Files in eeholmes/CoV19
Eli's package for figures and data on CoV-19 epidemic
.gitattributes
.github/workflows/getdata.yml
.gitignore
CFR.Rmd
CoV19.Rproj
DESCRIPTION
Forecasts.Rmd
NAMESPACE
R/add_vline.R
R/data.R
R/getdata.R
R/getdataitaly.R
R/getdatastates.R
R/getdatawa.R
R/getdataworld.R
R/getdataworld_oldjhu.R
R/getmitigations.R
R/plot1.R
R/plot2.R
R/plot3.R
R/plot4.R
R/regions.R
R/updatewebpage.R
R/walomb_plot.R
README.Rmd
README.md
README_files/figure-gfm/unnamed-chunk-1-1.png
README_files/figure-gfm/unnamed-chunk-2-1.png
README_files/figure-gfm/unnamed-chunk-3-1.png
README_files/figure-gfm/unnamed-chunk-4-1.png
Updates.Rmd
_site.yml
cz_plot.Rmd
data.Rmd
data/FIPS.RData
data/countydata.RData
data/countypop.RData
data/eunames.RData
data/gdp.RData
data/italy.RData
data/italypop.RData
data/mitigations.RData
data/popdata.RData
data/statepop.RData
data/states.RData
data/world.RData
data/worldpop.RData
docs/CFR.html
docs/CFR_files/figure-html/unnamed-chunk-10-1.png
docs/CFR_files/figure-html/unnamed-chunk-11-1.png
docs/CFR_files/figure-html/unnamed-chunk-12-1.png
docs/CFR_files/figure-html/unnamed-chunk-13-1.png
docs/CFR_files/figure-html/unnamed-chunk-14-1.png
docs/CFR_files/figure-html/unnamed-chunk-15-1.png
docs/CFR_files/figure-html/unnamed-chunk-17-1.png
docs/CFR_files/figure-html/unnamed-chunk-18-1.png
docs/CFR_files/figure-html/unnamed-chunk-19-1.png
docs/CFR_files/figure-html/unnamed-chunk-20-1.png
docs/CFR_files/figure-html/unnamed-chunk-3-1.png
docs/CFR_files/figure-html/unnamed-chunk-4-1.png
docs/CFR_files/figure-html/unnamed-chunk-7-1.png
docs/CFR_files/figure-html/unnamed-chunk-8-1.png
docs/CFR_files/figure-html/unnamed-chunk-9-1.png
docs/Forecasts.html
docs/Forecasts_files/figure-html/Asia-forecast-1.png
docs/Forecasts_files/figure-html/Asia-forecast-2.png
docs/Forecasts_files/figure-html/Asia-forecast-3.png
docs/Forecasts_files/figure-html/Austria-forecast-1.png
docs/Forecasts_files/figure-html/Balkans-forecast-1.png
docs/Forecasts_files/figure-html/Balkans-forecast-2.png
docs/Forecasts_files/figure-html/Balkans-forecast-3.png
docs/Forecasts_files/figure-html/Balkans-forecast-4.png
docs/Forecasts_files/figure-html/Balkans-forecast-5.png
docs/Forecasts_files/figure-html/Balkans-forecast-6.png
docs/Forecasts_files/figure-html/Balkans-forecast-7.png
docs/Forecasts_files/figure-html/CEurope-forecast-1.png
docs/Forecasts_files/figure-html/CEurope-forecast-2.png
docs/Forecasts_files/figure-html/CEurope-forecast-3.png
docs/Forecasts_files/figure-html/CEurope-forecast-4.png
docs/Forecasts_files/figure-html/Germanic-forecast-1.png
docs/Forecasts_files/figure-html/Germanic-forecast-2.png
docs/Forecasts_files/figure-html/Germanic-forecast-3.png
docs/Forecasts_files/figure-html/Germanic-forecast-4.png
docs/Forecasts_files/figure-html/Germany-forecast-1.png
docs/Forecasts_files/figure-html/Lomb-forecast-1.png
docs/Forecasts_files/figure-html/Mex-forecast-1.png
docs/Forecasts_files/figure-html/NAmer-forecast1-1.png
docs/Forecasts_files/figure-html/NAmer-forecast1-2.png
docs/Forecasts_files/figure-html/NAmer-forecast1-3.png
docs/Forecasts_files/figure-html/NAmer-forecast1-4.png
docs/Forecasts_files/figure-html/NAmer-forecast1-5.png
docs/Forecasts_files/figure-html/NAmer-forecast1-6.png
docs/Forecasts_files/figure-html/Russia-1.png
docs/Forecasts_files/figure-html/SAmer-forecast-1.png
docs/Forecasts_files/figure-html/SAmer-forecast-2.png
docs/Forecasts_files/figure-html/SAmer-forecast-3.png
docs/Forecasts_files/figure-html/SEurope-forecast-1.png
