Other writing: August 2021

What have I been writing when I haven’t been writing here?

Now you see me

  • Fedora Podcast, s02e08 — I appear on the Fedora Podcast to talk about my role as the Fedora Program Manager.

Stuff I wrote

The Open Organization

  • Fostering trust in our organization (video) — I join fellow Open Organization Ambassadors Jen Kelchner and Bryan Behrenshausen to discuss ways to help people feel empowered to propose their own solutions. I suggest leaders shut up for a little bit.
  • Open seems like it leads to hurt feelings (video) — I know that open organizations are places where people expect candid feedback and honest dialog. But that seems intimidating to me, because it seems like it can lead to harsh conversations and potentially hurt feelings. Is this true?

Fedora

Indiana COVID-19 update: 9 August 2021

I’d really hoped to not have to write another of these. The optimism I felt at the end of March when all the numbers were on the way down and vaccination was becoming widely available has now vanished. As the so-called delta variant races through the country, all of Indiana’s numbers are heading upward again.

Recent trends

After a slow downward trend to start the summer, the last few weeks have shown an increase in COVID-19 deaths.

Daily COVID-19 deaths in Indiana on a logarithmic scale with a 7-day moving average.

This is to be expected given the increase in cases and hospitalizations. In fact, the hospitalizations have increased faster than any time since the state started keeping records in early April of 2020.

Week-over-week (blue) and week-over-two-week (red) changes in COVID-19 cases.
Day-over-day (blue) and week-over-week (red) changes in COVID-19 hospitalizations.

The state had over 1,000 people in the hospital on Thursday (the latest data available) for the first time since May 4. If Friday was also above 1,000, that will mark the first time with consecutive 1,000+ days since mid-February. Hospitalizations have gone up 146% in the last month.

Indiana surrenders

The state used to update its COVID-19 dashboard daily. Then it stopped on Sundays. Now it’s just updated on weekdays. There’s no sign that the state government will do anything to require either masks or vaccination. Some local governments are re-implementing (or at least considering) mask mandates. I haven’t heard much about vaccination mandates except for at universities.

With schools starting or about to start, some districts have decided to have a mask mandate after all. (My kids school is among those, thankfully.) Others are leaving it up to individual families. Considering roughly half of K-12 students are not eligible to be vaccinated yet, this seems like a monumental policy failure. This is even more true if the delta variant is more severe in children than previous versions of the virus. At the moment, that appears to be more than a hypothetical.

It seems to me that the state has just surrendered. The governor is nowhere to be found on this, despite doing fairly well in the early days. In a recent press briefing, the state’s Health Commissioner was very diplomatic, but my interpretation of her answer to a few questions was “I wish we’d stop being dumb as a state and have some smart policy here. But my hands are tied without support from the Governor or the General Assembly.”

Projections

Unsurprisingly, the Institute for Health Metrics and Evaluation (IHME) forecast model continues the trends for the next few months. The latest model run projects a peak in daily deaths in the low-30s in mid-October. This is the “reference” scenario. The “worse” scenario peaks around 55. The worse scenario isn’t out of the question with an increase in in-person school and work. So much will depend on whether or not people wear masks and get vaccinated.

Observed and IHME-forecasted daily COVID-19 deaths

The good news is that if the reference scenario verifies, it will be lower than the previous two major peaks in deaths. The bad news is that a lot of people will still die unnecessarily.

As you may notice in the graph above, I had a long gap where I wasn’t adding new IHME model runs. Since it’s now clear that we won’t be done with COVID-19 any time soon, I’ll probably go back in the next few days and fill in that gap a bit. This way we can get a better sense of how the early summer model runs did.

Dashboard changes

I’ve made a few changes to my dashboard this weekend. First, I’ve changed the moving averages to be centered instead of trailing on all of the graphs. This keeps the last few days of data from distorting the trend.

In addition, I’ve added columns for a percentage change in deaths and cases week-over-week. The idea here is to produce a graph that shows the trends in cases, hospitalizations, and deaths. This would allow the viewer to see the relationship and delay between the three measures. To make it less noisy, it’s actually a comparison in the cumulative data over a seven-day window. That’s not necessary in the hospitalization data because that census is conducted every day. But cases are subject to a lot of variation throughout the week, and even the same-day-last-week comparisons seemed all over the place. Deaths are a relatively small number so small changes can be a big percentage.

