Merge remote-tracking branch 'origin/dev' into blog/holiday-surveys

Author: sgratzl

.gitignore

@@ -11,3 +11,5 @@
 /assets/jsconfig.json
 /static/uikit/**
 .DS_Store
+*.zip
+*.tgz

.release-it.json

@@ -0,0 +1,17 @@
+{
+  "hooks": {
+    "before:init": "npm run lint",
+    "before:release": "npm run build && npm run zip",
+    "after:release": "echo Successfully released ${name} v${version}."
+  },
+  "git": {
+    "tagName": "v${version}"
+  },
+  "npm": {
+    "publish": false
+  },
+  "github": {
+    "release": true,
+    "assets": ["website.zip"]
+  }
+}

README.md

@@ -104,3 +104,16 @@ In case you use new dependencies don't forget to either edit `environment.yml` o
 A Github action should runs when Rmd files changes so it will verify that the blog post can be built.
 However, the converted HTML file along with all generated images are committed to the repository.
 This simplifies the deployment and ensures that we have a blog post even when the API or data changes.
+
+
+### Release Process
+
+The release process is based on [release-it](https://github.com/release-it/release-it). To create a release, run
+
+1. create/checkout the release branch `release` and push to origin
+1. run `npm run release` and publish the release
+1. create a PR that merges the `release` branch in the `main` branch
+1. create a PR that merges the `main` branch back into the `dev` branch
+
+Then go to the release page and update short description of the changes made.
+

content/blog/2015-07-23-template-post.Rmd

@@ -9,8 +9,8 @@ tags:
 draft: true # remove this line in new blog posts
 authors: # list of author keys, see /data/authors.yaml
   - frida
-heroImage: /blog/images/blog-lg-img_hello-world.jpg
-heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg
+heroImage: /blog/images/blog-lg-img_hello-world.jpg # size: 1120x440 jpg and webp format
+heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg # size: 300x200 jpg and webp format
 summary: |
   Blog summary, the first 150 characters are used for the blog list
 acknowledgements: |

