Preview

incidence-1.6.0.zip

reconhub-incidence-96c38a5
- .Rbuildignore 312 Bytes
- .gitignore 130 Bytes
- .travis.yml 480 Bytes
- CONDUCT.md 1.4 kB
- DESCRIPTION 1.7 kB
- LICENSE 44 Bytes
- Makefile 952 Bytes
- NAMESPACE 1.8 kB
- NEWS.md 10.7 kB
- R
  - bootstrap.R 1.9 kB
  - check_boundaries.R 1.2 kB
  - check_dates.R 1.6 kB
  - check_dots.R 1.6 kB
  - check_groups.R 894 Bytes
  - check_interval.R 851 Bytes
  - check_timespan.R 718 Bytes
  - check_week.R 462 Bytes
  - conversion.R 5.7 kB
  - cumulate.R 1.3 kB
  - dim.R 166 Bytes
  - estimate_peak.R 3.4 kB
  - extract_info.R 2.7 kB
  - find_peak.R 1.5 kB
  - fit.R 7.7 kB
  - fit_optim_split.R 4.6 kB
  - get_counts.R 1.8 kB
  - get_dates.R 1.9 kB
  - get_fit.R 1.5 kB
  - get_info.R 2.0 kB
  - get_interval.R 3.2 kB
  - get_n.R 467 Bytes
  - get_timespan.R 562 Bytes
  - group_names.R 2.8 kB
  - incidence.R 12.7 kB
  - internals.R 1.7 kB
  - make_breaks.R 3.5 kB
  - make_incidence.R 2.8 kB
  - palettes.R 1.5 kB
  - plot.R 14.0 kB
  - pool.R 1.0 kB
  - print.R 3.4 kB
  - subset.R 3.7 kB
  - trim_observations.R 1.0 kB
  - valid_interval.R 2.0 kB
  - zzz.R 241 Bytes
- README.Rmd 9.5 kB
- README.md 13.9 kB
- _pkgdown.yml 1.7 kB
- appveyor.yml 848 Bytes
- artwork
  - banner.png 80.3 kB
  - logo
    - logo.png 19.6 kB
    - logo.svg 156.0 kB
  - workflow
    - workflow.svg 185.3 kB
    - workflow_script.R 129 Bytes
- bug_reports
  - issue_34.R 1.1 kB
- codecov.yml 15 Bytes
- cran-comments.md 468 Bytes
- demo
  - 00Index 56 Bytes
  - incidence-demo.R 3.1 kB
- docs
  - CONDUCT.html 6.6 kB
  - LICENSE-text.html 5.0 kB
  - articles
    - conversions.html 34.3 kB
    - conversions_files
      - figure-html
        
        example-1.png 31.2 kB
        
        iso-1.png 18.0 kB
        
        long-1.png 30.9 kB
        
        unnamed-chunk-3-1.png 11.6 kB
        
        unnamed-chunk-3-2.png 15.4 kB
        
        unnamed-chunk-4-1.png 17.6 kB
    - customize_plot.html 38.3 kB
    - customize_plot_files
      - figure-html
        
        EPIET1-1.png 11.0 kB
        
        colors1-1.png 22.8 kB
        
        colors2-1.png 26.7 kB
        
        colors3-1.png 43.3 kB
        
        default-1.png 14.8 kB
        
        default-2.png 26.6 kB
        
        default-3.png 44.7 kB
        
        grid1-1.png 44.7 kB
        
        grid2-1.png 71.6 kB
        
        incidence_pal1-1.png 23.2 kB
        
        legend1-1.png 64.3 kB
        
        pal2-1.png 36.0 kB
        
        palettes-1.png 44.2 kB
        
        palettes-2.png 26.8 kB
        
        scales1-1.png 17.1 kB
        
        scales2-1.png 23.9 kB
    - incidence_class.html 55.6 kB
    - incidence_class_files
      - figure-html
        
        i-1.png 18.2 kB
        
        sex-1.png 29.9 kB
    - incidence_fit_class.html 83.0 kB
    - incidence_fit_class_files
      - figure-html
        