docs/Forecasts_files/figure-html/SEurope-forecast-2.png
docs/Forecasts_files/figure-html/SEurope-forecast-3.png
docs/Forecasts_files/figure-html/SEurope-forecast-4.png
docs/Forecasts_files/figure-html/Scandinavia-forecast-1.png
docs/Forecasts_files/figure-html/Scandinavia-forecast-2.png
docs/Forecasts_files/figure-html/Scandinavia-forecast-3.png
docs/Forecasts_files/figure-html/UK-forecast-1.png
docs/Forecasts_files/figure-html/UK-forecast-2.png
docs/Forecasts_files/figure-html/USSR-1.png
docs/Forecasts_files/figure-html/USSR-2.png
docs/Forecasts_files/figure-html/denmark-forecast-1.png
docs/Forecasts_files/figure-html/states-forecast-cn-1.png
docs/Forecasts_files/figure-html/states-forecast-cn-2.png
docs/Forecasts_files/figure-html/states-forecast-cn-3.png
docs/Forecasts_files/figure-html/states-forecast-cn2-1.png
docs/Forecasts_files/figure-html/states-forecast-cn2-2.png
docs/Forecasts_files/figure-html/states-forecast-cn2-3.png
docs/Forecasts_files/figure-html/states-forecast-cn2-4.png
docs/Forecasts_files/figure-html/states-forecast-eastsouth-1.png
docs/Forecasts_files/figure-html/states-forecast-emid-1.png
docs/Forecasts_files/figure-html/states-forecast-fourcorners-1.png
docs/Forecasts_files/figure-html/states-forecast-fourcorners-2.png
docs/Forecasts_files/figure-html/states-forecast-fourcorners-3.png
docs/Forecasts_files/figure-html/states-forecast-fourcorners-4.png
docs/Forecasts_files/figure-html/states-forecast-fourcorners-5.png
docs/Forecasts_files/figure-html/states-forecast-mid-atlantic-1.png
docs/Forecasts_files/figure-html/states-forecast-midwest-1.png
docs/Forecasts_files/figure-html/states-forecast-midwest-2.png
docs/Forecasts_files/figure-html/states-forecast-midwest-3.png
docs/Forecasts_files/figure-html/states-forecast-midwest-4.png
docs/Forecasts_files/figure-html/states-forecast-mtnnorth-1.png
docs/Forecasts_files/figure-html/states-forecast-mtnsw-1.png
docs/Forecasts_files/figure-html/states-forecast-new-england-1.png
docs/Forecasts_files/figure-html/states-forecast-norcal-1.png
docs/Forecasts_files/figure-html/states-forecast-north-1.png
docs/Forecasts_files/figure-html/states-forecast-north-2.png
docs/Forecasts_files/figure-html/states-forecast-north-3.png
docs/Forecasts_files/figure-html/states-forecast-northeast-1.png
docs/Forecasts_files/figure-html/states-forecast-northeast-2.png
docs/Forecasts_files/figure-html/states-forecast-northeast-3.png
docs/Forecasts_files/figure-html/states-forecast-northeast-4.png
docs/Forecasts_files/figure-html/states-forecast-northeast-5.png
docs/Forecasts_files/figure-html/states-forecast-northeast-6.png
docs/Forecasts_files/figure-html/states-forecast-northeast-7.png
docs/Forecasts_files/figure-html/states-forecast-northeast-8.png
docs/Forecasts_files/figure-html/states-forecast-rockies-1.png
docs/Forecasts_files/figure-html/states-forecast-rockies-2.png
docs/Forecasts_files/figure-html/states-forecast-rockies-3.png
docs/Forecasts_files/figure-html/states-forecast-socal-1.png
docs/Forecasts_files/figure-html/states-forecast-south-1.png
docs/Forecasts_files/figure-html/states-forecast-south-2.png
docs/Forecasts_files/figure-html/states-forecast-south-3.png
docs/Forecasts_files/figure-html/states-forecast-south-4.png
docs/Forecasts_files/figure-html/states-forecast-south-5.png
docs/Forecasts_files/figure-html/states-forecast-south-6.png
docs/Forecasts_files/figure-html/states-forecast-southatlanticsouth-1.png
docs/Forecasts_files/figure-html/states-forecast-southca-1.png
