{"id":12735,"date":"2020-04-11T12:46:03","date_gmt":"2020-04-11T17:46:03","guid":{"rendered":"https:\/\/rud.is\/b\/?p=12735"},"modified":"2020-04-11T12:46:03","modified_gmt":"2020-04-11T17:46:03","slug":"new-package-cdccovidview-to-work-with-the-u-s-cdcs-new-covid-19-trackers-covidview-and-covid-net","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2020\/04\/11\/new-package-cdccovidview-to-work-with-the-u-s-cdcs-new-covid-19-trackers-covidview-and-covid-net\/","title":{"rendered":"New Package \u2014\u00a0{cdccovidview} \u2014 To Work with the U.S. CDC’s New COVID-19 Trackers: COVIDView and COVID-NET"},"content":{"rendered":"

The United States Centers for Disease Control (CDC from now on) has setup two new public surveillance resources for COVID-19. Together, COVIDView<\/a> and COVID-NET<\/a> provide similar weekly surveillance data as FluView<\/a> does for influenza-like illnesses (ILI).<\/p>\n

The COVIDView resources are HTML tables (O_O) and, while the COVID-NET interface provides a “download” button, there is no exposed API to make it easier for the epidemiological community to work with these datasets.<\/p>\n

Enter {cdccovidview} \u2014 https:\/\/cinc.rud.is\/web\/packages\/cdccovidview\/ \u2014 which scrapes the tables and uses the hidden API in the same way {cdcfluview}(https:\/\/cran.rstudio.com\/web\/packages\/cdcfluview\/index.html) does for the FluView data.<\/p>\n

Weekly case, hospitalization, and mortality data is available at the national, state and regional levels (where provided) and I tried to normalize the fields across each of the tables\/datasets (I hate to pick on them when they’re down, but these two sites are seriously sub-optimal from a UX and just general usage perspective).<\/p>\n

After you follow the above URL for information on how to install the package, it should “just work”. No API keys are needed, but the CDC may change the layout of tables and fields structure of the hidden API at any time, so keep an eye out for updates.<\/p>\n

Using it is pretty simple, just use one of the functions to grab the data you want and then work with it.<\/p>\n

