No, Your Vaccine Is Now Fully Operational

Another week is over, and for the past few years I’ve often said we all made it to the end of the week. When in reality, for the last few months, thousands of people were not. We’ve started using Monday to sort of recap the state of the pandemic in a select region of the country. And then we moved straight into how the New York Times addressed the US reaching the grim milestone of 500,000 deaths.

So I want to end this week with a little story told over at xkcd that tries to explain these new mRNA vaccines. Who doesn’t love science, science fiction, and humour woven together into a narrative? True, this isn’t really data visualisation, but it dovetails nicely into the work we’ve been doing and reviewing of late. Plus, levity. We all need levity.

These are not the cells you’re looking for.

You’ll want to click through to read it all.

Credit for the piece goes to Randall Munroe.

Another Look at 500,000

Yesterday we looked at how the New York Times covered the deaths of 500,000 Americans due to Covid-19. But I also read another article, this by the BBC, that attempted to capture the scale of the tragedy.

Instead of looking at the deaths in a timeline, the BBC approached it from a cumulative impact, i.e. 500,000 dead all in one go. To do this, they started with an illustration of 1,000 people. Then they zoomed out and showed how that group of 1,000 fit into a broader picture of 500,000.

We’re going to take a look at this in reverse, starting with the 500,000.

Half a statistic.

I think this part of the graphic works well. There’s just enough resolution to see individual pixels in the smaller squares, connecting us to the people. And of course the number 500 stacks nicely.

My quibble here might be whether the text overlay masks 8,000 people. Initially, I thought the design was akin to hollow square, but when I looked closer I could see the faint grey shapes of the boxes behind a white overlay. Perhaps it could be a bit clearer if the text fell at the end of all the boxes?

But overall, this part works well. So now let’s look at the top.

1,000 tragedies

This is where I have some issues.

When I first saw this, my eyes immediately went to the visual patterns. On the left and right there are rivers or columns of what look like guys in white t-shirts. Of course, once I focused on those, I saw other repeated patterns, the guy in the black jacket with his arms bent out, hands on his hips. The person in the wheelchair occupies a different amount of area and has a distinct shape and so that stood out too.

Upon even closer inspection, I noticed the pattern began to repeat itself. Every other line repeated itself and with the wheelchair person it was easy to see the images were sometimes just flipped to look different.

Now, allow me to let you in on a secret, unless you gave a designer a budget of infinite time, they wouldn’t illustrate 1,000 actual people to fill this box. We don’t have time for that. And I’ll also admit that not all designers are good illustrators—myself first and foremost. A good design team for an organisation that uses illustration should have either a full-time illustrator, or a designer who can capably illustrate things.

But this gets to my problem with the graphic. I normally can distance myself from reading a piece to critiquing it. But here, I immediately fixated on the illustrations, which is not a good sign.

There are three things I think that could have been done. The first two are relatively simple fixes whilst the third is a bit grander in scope.

First, I wonder if a little more time could have been spent with the illustrations. For one, white t-shirt guy, I don’t see his illustration reused, so why not change the colour of his t-shirt. Maybe in some instances make it purple, or orange, or some other colour. I think re-colouring the outfits of the people could actually solve this problem a good bit.

But second, if the patterns still appear visible to readers, mix it up a bit. I understand the lack of desire to spend time creating an individualised row for each row. Crafting each row person by person probably is out of the time requirements—though maybe the people above the designer(s) should know that content takes time to create. So what about repeating smaller blocks? I counted 20 rows, which means there should be 50 people per row. Make each row about ten blocks, and have several different blocks from which you can choose. Ideally, you have more blocks than you need per row, so not all figures are repeated, but if constrained, just make sure that no two rows have the same alignment of blocks.

Thirdly, and here’s the one that would really have required more time for the designer to do their job, make the illustrations meaningful. In a broad sense, we do have some statistics on the deaths in the United States. According to the CDC, 63% of deaths have been by white non-Hispanics, 15% by Black non-Hispanics, and 12% by Hispanic/Latino, 4% by Asian Americans, 1% by Native Americans, 0.3% by Hawaiian and Pacific Islander, and 4% by multiple non-Hispanic. Using those numbers, we would need 630 obviously white illustrations, 150 obviously Black, and so on.