        combine-1.png 24.5 kB
        
        fit_dates-1.png 24.5 kB
        
        fit_gender-1.png 110.8 kB
        
        incidence_by_gender-1.png 34.3 kB
        
        incidence_fit_list-1.png 33.9 kB
        
        list_stuff-1.png 132.8 kB
    - index.html 5.6 kB
    - overview.html 66.9 kB
    - overview_files
      - figure-html
        
        fit.both-1.png 32.5 kB
        
        fit1-1.png 16.5 kB
        
        gender-1.png 34.5 kB
        
        groupsub-1.png 36.8 kB
        
        hosp-1.png 37.1 kB
        
        i7outcome-1.png 42.7 kB
        
        incid1-1.png 17.2 kB
        
        interv-1.png 14.8 kB
        
        interv-2.png 17.9 kB
        
        interv-3.png 18.2 kB
        
        middle-1.png 19.3 kB
        
        optim-1.png 32.8 kB
        
        optim-2.png 33.9 kB
        
        optim2-1.png 132.8 kB
        
        optim2-2.png 102.9 kB
        
        stripes-1.png 17.4 kB
        
        tail-1.png 25.7 kB
        
        unnamed-chunk-2-1.png 28.5 kB
        
        unnamed-chunk-3-1.png 29.2 kB
  - authors.html 7.7 kB
  - docsearch.css 11.8 kB
  - docsearch.js 2.0 kB
  - figs
    - fit-plot-1-1.png 37.4 kB
    - fit-plot-2-1.png 34.8 kB
    - fit1-1.png 18.9 kB
    - gender-1.png 37.8 kB
    - i7outcome-1.png 45.1 kB
    - i7outcome_cum-1.png 37.3 kB
    - incid1-1.png 20.9 kB
    - optim-1.png 36.7 kB
    - optim-2.png 42.7 kB
    - pipe-fit-1.png 34.8 kB
    - start-1.png 18.9 kB
    - tail-1.png 23.1 kB
  - index.html 47.6 kB
  - link.svg 810 Bytes
  - news
    - index.html 28.1 kB
  - pkgdown.css 4.1 kB
  - pkgdown.js 3.4 kB
  - pkgdown.yml 239 Bytes
  - reference
    - accessors.html 11.3 kB
    - bootstrap-1.png 17.0 kB
    - bootstrap-2.png 17.9 kB
    - bootstrap.html 10.4 kB
    - conversions-1.png 22.7 kB
    - conversions.html 16.2 kB
    - cumulate-1.png 27.3 kB
    - cumulate-2.png 28.0 kB
    - cumulate.html 10.0 kB
    - estimate_peak-1.png 17.0 kB
    - estimate_peak-2.png 17.7 kB
    - estimate_peak-3.png 26.5 kB
    - estimate_peak-4.png 37.3 kB
    - estimate_peak.html 16.1 kB
    - find_peak-1.png 17.0 kB
    - find_peak-2.png 18.8 kB
    - find_peak-3.png 24.4 kB
    - find_peak.html 10.6 kB
    - fit-1.png 17.0 kB
    - fit-2.png 15.5 kB
    - fit-3.png 28.9 kB
    - fit-4.png 25.0 kB
    - fit-5.png 27.3 kB
    - fit-6.png 25.0 kB
    - fit-7.png 33.4 kB
    - fit-8.png 31.9 kB
    - fit-9.png 34.1 kB
    - fit.html 23.9 kB
    - get_counts.html 10.4 kB
    - get_dates.html 10.7 kB
    - get_fit.html 34.9 kB
    - group_names.html 13.9 kB
    - incidence-1.png 18.0 kB
    - incidence-2.png 16.5 kB
    - incidence-3.png 19.5 kB
    - incidence-4.png 25.8 kB
    - incidence.html 28.3 kB
    - index.html 11.5 kB
    - palettes-1.png 27.2 kB
    - palettes-2.png 71.4 kB
    - palettes-3.png 71.5 kB
    - palettes-4.png 71.9 kB
    - palettes.html 9.2 kB
    - plot.incidence-1.png 18.0 kB