I’m not going to bother putting the resulting graph in this post. It’s still a lot of spaghetti and not particularly informative. Later on I might play around with doing a second derivative. Perhaps showing how the rate of change is changing will be easier to understand.

Future dashboard changes

I’m beginning to hit annoyances with Google Sheets. In particular, inserting a new column (unless it’s at the far right of the data) means I have to re-adjust all of my graphs. I’ve been toying with the idea of using the Python Pandas package to do analysis and graphing. Then I could publish the graphs to a static website. It would also allow me to do a little more analysis, like listing the top 10 days for a particular stat or trend.

Another option I’ve been thinking about is splitting the sheet into multiple tabs. I could have a tab for the observations, another for models, etc. I’m not sure how well Google Sheets would like that, but it’s something to toy around with. It doesn’t seem like as much work as completely rebuilding it in a new system, but it’s also not trivial.

Given my lack of free time and the amount of effort that either of these options would require, I wouldn’t expect to see either happen for a while. However, it seems like I’ll be maintaining the dashboard for quite a while, so who knows?

New haiku in the Forecast Discussion Hall of Fame

A couple of friends independently directed me to a recent forecast discussion from Peachtree (Atlanta). Forecaster Kyle Thiem embraced his inner poet when he wrote the long-term discussion entirely in haiku. (Full disclosure: I didn’t count syllables to verify.) The discussion is now forever enshrined in the Forecast Discussion Hall of Fame.

Other writing: June 2021

What have I been writing when I haven’t been writing here?

Stuff I wrote

Fedora

LISA conference

Stuff I curated

Fedora

Other writing: May 2021

Stuff I wrote

Fedora

Open Organization

Stuff I curated

Fedora

Other writing: April 2021

What have I been writing when I haven’t been writing here?

Stuff I wrote

Fedora

Stuff I curated

Fedora

Other writing: March 2021

What have I been writing when I haven’t been writing here?

Now you see me!

Stuff I wrote

Fedora

Stuff I curated

Fedora

Indiana COVID-19 update: 27 March 2021

I haven’t written an update in nearly two full months. This is only slightly due to laziness. Mostly, it’s because the state’s numbers have been unremarkable. I mean that in a good way. We’ve consistently trended downward in infections (and positivity), hospitalizations, and deaths. However, we seem to have reached the floor and I’m concerned that the early indications suggest an increase. As usual, I am updating my dashboard most days.

Changes in trends

Five days in the past week (including the three most recent) had a daily increase in the hospitalization count. Two days had a 7% or greater daily increase. These are some of the largest increases on record. The hospitalization count is 12% higher than a week ago. Meanwhile, we’ve had a full week of week-over-week increases in positive cases. Only one day in the last 10 showed a week-over-week decline.

Daily and week-over-week changes in COVID-19 hospitalizations in Indiana.

Deaths continue to slowly trend downward, but if the increase in hospitalization holds, expect an uptick in deaths soon. After under-predicting the deaths during the surge in the fall, the Institute for Health Metrics and Evaluation (IHME) models are consistently over-predicting deaths. However, it does not appear that the most recent model run takes the end of the mask mandate (see “Changes in policy”), so it will be interesting to see how they fare in a month.

Observed and forecasted COVID-19 deaths in Indiana.

Changes in behavior

The IHME’s latest policy brief says mobility in Indiana is 8% below the pre-pandemic baseline. This is a big jump from the 20–25% of just a month or so ago. Meanwhile, mask usage has fallen slightly to 72%. Given these, it’s not hard to see why the numbers are picking back up again. These are both trends specifically called out as factoring into the “worst-case scenario.” (Note that the “reference scenario”—or most likely scenario—is what I plot on my dashboard.)

Changes in policy

Governor Holcomb announced earlier this week that the mask mandate will be gone on April 6. This is bad policy. While all Hoosiers 16+ will be eligible for vaccination beginning on March 31, the earliest a newly-eligible person will be fully vaccinated is April 14. And that assumes that the person can get the vaccine that day and that they receive the one-dose Johnson & Johnson vaccine. Recall that the CDC says people reach full vaccination two weeks after receiving the last shot.