If the designer had infinite time, the illustrations could also be made to try and capture age as well. Older people have been hit harder by this pandemic, and the illustrations could skew to cover that cohort. In other words, few young people. According to the CDC, fewer than 5% of deaths have been by people aged under 40. In other words, no baby illustrations needed.

That’s not to say babies haven’t died—87 deaths of people between 0 and 4 have been reported—but that when creating a representative average, they can be omitted, because that’s less than 0.1%, or not even 1 out of 1000.

To reiterate though, that third concept would take time to properly execute. And it would also require the skills to execute it properly. And I am no illustrator, so could I draw enough representative people to fake 1,000? Sure, but time and money.

The first two options are probably the most effective given I’d bet this was a piece thought up with little time to spare.

Credit for the piece goes to the BBC graphics team.

500,000 Deaths

The United States surpassed 500,000 deaths from Covid-19. On Sunday, in advance of that sobering statistic, the New York Times published a front-page graphic that dominated the layout.

Sunday front page for the New York Times

Usually a front-page graphic will make use of the four-colour process and present richly coloured graphics. This, however, starkly lays out the timeline of deaths in the United States in black and white.

Meaningful graphics do not need to reinvent the wheel. This takes each life lost as a black dot and then, starting at the top in February, plots each day.

Detail of the graphic

The colour here serves as the annotation. The red circle drawing attention to the first reported death. And down the side the tick marks for days. Red lines indicate 50,000 death increments. The labels tell the story, we’ve needed fewer and fewer days to reach each subsequent 50,000 milestone.

As the first wave intensifies in March and April, the space fills with black dots. But as we enter summer and deaths fell, the space lightens. Late autumn and winter bring more death and you can see clearly towards the bottom of the chart, as we approach today, the graphic is nearly solid black.

If we want to look towards a hopeful point in the content, we can see first that it took 17 days then 15 to reach 400,00 deaths and 450,000 deaths, respectively. But it took 19 days to reach 500,000. As a nation we appear to finally be on the downward slope of this wave.

Returning to the piece, it’s a gut punch of simplicity in design.

Credit for the piece goes to Lazaro Gambio, Lauren Leatherby, Bill Marsh, and Andrew Sondern.

Covid Update: 20 February

Another week, another snowstorm in the Northeast. This winter has been far busier than last, when Philadelphia saw no snow. Unfortunately, whilst people like me enjoy seeing the snow, it’s hampering with testing and vaccination.

Last week we saw some middling signs of improvement, but perhaps partially exaggerated by the closures caused by the storm. When we look back at the last week, despite the impact of a storm later in the week, it’s been a categorically positive week with respect to new cases.

New case curves for PA, NJ, DE, VA, & IL.

After the plateaus of the week before, most notably in the straight line in Pennsylvania, this week we saw the line for the seven-day average resume a sharp trajectory down. That isn’t to say we are seeing a slowdown in that reduction of new cases. Illinois best fits that, but we can see slight flattening of the downward curve also in Delaware and New Jersey. In Illinois’ case, that is still welcome as the state approaches early autumn levels of new case rates. In the remaining states, we still have a little ways to go before we reach those levels.

Deaths, on the other hand, remain a mixed bag of results. Last week we talked about a much improved picture from the week before with Delaware and Virginia in particular exhibiting significantly decreased rates.

Death curves for PA, NJ, DE, VA, & IL.

This week we saw some reversal of fortune in those two same states. In Delaware, the numbers of deaths have ticked back upwards and the seven-day average has made up about a third of the gains we saw. In Virginia, the upward swing can be largely—though not entirely—attributed to a one-day spike in numbers.

Whilst the other three states continued to see gradual improvements, the question over the coming week will be what trends emerge within Delaware and Virginia. Do the deaths increase and the situation worsen? Or will the increases prove a temporary aberration followed by a return to decreasing numbers of new deaths.

Finally with vaccines

The vaccination curves for PA, NJ, DE, VA, & IL.

