{"id":637,"date":"2022-04-14T09:00:02","date_gmt":"2022-04-14T09:00:02","guid":{"rendered":"http:\/\/www.johncmulligan.net\/blog\/?p=637"},"modified":"2022-04-14T14:55:18","modified_gmt":"2022-04-14T14:55:18","slug":"excess-mortality-and-covid-19","status":"publish","type":"post","link":"https:\/\/www.johncmulligan.net\/blog\/2022\/04\/14\/excess-mortality-and-covid-19\/","title":{"rendered":"Excess Mortality and COVID-19"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">New Interface<\/h2>\n\n\n\n<p>Below, I lay out the narrative for the by-cause-and-jurisdiction excess mortality graphs available at <a href=\"https:\/\/www.covid-excess-mortality.net\/\">https:\/\/www.covid-excess-mortality.net\/<\/a><\/p>\n\n\n\n<p>Here, a screenshot of a new interface I&#8217;m prototyping, that attempts to marry the use of surveillance algorithms with basic excess estimates. Feedback welcome! <a href=\"https:\/\/covid-dash-py.herokuapp.com\/\">https:\/\/covid-dash-py.herokuapp.com\/<\/a><\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><a href=\"https:\/\/www.covid-excess-mortality.net\/\" target=\"_blank\" rel=\"noreferrer noopener\"><img loading=\"lazy\" decoding=\"async\" width=\"2464\" height=\"1572\" src=\"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?fit=819%2C522\" alt=\"\" class=\"wp-image-722\" srcset=\"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?w=2464&amp;ssl=1 2464w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?resize=300%2C191&amp;ssl=1 300w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?resize=1024%2C653&amp;ssl=1 1024w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?resize=768%2C490&amp;ssl=1 768w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?resize=1536%2C980&amp;ssl=1 1536w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?resize=2048%2C1307&amp;ssl=1 2048w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2022\/04\/Screen-Shot-2022-04-14-at-9.49.21-AM.png?w=1638 1638w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><\/a><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">2020 Interface<\/h2>\n\n\n\n<p><strong>This app has been featured on KHOU&#8217;s pandemic coverage: <\/strong><a href=\"https:\/\/twitter.com\/KHOU\/status\/1446477984169439235\">https:\/\/twitter.com\/KHOU\/status\/1446477984169439235<\/a><\/p>\n\n\n\n<p>Use the app here: <a href=\"https:\/\/www.covid-excess-mortality.net\/\">https:\/\/www.covid-excess-mortality.net\/<\/a><\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"2394\" height=\"930\" src=\"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?fit=819%2C318\" alt=\"\" class=\"wp-image-662\" srcset=\"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?w=2394&amp;ssl=1 2394w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?resize=300%2C117&amp;ssl=1 300w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?resize=1024%2C398&amp;ssl=1 1024w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?resize=768%2C298&amp;ssl=1 768w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?resize=1536%2C597&amp;ssl=1 1536w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?resize=2048%2C796&amp;ssl=1 2048w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/01\/Screen-Shot-2021-01-29-at-4.48.50-PM.png?w=1638 1638w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><figcaption>One view on the Jan. 27 data<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Quick Overview<\/h2>\n\n\n\n<hr class=\"wp-block-separator\"\/>\n\n\n\n<ol class=\"wp-block-list\"><li>The CDC&#8217;s National Center for Health Statistics has been publishing <a href=\"https:\/\/data.cdc.gov\/NCHS\/Weekly-counts-of-death-by-jurisdiction-and-cause-o\/u6jv-9ijr\/\">granular historical mortality data relevant to COVID-19<\/a><\/li><li>There appears to be an undercount of US deaths caused by the pandemic.<\/li><\/ol>\n\n\n\n<h2 class=\"wp-block-heading\">Recent JAMA articles<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/jamanetwork.com\/journals\/jama\/fullarticle\/2774465\">COVID-19 may be the Leading Cause of Death in US<\/a> (Dec. 17)<\/li><li><a href=\"https:\/\/jamanetwork.com\/journals\/jama\/fullarticle\/2774445\">COVID-19 deaths in mauy be undercounted by as much as 60%<\/a> (Dec. 16)<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Visualization<\/h2>\n\n\n\n<p>This visualization shows:<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>In blue, the average number of deaths attributed to a selected cause(s) of death in a selected state(s), from 2015-19.<\/li><li>In orange, the number of weekly 2020-21 deaths in excess of that average (again, in that state\/s and attributed to that cause\/s).<\/li><\/ol>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1954\" height=\"1441\" src=\"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?fit=819%2C604\" alt=\"\" class=\"wp-image-670\" srcset=\"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?w=1954&amp;ssl=1 1954w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?resize=300%2C221&amp;ssl=1 300w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?resize=1024%2C755&amp;ssl=1 1024w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?resize=768%2C566&amp;ssl=1 768w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?resize=1536%2C1133&amp;ssl=1 1536w, https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2021\/03\/Screen-Shot-2021-03-11-at-10.13.31-PM.png?w=1638 1638w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><\/figure>\n\n\n\n<p>This graph suggests that ~7,100 people in Texas, whose 2020-21 deaths were attributed to Diabetes or Alzheimer&#8217;s, would likely not have died but for the pandemic.<\/p>\n\n\n\n<p>This could be read as a failure of infrastructure as hospitals are overwhelmed and people are under unprecedented stress during the COVID depression; or a failure of reporting mechanisms as COVID-related deaths are improperly coded. But in the context of an epidemic that has been fueled by deliberate misinformation, official negligence, and an utter disregard for the lives of anyone who can be opportunistically othered, I read these failures in reporting, prevention, and treatment as related aspects of a general failure of public health bordering on the necropolitical.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Live interface: <a href=\"https:\/\/www.covid-excess-mortality.net\/\">http:\/\/covid-excess-nchs.herokuapp.com\/ <\/a><\/li><li><a rel=\"noreferrer noopener\" aria-label=\"Underlying CDC data with good documentation (opens in a new tab)\" href=\"https:\/\/data.cdc.gov\/NCHS\/Weekly-counts-of-death-by-jurisdiction-and-cause-o\/u6jv-9ijr\/\" target=\"_blank\">Underlying CDC data with good documentation<\/a><\/li><li><a rel=\"noreferrer noopener\" aria-label=\"R application repository (opens in a new tab)\" href=\"https:\/\/github.com\/JohnMulligan\/covid_dashR\" target=\"_blank\">R application code<\/a><\/li><li><a rel=\"noreferrer noopener\" aria-label=\"And its git repository with weekly updates (opens in a new tab)\" href=\"https:\/\/weinbergerlab.github.io\/excess_pi_covid\/\" target=\"_blank\">Codebase with a more rigorous measure of excess mortality<\/a><\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>New Interface Below, I lay out the narrative for the by-cause-and-jurisdiction excess mortality graphs available at https:\/\/www.covid-excess-mortality.net\/ Here, a screenshot of a new interface I&#8217;m [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":651,"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,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-637","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"https:\/\/i0.wp.com\/www.johncmulligan.net\/blog\/wp-content\/uploads\/2020\/11\/Screen-Shot-2020-11-25-at-9.34.26-PM-2.png?fit=370%2C600&ssl=1","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p4eIi2-ah","_links":{"self":[{"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/posts\/637","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/comments?post=637"}],"version-history":[{"count":22,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/posts\/637\/revisions"}],"predecessor-version":[{"id":726,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/posts\/637\/revisions\/726"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/media\/651"}],"wp:attachment":[{"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/media?parent=637"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/categories?post=637"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.johncmulligan.net\/blog\/wp-json\/wp\/v2\/tags?post=637"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}