    - plot.incidence-10.png 100.5 kB
    - plot.incidence-2.png 17.0 kB
    - plot.incidence-3.png 16.5 kB
    - plot.incidence-4.png 19.9 kB
    - plot.incidence-5.png 26.5 kB
    - plot.incidence-6.png 25.8 kB
    - plot.incidence-7.png 35.9 kB
    - plot.incidence-8.png 40.7 kB
    - plot.incidence-9.png 101.2 kB
    - plot.incidence.html 21.5 kB
    - pool.html 10.4 kB
    - subset-1.png 15.7 kB
    - subset-2.png 17.0 kB
    - subset.html 11.2 kB
- figs
  - fit-plot-1-1.png 37.4 kB
  - fit-plot-2-1.png 34.8 kB
  - fit1-1.png 18.9 kB
  - gender-1.png 37.8 kB
  - i7outcome-1.png 45.1 kB
  - i7outcome_cum-1.png 37.3 kB
  - incid1-1.png 20.9 kB
  - optim-1.png 36.7 kB
  - optim-2.png 42.7 kB
  - pipe-fit-1.png 34.8 kB
  - start-1.png 18.9 kB
  - tail-1.png 23.1 kB
- incidence.Rproj 396 Bytes
- inst
  - CITATION 2.0 kB
  - WORDLIST 397 Bytes
- man
  - accessors.Rd 2.3 kB
  - bootstrap.Rd 1.4 kB
  - conversions.Rd 2.6 kB
  - cumulate.Rd 1.2 kB
  - estimate_peak.Rd 2.6 kB
  - find_peak.Rd 1.2 kB
  - fit.Rd 5.7 kB
  - get_counts.Rd 1.2 kB
  - get_dates.Rd 1.3 kB
  - get_fit.Rd 2.2 kB
  - group_names.Rd 1.9 kB
  - incidence.Rd 8.2 kB
  - palettes.Rd 899 Bytes
  - plot.incidence.Rd 3.9 kB
  - pool.Rd 844 Bytes
  - subset.Rd 1.7 kB
- misc
  - plotly-expl.R 827 Bytes
- tests
  - figs
    - deps.txt 67 Bytes
    - test-plotting
      - epiquares-single-plot.svg 52.0 kB
      - grouped-incidence-fit.svg 9.1 kB
      - grouped-incidence-plot-cumulative.svg 12.2 kB
      - grouped-incidence-plot-with-color-palette.svg 14.6 kB
      - grouped-incidence-plot-with-fit.svg 14.6 kB
      - grouped-incidence-plot-with-one-group.svg 16.2 kB
      - grouped-incidence-plot-with-specified-color.svg 14.6 kB
      - grouped-incidence-plot.svg 12.2 kB
      - incidence-fit-list-plot-with-split.svg 14.5 kB
      - incidence-fit-plot-with-split.svg 20.3 kB
      - incidence-fit.svg 7.1 kB
      - incidence-plot-by-month.svg 9.8 kB
      - incidence-plot-by-quarter.svg 6.5 kB
      - incidence-plot-from-posixct-data-with-fit.svg 17.9 kB
      - incidence-plot-from-posixct-data.svg 16.0 kB
      - incidence-plot-with-default-interval-cumulative.svg 15.6 kB
      - incidence-plot-with-default-interval.svg 15.2 kB
      - incidence-plot-with-interval-of-14-days.svg 8.1 kB
      - incidence-plot-with-interval-of-3-days-fit-and-specified-color.svg 10.3 kB
      - incidence-plot-with-isoweek-labels.svg 8.0 kB
      - incidence-plot-with-specified-color-and-alpha.svg 15.2 kB
      - incidence-plot-with-two-fitting-models.svg 17.9 kB
      - incidence-plot-without-isoweek-labels.svg 8.0 kB
      - split-optimum-plot-pooled.svg 6.4 kB
      - split-optimum-plot.svg 9.8 kB
  - testthat
    - data_cache
      - mfcat.rds 214 Bytes
      - mfdat.rds 508 Bytes
    - rds
      - df.rds 156 Bytes
      - df2.rds 122 Bytes
      - df3.rds 204 Bytes
      - df5.rds 211 Bytes
      - df6.rds 245 Bytes