The story to follow in Pennsylvania will be how distribution sites mistakenly administered second doses as first. 60,000 people awaiting their second dose will now have to wait—though still within the recommended window—for their second dose whilst 50,000 people will now have to wait for their first dose.

Otherwise, we continue to see an uptick in vaccinations. Last week we saw states make significant gains in their fully vaccinated populations. Virginia had passed 4% and Pennsylvania was about to hit the same milestone. This week begins with Virginia at nearly 5.5% and Pennsylvania almost at 5%, sitting on 4.77%. We need to keep in mind that this excludes any new vaccinations from the city, which doesn’t report vaccination data at the weekend. Illinois is now the lagging state at 4.29%.

Credit for the piece is mine.

Covid Update: 15 February

Last week we discussed the potential impact of a major nor’easter that struck the East Coast and interrupted testing and vaccination operations in the states we cover: Pennsylvania, New Jersey, Delaware, Virginia, and Illinois (affected by the storm as one of the components moved east across the Midwest).

The possibility of an exaggerated downward trajectory concerned me and that it could be followed with an uptick in new cases and deaths. So a week later, where are we?

New case curves for PA, NJ, DE, VA, & IL.

We can see something in the middle. With the exception of Illinois, which has continued its downward trend for new cases, we saw a brief interruption last week. In some cases, like Pennsylvania, that emerged as a rolling seven-day average that began and ended the workweek with the same exact number. And without a lot of variation during the week, you can see that pattern as the flat line towards the end of the chart. As numbers resumed heading down, you can see that beginning of a downward direction at the line’s very end.

In the remaining states of New Jersey, Delaware, and Virginia we saw brief upticks in the seven-day averages with daily spikes of new cases. None of these upticks came anywhere close enough to be threatening—though any upward tick should be monitored—but they were all significant enough to be seen as the quick, upward pointing jogs in the lines. But as we entered the weekend, those numbers also began to drop again.

Next we look at deaths. Last week I described a muddled picture. Delaware and Virginia had begun to rebound and reach or approach new peaks whilst Pennsylvania and Illinois continued to see steady but significant declines. New Jersey fell somewhere between the two. What about this week?

Death curves for PA, NJ, DE, VA, & IL.

This week is an improved picture. We did see the potential interruption from the storm—Pennsylvania’s death trend evinces the disruption with the same straight line pattern we saw with new cases. But, overall, numbers continue to trend down. Delaware and Virginia show dramatic improvement with steep drops over the last week. And whilst Illinois continues to show steadily declining numbers, New Jersey now falls somewhere near the top of the pile. Its death rate continues to decline very slowly, relative to the other states. But it is heading down.

Finally, a look at vaccinations for Pennsylvania, Virginia, and Illinois.

Last week we talked about how the states all reached at least 2% over the course of the week. Even better news this week.

Vaccination curves for PA, VA, & IL.

Last week we needed approximately one week to climb one percentage point from 1% to 2%. This week in the same one week time period we saw Virginia climb two percentage points from 2% to 4%. Illinois has slowed its vaccination efforts as it’s still in the mid 3% range. And Pennsylvania is tricky. Because the city of Philadelphia does not report its data on the weekend, we have an incomplete picture until after I post this on Mondays. Even though today is Tuesday, yesterday was a holiday so the same pattern holds true. I would suspect, however, the Commonwealth surpasses 4% later today when the new numbers are released or it comes near to reaching that level.

Credit for the piece is mine.

Covid Update: 7 February

I missed last week’s posting on an update to Covid-19. Two weeks on from the last post, things in the states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois continue to improve, albeit with a few fits and starts. But the downward trend nonetheless can be seen in the new cases charts.

Consider that in the charts from two weeks ago, we saw downward slopes, but a look at the charts in the two weeks hence shows some blips.

Another thing to keep in mind is that a major snowstorm disrupted testing and vaccinating operations in the northeastern states of Pennsylvania, New Jersey, and Delaware. The storm, which also hit northern Illinois and Virginia, also likely impacted those states but to lesser degrees.

New cases curves for PA, NJ, DE, VA, & IL.

That means the downward trends in new cases could be slightly exaggerated in those states. Consequently, rebounds next week should be taken with a grain of salt. Indeed, Sunday’s data releases from the tri-state area were greater than we might normally see with weekend data.