content/blog/2021-01-21-unpack-cfr.Rmd

@@ -0,0 +1,328 @@
+@article{beigel2020remdesivir,
+  title={Remdesivir for the treatment of Covid-19—preliminary report},
+  author={Beigel, John H and Tomashek, Kay M and Dodd, Lori E and Mehta, Aneesh K and Zingman, Barry S and Kalil, Andre C and Hohmann, Elizabeth and Chu, Helen Y and Luetkemeyer, Annie and Kline, Susan and others},
+  journal={New England Journal of Medicine},
+  year={2020},
+  publisher={Mass Medical Soc}
+}
+
+@article{recovery2020dexamethasone,
+  title={Dexamethasone in hospitalized patients with {COVID}-19—preliminary report},
+  author={RECOVERY Collaborative Group},
+  journal={New England Journal of Medicine},
+  year={2020},
+  publisher={Mass Medical Soc}
+}
+
+
+
+@misc{florida_line_data,
+ author = {{Florida Department of Health}},
+ year = {2020},
+ title = {Florida Case Line Data},
+ url = {https://www.arcgis.com/home/item.html?id=4cc62b3a510949c7a8167f6baa3e069d},
+ urldate = {2020-09-07}
+}
+
+@misc{cdc_data,
+ author = {{CDC Case Surveillance Task Force}},
+ year = {2020},
+ title = {COVID-19 Case Surveillance Data},
+ urldate = {2020-09-07}
+}
+
+@misc{moser2020changing,
+ author = {Whet, Moser},
+ year = {2020},
+ title = {{Why Changing COVID-19 Demographics in the US Make Death Trends Harder to Understand}},
+ journal = {The COVID Tracking Project Blog},
+ url = {https://covidtracking.com/blog/why-changing-covid-19-demographics-in-the-us-make-death-trends-harder-to},
+ urldate = {2020-08-27}
+}
+
+% https://www.wired.com/story/bill-gates-on-covid-most-us-tests-are-completely-garbage/
+
+@misc{levy2020gates,
+ author = {Levy, Steven},
+ year = {2020},
+ title = {{Bill Gates on Covid: Most US Tests Are ‘Completely Garbage’}},
+ journal = {Wired Magazine},
+ url = {https://www.wired.com/story/bill-gates-on-covid-most-us-tests-are-completely-garbage/},
+ urldate = {2020-08-27}
+}
+
+@misc{wu2020groundhog,
+ author = {Wu, Katherine J.},
+ year = {2020},
+ title = {{‘It’s Like Groundhog Day’: Coronavirus Testing Labs Again Lack Key Supplies}},
+ journal = {The New York Times},
+ url = {https://www.nytimes.com/2020/07/23/health/coronavirus-testing-supply-shortage.html},
+ urldate = {2020-08-27}
+}
+
+@misc{covidcast2020api,
+author = {CMU Delphi Project},
+year= {2020},
+url = {https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html},
+urldate = {2020-08-27}
+}
+
+
+@misc{cdc_national,
+title = {COVID-19 Case Surveillance Public Use Data},
+author = {CDC Case Surveillance Task Force},
+year= {2020},
+url = {https://data.cdc.gov/Case-Surveillance/COVID-19-Case-Surveillance-Public-Use-Data/vbim-akqf},
+urldate = {2020-09-07}
+}
+
+@misc{usafacts, title={Coronavirus Outbreak Stats \& Data}, url={https://usafacts.org/issues/coronavirus/}, author={USAFacts}, year={2020}, month={Aug}} 
+
+@misc{uw2020testing,
+author={UW Medicine},
+title = {{COVID-19 Testing for Hospital Patients}},
+year={2020},
+url = {https://www.uwmedicine.org/coronavirus/inpatient-screening},
+urldate = {2020-08-27}
+}
+
+
+@ARTICLE{hospitalization_monitor,
+  
+AUTHOR={Mallow, Peter J. and Jones, Michael},   
+	 
+TITLE={When Second Best Might Be the Best: Using Hospitalization Data to Monitor the Novel Coronavirus Pandemic},      
+	
+JOURNAL={Frontiers in Public Health},      
+	
+VOLUME={8},      
+
+PAGES={348},     
+	
+YEAR={2020},      
+	  
+URL={https://www.frontiersin.org/article/10.3389/fpubh.2020.00348},       
+	
+DOI={10.3389/fpubh.2020.00348},      
+	
+ISSN={2296-2565},   
+   
