Here are notes and links I personally find useful, all gathered in one place. Mostly, I kept looking at webcams to see whether people are practicing social distancing and decided to put them all in one page. I also gather data when nervous, so I also have plots of things like testing, activity, and cases over time so I can see the info directly myself (for example, Knox County Health Department plots cases per day with a trendline, but so far their trendline is only a straight line - I was curious if a more flexible fitting might be more informative). I am not an epidemiologist, so please do not draw any advice from this page (and I’ve been careful NOT to do projections or anything like that – there is a lot that goes into modeling, see this video by my colleague Nina Fefferman, who unlike me is an expert in this, for more on models). This is just me poking around with the data to make myself feel better – the raw code is here if you’d like to examine it yourself.
Other sources for data and other information:
And sections of my page:
The following plots are created in R using data from https://covid19datahub.io (Guidotti, E., Ardia, D., (2020), “COVID-19 Data Hub”, Working paper, doi: 10.13140/RG.2.2.11649.81763), as well as information from Google and the state of Tennessee dataset page and plotting and analysis using the
dplyr packages. Plots created on 2020-09-22 10:45:30. I use
geom_smooth() function for the smoothed regression plots with its default formula, which uses loess smoothing for this many points. This is not based on a model of disease spread or anything similarly sophisticated, just drawing a smooth curve to summarize noisy points (see here for more details).
The number of new and active cases should be not be going up if things are well-controlled, and ideally should be going down. The number of active cases is the number of positive cases minus the total of recovered or deceased cases: note it is from those tested and shown to be positive, but there are likely more people with covid who have not been tested. This uses data from https://www.tn.gov/health/cedep/ncov/data/downloadable-datasets.html. Note that the number of active cases in Knox County reported by the state differs from the county website, sometimes dramatically (on June 16, the county website said 102 active cases, while the state says 178, for example) – I suspect this is based on the number of recovered cases not being updated as quickly in the state data, but I do not know. Knox County does not seem to offer a download of their data through time, so I am using the state’s data. The number of new cases per day seems to align fairly well, but not perfectly, between the state and county data, too.
Around Sept. 4, the reported number of active cases dramatically dropped: Knox calculations of what constituted an active case changed from being based on recoveries to just a certain number of days after a positive test. So do not compare numbers across that date boundary.
I plot three regions
For many of these plots, I am now showing the smoothed curves rather than line connecting the raw points per day – these can jump around quite a bit (such as for things like tests per day). However, where the loess smoothing seems to be obscuring rather than clarifying, I just plot the line connecting the points.
Here are the same plots, but normalized so it’s per 100,000 residents in each area per day (making it easier to see patterns in less populous areas):
Testing is a key part of getting a handle on the pandemic. Here are Knox County, Oak Ridge’s counties (Anderson and Roane), and all the East TN counties combined (the same ones used for regional hospital reporting for bed availability). This plots shows the daily number of tests per 100,000 residents.
Another way to look at testing (or disease spread) is to look at the proportion of positive tests (“positivity rate”): they can go up if a greater proportion of symptomatic people are being tested and/or if the frequency of the disease is increasing. Updated WHO guidelines recommend testing should be 5% positive or lower (black line). Remember that the solid lines are smoothed across days but may still reflect recent points more so than a seven day average would.
Many of the local schools are adopting a hybrid approach, where families can choose whether to send their kids to school or do online learning (sometimes with reduced options). The New York Times reports on July 14, 2020, that, “As education leaders decide whether to reopen classrooms in the fall amid a raging pandemic, many are looking to a standard generally agreed upon among epidemiologists: To control community spread of the coronavirus, the average daily infection rate among those who are tested should not exceed 5 percent.” Many districts nationally are not hitting that goal, but a question is whether local ones will. The first district to open in our area was Oak Ridge public schools, who had a start date for students in person on July 29, 2020. Following the procedure of the NYT‘s article, I am plotting the seven day average of positivity rate for tests for the counties including Oak Ridge’s counties (Roane and Anderson). The black line is the seven day rolling mean (total new confirmed / total new tests, not a mean of this ratio per day), the blue line is this smoothed, the dotted line is the 5% threshold, and the green rectangle is the goal and starts at the start of school – the positivity should be in that rectangle to meet epidemiologists’ goals. Oak Ridge is giving families options of whether to enroll their children in online or in person school: their plan, and the way to choose either mode, is here. They have updated their in person plan to require masks when possible but not social distancing; when individuals test positive, the possibly affected parts of the building will be closed for 2-5 days. We’ve opted for the online option for our family.