docs/Forecasts_files/figure-html/states-forecast-southcentral-1.png
docs/Forecasts_files/figure-html/states-forecast-southcentral-2.png
docs/Forecasts_files/figure-html/states-forecast-southcentral-3.png
docs/Forecasts_files/figure-html/states-forecast-southeast-1.png
docs/Forecasts_files/figure-html/states-forecast-southeast-2.png
docs/Forecasts_files/figure-html/states-forecast-southeast-3.png
docs/Forecasts_files/figure-html/states-forecast-southeast-4.png
docs/Forecasts_files/figure-html/states-forecast-southeast-5.png
docs/Forecasts_files/figure-html/states-forecast-usouthatlantic-1.png
docs/Forecasts_files/figure-html/states-forecast-westcoast-1.png
docs/Forecasts_files/figure-html/states-forecast-westcoast-2.png
docs/Forecasts_files/figure-html/states-forecast-westcoast-3.png
docs/Forecasts_files/figure-html/states-forecast-westnosocal-1.png
docs/Forecasts_files/figure-html/states-forecast-westsouth-1.png
docs/Forecasts_files/figure-html/states-forecast-wmid-1.png
docs/Forecasts_files/figure-html/states-forecast-wmid2-1.png
docs/Updates.html
docs/cz_plot.html
docs/cz_plot_files/figure-html/au_plot-1.png
docs/cz_plot_files/figure-html/au_plot2-1.png
docs/cz_plot_files/figure-html/cz_plot-1.png
docs/cz_plot_files/figure-html/cz_plot2-1.png
docs/cz_plot_files/figure-html/ge_plot-1.png
docs/cz_plot_files/figure-html/ge_plot2-1.png
docs/cz_plot_files/figure-html/pl_plot-1.png
docs/cz_plot_files/figure-html/pl_plot2-1.png
docs/data.html
docs/data_files/figure-html/unnamed-chunk-5-1.png
docs/epidemic_states.html
docs/epidemic_states_files/figure-html/unnamed-chunk-1-1.png
docs/epidemic_states_files/figure-html/unnamed-chunk-2-1.png
docs/epidemic_states_files/figure-html/unnamed-chunk-3-1.png
docs/index.html
docs/ny_plot.html
docs/ny_plot_files/figure-html/ny_plot-1.png
docs/plots.html
docs/plots_files/figure-html/unnamed-chunk-1-1.png
docs/plots_files/figure-html/unnamed-chunk-2-1.png
docs/plots_files/figure-html/unnamed-chunk-3-1.png
docs/plots_files/figure-html/unnamed-chunk-4-1.png
docs/site_libs/anchor-sections-1.0/anchor-sections.css
docs/site_libs/anchor-sections-1.0/anchor-sections.js
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap.min.css
docs/site_libs/bootstrap-3.3.5/css/cerulean.min.css
docs/site_libs/bootstrap-3.3.5/css/cosmo.min.css
docs/site_libs/bootstrap-3.3.5/css/darkly.min.css
docs/site_libs/bootstrap-3.3.5/css/flatly.min.css
docs/site_libs/bootstrap-3.3.5/css/fonts/Lato.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/LatoBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
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docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoLight.ttf
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docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansPro.ttf
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docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProItalic.ttf
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docs/site_libs/bootstrap-3.3.5/css/fonts/Ubuntu.ttf
docs/site_libs/bootstrap-3.3.5/css/journal.min.css
docs/site_libs/bootstrap-3.3.5/css/lumen.min.css
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docs/site_libs/bootstrap-3.3.5/css/readable.min.css
docs/site_libs/bootstrap-3.3.5/css/sandstone.min.css
docs/site_libs/bootstrap-3.3.5/css/simplex.min.css
docs/site_libs/bootstrap-3.3.5/css/spacelab.min.css
docs/site_libs/bootstrap-3.3.5/css/united.min.css
docs/site_libs/bootstrap-3.3.5/css/yeti.min.css
