def.Rd 1.8 kB
  - generation_times.Rd 451 Bytes
  - get_dist.Rd 704 Bytes
  - get_generation_time.Rd 694 Bytes
  - get_incubation_period.Rd 704 Bytes
  - get_raw_result.Rd 597 Bytes
  - get_regional_results.Rd 2.1 kB
  - get_regions.Rd 463 Bytes
  - global_map.Rd 3.3 kB
  - growth_to_R.Rd 638 Bytes
  - incubation_periods.Rd 463 Bytes
  - lognorm_dist_def.Rd 1.6 kB
  - make_conf.Rd 694 Bytes
  - map_prob_change.Rd 552 Bytes
  - plot_estimates.Rd 2.3 kB
  - plot_summary.Rd 721 Bytes
  - process_region.Rd 743 Bytes
  - process_regions.Rd 518 Bytes
  - regional_epinow.Rd 3.2 kB
  - regional_summary.Rd 2.7 kB
  - report_cases.Rd 3.0 kB
  - report_plots.Rd 1.7 kB
  - report_summary.Rd 742 Bytes
  - run_region.Rd 1.4 kB
  - sample_approx_dist.Rd 2.9 kB
  - setup_future.Rd 1.4 kB
  - setup_logging.Rd 1.6 kB
  - simulate_cases.Rd 5.5 kB
  - stop_timeout.Rd 273 Bytes
  - summarise_key_measures.Rd 960 Bytes
  - summarise_results.Rd 954 Bytes
  - theme_map.Rd 1.5 kB
- src
  - Makevars 751 Bytes
  - Makevars.win 727 Bytes
  - RcppExports.cpp 1.1 kB
  - stanExports_estimate_infections.cc 2.0 kB
  - stanExports_estimate_infections.h 131.1 kB
  - stanExports_exp.cc 2.0 kB
  - stanExports_exp.h 13.3 kB
  - stanExports_gamma.cc 2.0 kB
  - stanExports_gamma.h 22.1 kB
  - stanExports_lnorm.cc 2.0 kB
  - stanExports_lnorm.h 15.4 kB
- tests
  - spelling.R 161 Bytes
  - testthat
    - test-create_stan_args.R 830 Bytes
    - test-epinow.R 2.4 kB
    - test-estimate_infections.R 3.9 kB
    - test-get_dist.R 373 Bytes
    - test-regional_epinow.R 2.6 kB
    - test-setup_future.R 1.1 kB
  - testthat.R 58 Bytes