+ABSTRACT={The novel coronavirus' high rate of asymptomatic transmission combined with a lack of testing kits call for a different approach to monitor its spread and severity. We proposed the use of hospitalizations and hospital utilization data to monitor the spread and severity. A proposed threshold of a declining 7-day moving average over a 14-day period, “7&14” was set to communicate when a wave of the novel coronavirus may have passed. The state of Ohio was chosen to illustrate this threshold. While not the ideal solution for monitoring the spread of the epidemic, the proposed approach is an easy to implement framework accounting for limitations of the data inherent in the current epidemic. Hospital administrators and policy makers may benefit from incorporating this approach into their decision making.}
+}
+
+@misc{propublica_hosp,
+ author = {Ornstein, Charles},
+ year = {2020},
+ title = {{How Many People in the U.S. Are Hospitalized With COVID-19? Who Knows?}},
+ journal = {ProPublica},
+ url = {https://www.propublica.org/article/how-many-people-in-the-us-are-hospitalized-with-covid-19-who-knows},
+ urldate = {2020-08-31}
+}
+
+ @inbook{uptodate_eval, 
+ place={Waltham, MA}, 
+ title={{Coronavirus disease 2019 (COVID-19): Outpatient evaluation and management in adults}}, 
+ booktitle={UpToDate}, 
+ publisher={UpToDate}, 
+ author={Cohen, Pieter and Elmore, Joann G and Blau, Jessamyn and Bloom, Allyson}, 
+ year={2020}}
+ 
+@article{phua_icu_manage, 
+title={{Intensive care management of coronavirus disease 2019 (COVID-19): challenges and recommendations}}, volume={8}, DOI={10.1016/s2213-2600(20)30161-2}, number={5}, journal={The Lancet Respiratory Medicine}, author={Phua, Jason and Weng, Li and Ling, Lowell and Egi, Moritoki and Lim, Chae-Man and Divatia, Jigeeshu Vasishtha and Shrestha, Babu Raja and Arabi, Yaseen M and Ng, Jensen and Gomersall, Charles D and et al.}, year={2020}, pages={506–517}}
+
+@article{lancet_death_pathways, 
+title={{Understanding pathways to death in patients with COVID-19}}, 
+volume={8}, 
+DOI={10.1016/s2213-2600(20)30165-x}, 
+number={5}, 
+journal={The Lancet Respiratory Medicine}, 
+author={Vincent, Jean-Louis and Taccone, Fabio S}, year={2020}, 
+pages={430–432}}
+ 
+@article{nature_death_indicator, 
+title={{Why daily death tolls have become unusually important in understanding the coronavirus pandemic}}, 
+DOI={10.1038/d41586-020-01008-1}, 
+journal={Nature}, 
+author={Subbaraman, Nidhi}, 
+year={2020}, 
+month={Apr}}
+  
+@misc{covid_tracking_project, url={https://covidtracking.com/}, journal={{The COVID Tracking Project}}, publisher={The Atlantic}, author={Meyer, Robinson and Madrigal, Alexis}, year={2020}}
+
+ @article{gender_age_differential, series={Correspondence}, title={Sex differential in COVID-19 mortality varies markedly by age}, volume={396}, number={10250}, journal={The Lancet}, author={Bhopal, Sunil  S and Bhopal, Raj}, year={2020}, collection={Correspondence}} 
+ 
+@misc{backlog_april_quest, title={Documents show backlog of 160,000 coronavirus tests at just one lab company}, url={https://www.cnn.com/2020/04/01/politics/testing-backlog-coronavirus-quest-invs/index.html}, author={Griffin, Drew and Devine, Curt and Bronstein, Scott and Black, Nelli}, year={2020}, month={Apr}} 
+
+@misc{backlog_illinois, title={Backlog of Tests Worked Through – 5,368 New Confirmed Cases of Coronavirus Disease}, url={http://www.dph.illinois.gov/news/backlog-tests-worked-through-%E2%80%93-5368-new-confirmed-cases-coronavirus-disease}, 
+author={Illinois Department of Health}} 
+
+@misc{backlog_nytimes, title={Testing Backlogs May Cloud the True Spread of the Coronavirus}, url={https://www.nytimes.com/2020/07/19/health/coronavirus-testing-viral-spread.html}, author={Wu, Katherine J.}, year={2020}, month={Jul}} 
+
+ @misc{data_problems_nyt, 
+ title={Why Can't We See All of the Government's Virus Data?}, 
+ url={https://www.nytimes.com/2020/10/23/opinion/coronavirus-data-secrecy.html}, 
+ author={Murray, Christopher J.L.}, 
+ year={2020}, 