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
docs/site_libs/bootstrap-3.3.5/js/bootstrap.js
docs/site_libs/bootstrap-3.3.5/js/bootstrap.min.js
docs/site_libs/bootstrap-3.3.5/js/npm.js
docs/site_libs/bootstrap-3.3.5/shim/html5shiv.min.js
docs/site_libs/bootstrap-3.3.5/shim/respond.min.js
docs/site_libs/font-awesome-5.1.0/css/all.css
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docs/site_libs/highlightjs-9.12.0/default.css
docs/site_libs/highlightjs-9.12.0/highlight.js
docs/site_libs/highlightjs-9.12.0/textmate.css
docs/site_libs/jquery-1.11.3/jquery.min.js
docs/site_libs/navigation-1.1/codefolding.js
docs/site_libs/navigation-1.1/sourceembed.js
docs/site_libs/navigation-1.1/tabsets.js
docs/state_plots.html
docs/state_plots_files/figure-html/unnamed-chunk-10-1.png
docs/state_plots_files/figure-html/unnamed-chunk-11-1.png
docs/state_plots_files/figure-html/unnamed-chunk-12-1.png
docs/state_plots_files/figure-html/unnamed-chunk-13-1.png
docs/state_plots_files/figure-html/unnamed-chunk-14-1.png
docs/state_plots_files/figure-html/unnamed-chunk-2-1.png
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docs/state_plots_files/figure-html/unnamed-chunk-5-1.png
docs/state_plots_files/figure-html/unnamed-chunk-6-1.png
docs/state_plots_files/figure-html/unnamed-chunk-7-1.png
docs/state_plots_files/figure-html/unnamed-chunk-8-1.png
docs/state_plots_files/figure-html/unnamed-chunk-9-1.png
docs/styles.css
docs/updates/2020-04-28-Perspective.Rmd
docs/updates/2020-04-28-Perspective.html
docs/updates/2020-04-29-Rural.Rmd
docs/updates/2020-04-29-Rural.html
docs/updates/2020-05-01-Forecast-Models.Rmd
docs/updates/2020-05-01-Forecast-Models.html
docs/updates/2020-05-04-Patterns.Rmd
docs/updates/2020-05-04-Patterns.html
docs/updates/2020-05-06-Changing-CFR.Rmd
docs/updates/2020-05-06-Changing-CFR.html
docs/updates/2020-05-13-Fitting-SIR-Models.Rmd
docs/updates/2020-05-17-Patterns.Rmd
docs/updates/2020-05-17-Patterns.html
docs/updates/2020-05-18-Density.Rmd
docs/updates/2020-05-25-Patterns.Rmd
docs/updates/2020-06-10-Patterns.Rmd
docs/updates/2020-06-10-Patterns.html
docs/updates/2020-06-17-Going-Up.Rmd
docs/updates/2020-06-17-Going-Up.html
docs/updates/2020-06-28-AZ-TX-NJ.Rmd
docs/updates/2020-06-28-AZ-TX-NJ.html
docs/updates/2020-07-15-AZ-TX-FL.Rmd
docs/updates/2020-07-15-AZ-TX-FL.html
docs/updates/2020-10-24.Rmd
docs/updates/2020-10-24.html
docs/updates/2020-10-25.Rmd
docs/updates/2020-10-26-Fall-Surge.Rmd
docs/updates/2020-10-26-Fall-Surge.html
docs/updates/2020-10-30-Changing-Positivity.Rmd
docs/updates/2020-10-30-Changing-Positivity.html
docs/updates/Forecast-Functions-2.Rmd
docs/updates/Forecast-Functions-3.Rmd
docs/updates/Forecast-Functions.Rmd
docs/updates/Screen Shot 2020-05-17 at 9.06.48 AM.png
docs/updates/cases_per_100k_US.png
docs/updates/day10.R
docs/updates/day11.R
docs/updates/day12.R
docs/updates/day15.R
docs/updates/day17.R
docs/updates/day18.R
docs/updates/day19.R
docs/updates/day2.R
docs/updates/day20.R
docs/updates/day21.R
docs/updates/day22.R
docs/updates/day23.R
docs/updates/day3.R
docs/updates/day4.R
docs/updates/day6.R
docs/updates/day7.R
docs/updates/day8.R
docs/updates/day9.R
docs/updates/king-co-geography.gif
docs/walomb_plot.html
docs/walomb_plot_files/figure-html/italy_plot-1.png
docs/walomb_plot_files/figure-html/king_plot-1.png
docs/walomb_plot_files/figure-html/unnamed-chunk-2-1.png
docs/walomb_plot_files/figure-html/wa_plot-1.png
docs/walomb_plot_files/figure-html/world_plot-1.png