In other words, in the impossibly-best case scenario, the mask mandate ends a week before the state’s (adult) population is fully vaccinated. The more likely case is that we don’t hit the 70% threshold for weeks, perhaps months. Holcomb says “Hoosiers know the science” and will continue to wear masks and follow distancing guidelines once the mandate becomes an advisory. I wonder what Hoosiers the governor has been talking to. Considering how many crowded restaurant parking lots and improperly-worn masks I’ve seen in the past week, I don’t believe him.

This is infuriating, because a mask mandate is essentially free. This is particularly true given how little effort the state put in to enforcing it. Ending the mandate early sends the wrong message. We can only hope that vaccinations outpace the virus. We deserve better than this.

Other writing: February 2021

Where have I been writing when I haven’t been writing here?

Stuff I wrote

Fedora

Stuff I curated

Fedora

Indiana COVID-19 update: 5 February 2021

On Wednesday, the Indianapolis Star reported that a state audit discovered just over 1,500 “missing” COVID-19 deaths. These deaths were added to the Indiana State Department of Health’s dashboard on Thursday. The state “snuck” them in, not including them in the “newly reported” deaths for that day’s update. Fortunately, I had the data before and after and was able to produce some information on my dashboard.

It wasn’t as good as we thought

“Missing” COVID-19 deaths by day

The missing deaths stretch as far back as early April, but the bulk came in November through January. This is also when the overall death rate was the highest. On the whole, approximately 15% of COVID-19 deaths were not included on the state’s dashboard prior to February 4. But on 48 days, the missing deaths exceeded 20%. On December 18, 31 deaths (29% of the total) were missing. Instead of having a peak death count of 97, we’ve instead exceeded 100 deaths on several days with a peak of 118.

COVID-19 deaths per day before and after the “missing” deaths were included

I wrote in the last update that I thought deaths were missing, particularly given the abrupt drop in December. It turns out that I was more right than I could have imagined. “I’m not trying to sound like a conspiracy theorist,” I wrote. “I don’t think there was any malfeasance.” I’m trying very hard to continue believing that.

At the very least, this represents appalling incompetence. This isn’t just a problem for making graphs. The death toll of this pandemic is serious. Losing 15% of the deaths is not only disrespectful to the dead and their families, but it robs decision-makers of reliable data. What decisions would have been made differently if we knew the true death toll.

Of course, we may never be sure of the true death toll, particularly early in the pandemic. At the time, testing was scarce. I’ve heard anecdotes from several reliable friends of loved ones not getting testing after death. We can compare 2020’s overall death to previous years, but that will not be definitive.

The future

The good news is that the overall numbers continue to trend in the right direction. Yesterday, hospitalizations were below 1500 for the first time since October 20. Deaths, new cases, hospitalization, and positivity all continue to drop. Mask usage is up and mobility remains 20% below the baseline, per the Institute of Health Metrics and Evaluation (IHME). Perversely, the corrected death totals represent a positive of sorts: the recent model runs have proven more accurate than it appeared.

Observed and forecast COVID-19 deaths in Indiana by day

As best I can tell, IHME’s most recent model run did not include the adjusted death totals, so it will be interesting to see how much changes in the next update. The observed death trend is dropping at a faster rate than the models would suggest, but that may flatten a bit over the coming days. Still, the trends are encouraging.

Causes for concern

But all is not well. Although IHME’s latest model run does not show an increase in deaths through the end of May, they say some states will see that. But even more worrying, it appears some of the new variants may lead to reinfection in people who already have immunity.

The Novavax Phase III trial in South Africa placebo arm found that prior infection
provided no protection from variant B.1.351. The implication of this finding is that herd
immunity is only variant-specific; if this finding is confirmed in the Johnson & Johnson
placebo arm data, our worse scenario is likely too optimistic.

IHME COVID-19 Policy Brief for the United States, 3 February 2021

With the next update, IHME will incorporate cross-variant reinfection into the model. I’ll continue to update my dashboard with the new model runs as they’re available.