Harvard’s Edmond J. Safra Center for Ethics and the Harvard Global Health Institute have created (July 19, 2020) guidelines for schools reopening (see also their full report PDF). They distinguish students by age group: “With COVID-19, people 18 and younger have far lower risk of death, hospitalization, and severe outcomes and are also less likely to get infected. Within this group, students in the younger age band of 10 and under also transmit at lower rates. This last point about lower rates of transmission may also pertain to people 15 and younger, a point that research should clarify in coming weeks. Keeping levels of risk low for young children via pandemic resilient teaching and learning spaces is more readily achievable than doing so for high school age students and the adult educators and staff in the school building.” They provide suggestions on building ventilation, social distancing, and more, and mention the utility of looking at multiple metrics (such as positivity rate, hospitalization, and more), but focus on daily new cases per 100,000 people (with a caution about missing cases if testing is not adequate; for example, if positivity rate is above 10%). The plot below has summaries of their recommendations for priority for which grade levels can meet in person, if there are conditions for pandemic resistant teaching and learning. The black line is the rolling seven day average of new cases per day for the counties containing Oak Ridge (Roane and Anderson), the blue line is this smoothed.
Tennessee now breaks out covid test results for school age children (age 5-18). The number of tests in this age group and the underlying population size aren’t known to me, so things like positivity rate and proportion of students infected cannot be determined, but the raw number of students infected can be shown:
As of the last time the data were updated (likely 6 days ago), regional hospitals had 46 ICU beds available of 278 total, and 134 available ventilators out of 243 total. This is based on 19 acute care hospitals in the East TN region; based on the 14 counties these hospitals are in, these serve at least 1,235,720 people. When a line hits 100%, the local hospitals are theoretically full for that resource (for all patients, not just covid patients), though there is surge capacity on top of this. Note that these data are updated only weekly, so current conditions maybe be much better or worse than these plots show. Data on capacity from Knox County’s dashboard, data on hospitalizations and testing over time from the state data.
Trends in hospitalization of covid patients over time. The vertical dotted line shows the last day with updated capacity information, when there were 46 ICU beds available (ignoring surge capacity) for people in the East Tennessee region.
Which age groups are being infected is an important question as local schools open up. These are data from Knox county alone. Note that one important bias here could be testing rate: if two year olds aren’t being tested as often as forty year olds, the age 0-10 results will be lower than the actual rate of infection, for example.
Another question is what is happening at UT as campus opens up and testing ramps up. There is some information available at https://www.utk.edu/coronavirus/guides/data-monitoring-and-contingency-options, of which I show one figure below. There are also reports in the news media, such as this article from Aug. 18 showing that 23 of 91 football players (over 25%) have had positive covid tests since returning but before the start of classes. For context, if the other undergraduates get infected at the same proportion (and assuming the number of undergraduates is the same as Fall 2019), that would be 5,863 cases, slightly more than all the confirmed and probable cases in Knox County (5,686 cases) up to Aug. 18, 2020. New York has set a threshold of 100 cases or 5% positive tests for colleges to move online; UT has had over that many active cases; its positivity rate is not public (as of now). However, UT clearly is not bound by New York rules. UT is suspending student groups violating rules and potentially punishing students who do not comply with covid rules, which might help prevent spread.
UT’s webcam of the Rock, a campus landmark, to see how UT’s community is choosing to protect others. You will have to click to start the stream.