+ month={Oct}} 
+ 
+ 
+ @article{horwitz2020trends,
+  title={Trends in Covid-19 risk-adjusted mortality rates in a single health system},
+  author={Horwitz, Leora and Jones, Simon A and Cerfolio, Robert J and Francois, Fritz and Greco, Joseph and Rudy, Bret and Petrilli, Christopher M},
+  journal={medRxiv},
+  year={2020},
+  publisher={Cold Spring Harbor Laboratory Press}
+}
+
+@article{chen2020sars,
+  title={SARS-CoV-2 Neutralizing Antibody LY-CoV555 in Outpatients with Covid-19},
+  author={Chen, Peter and Nirula, Ajay and Heller, Barry and Gottlieb, Robert L and Boscia, Joseph and Morris, Jason and Huhn, Gregory and Cardona, Jose and Mocherla, Bharat and Stosor, Valentina and others},
+  journal={New England Journal of Medicine},
+  year={2020},
+  publisher={Mass Medical Soc}
+}
+
+@article{agarwal2020convalescent,
+  title={Convalescent plasma in the management of moderate covid-19 in adults in India: open label phase II multicentre randomised controlled trial (PLACID Trial)},
+  author={Agarwal, Anup and Mukherjee, Aparna and Kumar, Gunjan and Chatterjee, Pranab and Bhatnagar, Tarun and Malhotra, Pankaj},
+  journal={bmj},
+  volume={371},
+  year={2020},
+  publisher={British Medical Journal Publishing Group}
+}
+
+@misc{dyer2020covid,
+  title={Covid-19: Eli Lilly pauses antibody trial for safety reasons},
+  author={Dyer, Owen},
+  year={2020},
+  publisher={British Medical Journal Publishing Group}
+}
+
+@article{self2020effect,
+  title={Effect of Hydroxychloroquine on Clinical Status at 14 Days in Hospitalized Patients With COVID-19: A Randomized Clinical Trial},
+  author={Self, Wesley H and Semler, Matthew W and Leither, Lindsay M and Casey, Jonathan D and Angus, Derek C and Brower, Roy G and Chang, Steven Y and Collins, Sean P and Eppensteiner, John C and Filbin, Michael R and others},
+  journal={JAMA},
+  year={2020}
+}
+
+@article{horby2020effect,
+  title={Effect of Hydroxychloroquine in Hospitalized Patients with COVID-19: Preliminary results from a multi-centre, randomized, controlled trial.},
+  author={Horby, Peter and Mafham, Marion and Linsell, Louise and Bell, Jennifer L and Staplin, Natalie and Emberson, Jonathan R and Wiselka, Martin and Ustianowski, Andrew and Elmahi, Einas and Prudon, Benjamin and others},
+  journal={MedRxiv},
+  year={2020},
+  publisher={Cold Spring Harbor Laboratory Press}
+}
+
+@article{dennis2020improving,
+  title={Improving COVID-19 critical care mortality over time in England: A national cohort study, March to June 2020},
+  author={Dennis, John and McGovern, Andrew and Vollmer, Sebastian and Mateen, Bilal A},
+  journal={medRxiv},
+  year={2020},
+  publisher={Cold Spring Harbor Laboratory Press}
+}
+
+@article{pachetti2020impact,
+  title={Impact of lockdown on Covid-19 case fatality rate and viral mutations spread in 7 countries in Europe and North America},
+  author={Pachetti, Maria and Marini, Bruna and Giudici, Fabiola and Benedetti, Francesca and Angeletti, Silvia and Ciccozzi, Massimo and Masciovecchio, Claudio and Ippodrino, Rudy and Zella, Davide},
+  journal={Journal of Translational Medicine},
+  volume={18},
+  number={1},
+  pages={1--7},
+  year={2020},
+  publisher={BioMed Central}
+}
+
+@article{piubelli2020overall,
+  title={Overall decrease in SARS-CoV-2 viral load and reduction in clinical burden: the experience of a hospital in northern Italy},
+  author={Piubelli, Chiara and Deiana, Michela and Pomari, Elena and Silva, Ronaldo and Bisoffi, Zeno and Formenti, Fabio and Perandin, Francesca and Gobbi, Federico and Buonfrate, Dora},
+  journal={Clinical Microbiology and Infection},
+  year={2020},
+  publisher={Elsevier}
+}
+