library(cdccovidview)\nlibrary(hrbrthemes)\nlibrary(tidyverse)\n\nhosp <- laboratory_confirmed_hospitalizations()\n\nhosp\n## # A tibble: 4,590 x 8\n##    catchment      network   year  mmwr_year mmwr_week age_category cumulative_rate weekly_rate\n##    <chr>          <chr>     <chr> <chr>     <chr>     <chr>                  <dbl>       <dbl>\n##  1 Entire Network COVID-NET 2020  2020      10        0-4 yr                   0           0  \n##  2 Entire Network COVID-NET 2020  2020      11        0-4 yr                   0           0  \n##  3 Entire Network COVID-NET 2020  2020      12        0-4 yr                   0           0  \n##  4 Entire Network COVID-NET 2020  2020      13        0-4 yr                   0.3         0.3\n##  5 Entire Network COVID-NET 2020  2020      14        0-4 yr                   0.6         0.3\n##  6 Entire Network COVID-NET 2020  2020      15        0-4 yr                  NA          NA  \n##  7 Entire Network COVID-NET 2020  2020      16        0-4 yr                  NA          NA  \n##  8 Entire Network COVID-NET 2020  2020      17        0-4 yr                  NA          NA  \n##  9 Entire Network COVID-NET 2020  2020      18        0-4 yr                  NA          NA  \n## 10 Entire Network COVID-NET 2020  2020      19        0-4 yr                  NA          NA  \n## # \u2026 with 4,580 more rows\n\nc(\n  \"0-4 yr\", \"5-17 yr\", \"18-49 yr\", \"50-64 yr\", \"65+ yr\", \"65-74 yr\", \"75-84 yr\", \"85+\"\n) -> age_f\n\nmutate(hosp, start = mmwr_week_to_date(mmwr_year, mmwr_week)) %>%\n  filter(!is.na(weekly_rate)) %>%\n  filter(catchment == \"Entire Network\") %>%\n  select(start, network, age_category, weekly_rate) %>%\n  filter(age_category != \"Overall\") %>%\n  mutate(age_category = factor(age_category, levels = age_f)) %>%\n  ggplot() +\n  geom_line(\n    aes(start, weekly_rate)\n  ) +\n  scale_x_date(\n    date_breaks = \"2 weeks\", date_labels = \"%b\\n%d\"\n  ) +\n  facet_grid(network~age_category) +\n  labs(\n    x = NULL, y = \"Rates per 100,000 pop\",\n    title = \"COVID-NET Weekly Rates by Network and Age Group\",\n    caption = sprintf(\"Source: COVID-NET: COVID-19-Associated Hospitalization Surveillance Network, Centers for Disease Control and Prevention.\\n<https:\/\/gis.cdc.gov\/grasp\/COVIDNet\/COVID19_3.html>; Accessed on %s\", Sys.Date())\n  ) +\n  theme_ipsum_es(grid=\"XY\")\n<\/code><\/pre>\n
\"\"<\/a><\/p>\n
FIN<\/h3>\n
This is brand new and — as noted — things may change or break due to CDC site changes. I may have also missed a table or two (it’s a truly terrible site).<\/p>\n
If you notice things are missing or would like a different interface to various data endpoints, drop an issue or PR wherever you’re most comfortable.<\/p>\n
Stay safe!<\/p>\n","protected":false},"excerpt":{"rendered":"
The United States Centers for Disease Control (CDC from now on) has setup two new public surveillance resources for COVID-19. Together, COVIDView and COVID-NET provide similar weekly surveillance data as FluView does for influenza-like illnesses (ILI). The COVIDView resources are HTML tables (O_O) and, while the COVID-NET interface provides a “download” button, there is no […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":3,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":""},"categories":[91],"tags":[],"class_list":["post-12735","post","type-post","status-publish","format-standard","hentry","category-r"],"yoast_head":"\nNew Package \u2014\u00a0{cdccovidview} \u2014 To Work with the U.S. CDC's New COVID-19 Trackers: COVIDView and COVID-NET - rud.is<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/rud.is\/b\/2020\/04\/11\/new-package-cdccovidview-to-work-with-the-u-s-cdcs-new-covid-19-trackers-covidview-and-covid-net\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"New Package \u2014\u00a0{cdccovidview} \u2014 To Work with the U.S. CDC's New COVID-19 Trackers: COVIDView and COVID-NET - rud.is\" \/>\n<meta property=\"og:description\" content=\"The United States Centers for Disease Control (CDC from now on) has setup two new public surveillance resources for COVID-19. 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Around the\u2026","rel":"","context":"In "Data Analysis"","block_context":{"text":"Data Analysis","link":"https:\/\/rud.is\/b\/category\/data-analysis-2\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3215,"url":"https:\/\/rud.is\/b\/2015\/01\/10\/new-r-package-cdcfluview-retrieve-flu-data-from-cdcs-fluview-portal\/","url_meta":{"origin":12735,"position":1},"title":"New R Package: cdcfluview \u2014 Retrieve Flu Data from CDC’s FluView Portal","author":"hrbrmstr","date":"2015-01-10","format":false,"excerpt":"**NOTE** If there's a particular data set from http:\/\/www.cdc.gov\/flu\/weekly\/fluviewinteractive.htm that you want and that isn't in the pacakge, please file it as an issue and be as specific as you can (screen shot if possible). ----- Towards the end of 2014 I had been tinkering with flu data from the\u2026","rel":"","context":"In "DataVis"","block_context":{"text":"DataVis","link":"https:\/\/rud.is\/b\/category\/datavis-2\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":7020,"url":"https:\/\/rud.is\/b\/2017\/11\/06\/taking-a-shot-at-cdcfluview-v0-7-0-a-k-a-the-dangers-of-relying-on-hidden-apis\/","url_meta":{"origin":12735,"position":2},"title":"Taking a Shot at cdcfluview v0.7.0 (a.k.a. The Dangers of Relying on ‘Hidden’ APIs)","author":"hrbrmstr","date":"2017-11-06","format":false,"excerpt":"Unlike @noamross, I am not an epidemiologist (NOTE: Noam battles pandemics before breakfast, so be super nice to him) but I do like to find kindred methodologies in other disciplines to help foster the growth of cybersecurity into something beyond it's current Barnum & Bailey state. I also love finding\u2026","rel":"","context":"In "R"","block_context":{"text":"R","link":"https:\/\/rud.is\/b\/category\/r\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/11\/unnamed-chunk-5-4.png?fit=672%2C480&ssl=1&resize=350%2C200","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/11\/unnamed-chunk-5-4.png?fit=672%2C480&ssl=1&resize=350%2C200 1x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/11\/unnamed-chunk-5-4.png?fit=672%2C480&ssl=1&resize=525%2C300 1.5x"},"classes":[]},{"id":3262,"url":"https:\/\/rud.is\/b\/2015\/02\/04\/a-step-to-the-right-in-r-assignments\/","url_meta":{"origin":12735,"position":3},"title":"A Step to the Right in R Assignments","author":"hrbrmstr","date":"2015-02-04","format":false,"excerpt":"I received an out-of-band question on the use of `%%` in my [CDC FluView](rud.is\/b\/2015\/01\/10\/new-r-package-cdcfluview-retrieve-flu-data-from-cdcs-fluview-portal\/) post, and took the opportunity to address it in a broader, public fashion. 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