When we at deaths, however, we see a more muddled picture.

Death curves in PA, NJ, DE, VA, & IL.

In states like Delaware and Virginia, the average death rate is now higher than it was two weeks ago. In New Jersey, the rate is down slightly, but after two weeks of it being largely up and so all in all, largely a wash. Instead, it’s only in Pennsylvania and Illinois where we any real improvements in the average death rate. Both states are down and look to continue heading down.

Finally, we look at vaccinations and the percent of state populations that have been fully vaccinated.

The fully vaccinated percentage of the populations of PA, VA, & IL.

Two weeks ago, Pennsylvania and Illinois had just reached 1%. Neither New Jersey nor Delaware is reporting similar data, so both those states remain outside our consideration set. But, all three remaining states—Pennsylvania, Virginia, and Illinois—are now over 2%. Pennsylvania reports at least 2.5%—the city of Philadelphia reports separately from the statewide Department of Health, but does not update its figures at the weekend and so is likely higher. Both Virginia and Illinois have reached 2.3% full vaccination.

Credit for the piece is mine.

Viral Mutations

With Covid-19, one of the big challenges we face is the rapid mutations in the viral genetic code that have produced several beneficial—from the virus’ standpoint—adaptations. Several days ago the New York Times published a nice, illustrated piece that showed just what these mutations look like.

Of course, these were not just nice illustrations of protein molecules, but the screenshot below is of the code itself and you can see how just a few alterations can produce subtle, but impactful, effects.

In a biological sense, these mutations are nothing new. In fact, humanity wouldn’t be humanity but for mutations. Rather we are seeing evolution play out in front of our eyes—albeit eyes locked in the same household for nearly a year now—as the virus evolves adaptations better suited to spreading and surviving in a host population.

The piece includes several illustrations, but begins with an overall, simplified diagram of the virus and where its genetic code lies. And then breaks that code down similar to a stacked bar chart.

Designers identify where in the code the different mutations occur and the type of mutation. Later on in the piece we see a map of where this particular variant can be found.

I might come back to that map later, so I won’t comment too much on it here.

But I think this piece does a great job of showcasing just what we mean when we talk about virus mutations. It’s really just a beneficial slip up in the genetic alphabet.

Credit for the piece goes to Jonathan Corum and Carl Zimmer.

Covid-19 Update: 24 January

Last week we saw some indications that the recent surge was beginning to ebb in Pennsylvania, Delaware, and Illinois with the same in New Jersey, but to a slight degree less so. Only Virginia presented us with data that showed its surge continuing unabated.

So this week we have some generally good news to look at.

New case curves for PA, NJ, DE, VA, & IL.

The drop in Pennsylvania, New Jersey, and Illinois appears real and sustained. Even in Virginia, we are beginning to see some signs of a decline in new cases—albeit it after a week of record reports of new cases.

Of course we should also mention that even though we are seeing declines in new cases, in no state are we close to approach low levels of community spread. Things are still bad out there, but they have gone from catastrophic spread to merely a disaster. Illinois is probably the closest to reaching summer-like levels of viral spread.

Deaths, however, because they lag behind new cases, are just now beginning to show signs of ebbing.

Death curves in PA, NJ, DE, VA & IL.

If last week’s pattern with new cases was that we were seeing positive trends in four states, we can say this week we are seeing positive trends in deaths for the same four states. Virginia is, again, the outlier.

Though I would be remiss if I noted that the declines in deaths is not nearly as pronounced as in new cases. In Pennsylvania, the seven-day trend for new deaths has appeared to have crested. But in New Jersey, recent days have suggested the decline may not be as steady. Only in Illinois are we really seeing a sustained downward trend in deaths.

And Virginia just Saturday saw its seven-day trend reach another new record, over 50 deaths per day.

But what about vaccinations?

Firstly, we still only have data for the three states of Pennsylvania, Virginia, and Illinois. Secondly, keep in mind that I am looking only at people reported fully vaccinated, i.e. they have had both their shots—both Pfizer’s and Moderna’s vaccines require two shots.

Vaccination curves in PA, VA, & IL.