+ @misc{trump_statement, title={Remarks by President Trump in Press Briefing on COVID-19}, url={https://www.whitehouse.gov/briefings-statements/remarks-president-trump-press-briefing-covid-19/}, author={Trump, Donald}, year={2020}, month={Jul}} 
+ 
+  @misc{factcheck_mcdonald_2020, title={Trump Misleads on Reasons for Falling COVID-19 Fatality Rate}, url={https://www.factcheck.org/2020/09/trump-misleads-on-reasons-for-falling-covid-19-fatality-rate/}, journal={FactCheck.org}, author={McDonald, Jessica}, year={2020}, month={Sep}} 
+  
+@article{madsen2020remdesivir,
+title={Remdesivir for the Treatment of Covid-19-Final Report},
+author={Madsen, Lone Wulff and others},
+journal={The New England Journal of Medicine},
+year={2020},
+publisher={Massachusetts Medical Society}
+}
+
+@article{monoclonal_eua, 
+ title={Coronavirus (COVID-19) Update: FDA Authorizes Monoclonal Antibody for Treatment of COVID-19},
+ author={{U.S. Food and Drug Administration}},
+ url={https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-monoclonal-antibody-treatment-covid-19}, 
+ year={2020}, 
+ month={Nov}}
+ 
+ @article{regeneron_monoclonal_eua, 
+ title={Coronavirus (COVID-19) Update: FDA Authorizes Monoclonal Antibodies for Treatment of COVID-19},
+ author={{U.S. Food and Drug Administration}},
+ url={https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-monoclonal-antibodies-treatment-covid-19}, 
+ year={2020}, 
+ month={Nov}}
+ 
+@article{regeneron_press,
+title={Regeneron's Casirivimab and Imdevimab Antibody Cocktail for COVID-19 is First Combination Therapy to Receive FDA Emergency Use Authorization},
+author={{Regeneron}},
+url={https://investor.regeneron.com/news-releases/news-release-details/regenerons-regen-cov2-first-antibody-cocktail-covid-19-receive}, year={2020}, month={Nov}} 
+ 
+@book{bootstrap_davison_hinkley_1997, place={Cambridge}, series={Cambridge Series in Statistical and Probabilistic Mathematics}, title={Bootstrap Methods and their Application}, DOI={10.1017/CBO9780511802843}, publisher={Cambridge University Press}, author={Davison, A. C. and Hinkley, D. V.}, year={1997}, collection={Cambridge Series in Statistical and Probabilistic Mathematics}}
+
+@article{fan2020decreased,
+  title={Decreased Case Fatality Rate of COVID-19 in the Second Wave: A study in 53 countries or regions},
+  author={Fan, Guihong and Yang, Zhichun and Lin, Qianying and Zhao, Shi and Yang, Lin and He, Daihai},
+  journal={Transboundary and emerging diseases},
+  year={2020},
+  publisher={Wiley Online Library}
+}
+
+
+@misc{madrigal2020second,
+ author = {Madrigal, Alexis},
+ year = {2020},
+ title = {A Second Coronavirus Death Surge Is Coming},
+ journal = {The Atlantic},
+ url = {https://www.theatlantic.com/health/archive/2020/07/second-coronavirus-death-surge/614122/},
+ urldate = {2020-08-27}
+}
+
+
+@misc{thomp2020,
+ author = {Thompson, Derek},
+ year = {2020},
+ title = {COVID-19 Cases Are Rising, So Why Are Deaths Flatlining?},
+ journal = {The Atlantic},
+ url = {https://www.theatlantic.com/ideas/archive/2020/07/why-covid-death-rate-down/613945/},
+ urldate = {2020-07-09}
+}
+
+
+@misc{mad2020,
+ author = {Madrigal, Alexis and Moser, Whet},
+ year = {2020},
+ title = {How Many Americans Are About to Die?},
+ urldate = {2020-11-19}
+}
+
+@article{eldeclining,
+  title={Declining Trend in the Initial SARS-CoV-2 Viral Load Over Time: Observations From Detroit, Michigan},
+  author={El Zein, S}
+}
+
+@article {Mahasem1327_agedeathrate,
+	author = {Mahase, Elisabeth},
+	title = {Covid-19: death rate is 0.66\% and increases with age, study estimates},
+	volume = {369},
+	elocation-id = {m1327},
+	year = {2020},
+	doi = {10.1136/bmj.m1327},
+	publisher = {BMJ Publishing Group Ltd},
+	URL = {https://www.bmj.com/content/369/bmj.m1327},
+	eprint = {https://www.bmj.com/content/369/bmj.m1327.full.pdf},
+	journal = {BMJ}
+}