docs/walomb_plot_files/figure-html/world_plot-10.png
docs/walomb_plot_files/figure-html/world_plot-11.png
docs/walomb_plot_files/figure-html/world_plot-12.png
docs/walomb_plot_files/figure-html/world_plot-13.png
docs/walomb_plot_files/figure-html/world_plot-14.png
docs/walomb_plot_files/figure-html/world_plot-15.png
docs/walomb_plot_files/figure-html/world_plot-16.png
docs/walomb_plot_files/figure-html/world_plot-17.png
docs/walomb_plot_files/figure-html/world_plot-18.png
docs/walomb_plot_files/figure-html/world_plot-19.png
docs/walomb_plot_files/figure-html/world_plot-2.png
docs/walomb_plot_files/figure-html/world_plot-20.png
docs/walomb_plot_files/figure-html/world_plot-21.png
docs/walomb_plot_files/figure-html/world_plot-22.png
docs/walomb_plot_files/figure-html/world_plot-23.png
docs/walomb_plot_files/figure-html/world_plot-24.png
docs/walomb_plot_files/figure-html/world_plot-25.png
docs/walomb_plot_files/figure-html/world_plot-26.png
docs/walomb_plot_files/figure-html/world_plot-27.png
docs/walomb_plot_files/figure-html/world_plot-28.png
docs/walomb_plot_files/figure-html/world_plot-29.png
docs/walomb_plot_files/figure-html/world_plot-3.png
docs/walomb_plot_files/figure-html/world_plot-30.png
docs/walomb_plot_files/figure-html/world_plot-31.png
docs/walomb_plot_files/figure-html/world_plot-32.png
docs/walomb_plot_files/figure-html/world_plot-33.png
docs/walomb_plot_files/figure-html/world_plot-4.png
docs/walomb_plot_files/figure-html/world_plot-5.png
docs/walomb_plot_files/figure-html/world_plot-6.png
docs/walomb_plot_files/figure-html/world_plot-7.png
docs/walomb_plot_files/figure-html/world_plot-8.png
docs/walomb_plot_files/figure-html/world_plot-9.png
epidemic_states.Rmd
index.Rmd
man/add_vline.Rd
man/getdata.Rd
man/getdataitaly.Rd
man/getdatastates.Rd
man/getdatawa.Rd
man/getdataworld.Rd
man/getdataworld_oldjhu.Rd
man/italy.Rd
man/plot1.Rd
man/plot2.Rd
man/plot3.Rd
man/plot4.Rd
man/regions.Rd
man/states.Rd
ny_plot.Rmd
plots.Rmd
state_plots.Rmd
styles.css
updates/2020-04-28-Perspective.Rmd
updates/2020-04-28-Perspective.html
updates/2020-04-29-Rural.Rmd
updates/2020-04-29-Rural.html
updates/2020-05-01-Forecast-Models.Rmd
updates/2020-05-01-Forecast-Models.html
updates/2020-05-04-Patterns.Rmd
updates/2020-05-04-Patterns.html
updates/2020-05-06-Changing-CFR.Rmd
updates/2020-05-06-Changing-CFR.html
updates/2020-05-13-Fitting-SIR-Models.Rmd
updates/2020-05-17-Patterns.Rmd
updates/2020-05-17-Patterns.html
updates/2020-05-18-Density.Rmd
updates/2020-05-25-Patterns.Rmd
updates/2020-06-10-Patterns.Rmd
updates/2020-06-10-Patterns.html
updates/2020-06-17-Going-Up.Rmd
updates/2020-06-17-Going-Up.html
updates/2020-06-28-AZ-TX-NJ.Rmd
updates/2020-06-28-AZ-TX-NJ.html
updates/2020-07-15-AZ-TX-FL.Rmd
updates/2020-07-15-AZ-TX-FL.html
updates/2020-10-24.Rmd
updates/2020-10-24.html
updates/2020-10-25.Rmd
updates/2020-10-26-Fall-Surge.Rmd
updates/2020-10-26-Fall-Surge.html
updates/2020-10-30-Changing-Positivity.Rmd
updates/2020-10-30-Changing-Positivity.html
updates/Forecast-Functions-2.Rmd
updates/Forecast-Functions-3.Rmd
updates/Forecast-Functions.Rmd
updates/Screen Shot 2020-05-17 at 9.06.48 AM.png
updates/cases_per_100k_US.png
updates/day10.R
updates/day11.R
updates/day12.R
updates/day15.R
updates/day17.R
updates/day18.R
updates/day19.R
updates/day2.R
updates/day20.R
updates/day21.R
updates/day22.R
updates/day23.R
updates/day3.R
updates/day4.R
updates/day6.R
updates/day7.R
updates/day8.R
updates/day9.R
updates/king-co-geography.gif
walomb_plot.Rmd