      - dfl.rds 197 Bytes
      - fit.i.rds 2.8 kB
      - fit.i.sex.rds 4.4 kB
      - incidence.res1.rds 181 Bytes
      - incidence.res2.rds 166 Bytes
      - incidence.res3.rds 383 Bytes
      - incidence.res4.rds 486 Bytes
      - incidence.res5.rds 178 Bytes
      - incidence.res6.rds 165 Bytes
      - incidence.res7.rds 246 Bytes
      - incidence.res8.rds 254 Bytes
      - o.fit.i.rds 21.2 kB
      - o.fit.i.sex.rds 23.7 kB
      - print.fit.i.rds 356 Bytes
      - print.fit.sex.rds 412 Bytes
      - print1.rds 231 Bytes
      - print2.rds 239 Bytes
      - print3.rds 268 Bytes
      - ref_date_breaks_iso.rds 142 Bytes
      - res.g.1.rds 198 Bytes
      - res.g.2.rds 184 Bytes
      - res.g.3.rds 213 Bytes
      - x.sub1.rds 175 Bytes
      - x.sub2.rds 193 Bytes
      - x.sub3.rds 192 Bytes
      - x.sub4.rds 188 Bytes
      - x.sub5.rds 168 Bytes
      - y.sub1.rds 249 Bytes
    - test-accessors.R 7.8 kB
    - test-bootstrap.R 2.3 kB
    - test-conversions.R 2.3 kB
    - test-cumulate.R 409 Bytes
    - test-fit.R 2.3 kB
    - test-incidence.R 13.6 kB
    - test-non-exported.R 2.3 kB
    - test-palettes.R 583 Bytes
    - test-plot.R 4.8 kB
    - test-pool.R 379 Bytes
    - test-standards.R 1.1 kB
    - test-subset.R 3.1 kB
  - testthat.R 62 Bytes
- vignettes
  - conversions.Rmd 4.3 kB
  - customize_plot.Rmd 6.6 kB
  - figs-class
    - i-1.png 17.4 kB
    - sex-1.png 30.2 kB
  - figs-conversion
    - example-1.png 31.6 kB
    - iso-1.png 18.3 kB
    - long-1.png 31.5 kB
    - unnamed-chunk-3-1.png 11.7 kB
    - unnamed-chunk-3-2.png 15.6 kB
    - unnamed-chunk-4-1.png 17.8 kB
  - figs-custom
    - colors1-1.png 15.1 kB
    - colors2-1.png 27.3 kB
    - colors3-1.png 44.3 kB
    - default-1.png 15.1 kB
    - default-2.png 27.2 kB
    - default-3.png 45.5 kB
    - grid1-1.png 45.5 kB
    - grid2-1.png 72.3 kB
    - incidence_pal1-1.png 23.7 kB
    - legend1-1.png 64.9 kB
    - pal1-1.png 23.9 kB
    - pal2-1.png 36.6 kB
    - palettes-1.png 44.9 kB
    - palettes-2.png 27.6 kB
    - scales1-1.png 16.8 kB
    - scales2-1.png 24.0 kB
  - figs-fit
    - combine-1.png 23.9 kB
    - fit_dates-1.png 23.9 kB
    - fit_gender-1.png 112.4 kB
    - incidence_by_gender-1.png 35.8 kB
    - incidence_fit_list-1.png 33.9 kB
    - list_stuff-1.png 133.4 kB
  - figs-overview
    - fit.both-1.png 32.4 kB
    - fit1-1.png 16.6 kB
    - gender-1.png 36.3 kB
    - groupsub-1.png 40.6 kB
    - hosp-1.png 37.8 kB
    - i7outcome-1.png 43.3 kB
    - incid1-1.png 18.1 kB
    - interv-1.png 15.1 kB
    - interv-2.png 17.8 kB
    - interv-3.png 18.2 kB
    - middle-1.png 19.4 kB
    - optim-1.png 32.9 kB
    - optim-2.png 33.9 kB
    - optim2-1.png 133.4 kB
    - optim2-2.png 104.2 kB
    - stripes-1.png 19.2 kB
    - tail-1.png 25.6 kB
    - unnamed-chunk-2-1.png 29.3 kB
    - unnamed-chunk-3-1.png 29.3 kB
  - incidence_class.Rmd 5.7 kB
  - incidence_fit_class.Rmd 9.7 kB
  - overview.Rmd 9.3 kB