There’s not a lot to report on yet, other than that both Pennsylvania and Illinois reached the 1% threshold. I think that for most people, however, that you can begin to see their respective lines easing off the 0% baseline. Virginia lags behind those two states, however, with just 0.5% of its population reported as fully vaccinated.

I’m curious to see if I cannot find some additional/alternative data sources for New Jersey and Delaware next weekend. I don’t love the idea of mixing data sources, but after a few weeks, we haven’t really seen any improvements to the data sharing from those states.

That said, I should also note that the new US administration has identified data transparency as an issue—or the lack thereof—in the current vaccination programme and is working to develop national and state-level dashboards to inform the public.

Credit for the piece is mine.

Covid-19 Update: 18 January

Last week we saw that in the weeks after Christmas, new cases and deaths rebounded in the five states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois. The question was how bad would things continue to get? Would these rebounds sustain themselves?

A week later we can see a glimmer of good news in that with new cases, these rebounds appear to have crested and are now ebbing back down. At least in four states.

In Virginia, unfortunately, we see that new cases continue to climb with a new record of nearly 10,000 cases reported late last week. More broadly, this is the dilemma that confronts the United States. We have states like Pennsylvania, Delaware, and Illinois where we are bringing the virus back to heel. But in other states like Virginia, things continue to get worse.

New Jersey is somewhere in the middle. It appears to just possibly be cresting with its average actually ticking higher the last few days despite falling daily new cases. We will need to see how the Garden State plays out over the course of this week.

When we look at deaths, we continue to see the grim numbers pile up.

Deaths, of course, lag new cases by 2–4 weeks, sometimes as many as six or longer. In most of our five states, the average rate of deaths appears to be cresting or peaking. In Pennsylvania the curve may have peaked. In Delaware, we have seen a plateau and in Illinois we see the best news of a resumed decline.

In both New Jersey and Virginia, however, we see deaths continuing to climb, and in some cases by significant amounts.

If cases really have peaked in some of these states over the last week, we may expect deaths to continue to rise over the course of this week before beginning to fall again.

I also want to add two new graphics today. I have been trying to figure out how to cover the vaccination programme of the five states. Unfortunately, they do not all report the same data in the same way.

The graphic that perhaps makes the most sense is the one that looks the emptiest at the moment.

In order to resume “normal” lives, we need to achieve herd immunity. When we reach that level, the virus starves of new hosts and dies out. Broadly speaking, we have two ways of achieving herd immunity.

Option 1, let the virus run rampant and takes its course through the population. The benefit is that society remains open and people can return to cafes, pubs, shops, and museums. The cost is that millions get sick and hundreds of thousands die. Sadly, this is the route taken by Sweden and, unofficially, the United States.

Option 2, vaccinate the population. The benefit here is that millions do not get sick and hundreds of thousands do not die. The cost is that in order to wait for a vaccine and vaccination we would need to close cafes, pubs, shops, and museums.

The reality is that we chose something between the two. In the initial months, after we (belatedly) recognised the threat of the virus, we shut down our economies and stayed home. We chose option 2. You can see in the state charts above how that quickly helped us curb the spread of new infections.

Unfortunately, then the Trump administration chose to follow option 1 and encouraged states to “reopen” their economies. And because we never got the virus fully under control, we sowed the seeds for the explosive growth this autumn and winter.

But the vaccines are now here and the best bet is to vaccinate the population. How many people do we need to vaccinate? The exact number depends upon the infectiousness of the virus. Measles, one of the most infectious viruses out there, requires near 100% vaccination rates to achieve herd immunity. Thankfully, this coronavirus is not as infectious as measles. Early estimates placed the range at 60–70%. But lately, some epidemiologists have indicated the true number may be higher. Dr. Fauci of the National Institutes of Health (NIH) has said the true number is likely 70–85%.

This is why the new strains of the coronavirus we have identified in South Africa and the United Kingdom worry folks. Both appear to be more transmissible than earlier strains. Neither strain appears to be more lethal in its own right—although more cases means more people will die—but this increased infectiousness could mean we need an ever higher level of herd immunity, which means more vaccinations. And we’re already seeing the anti-vaccination support rising to somewhere in the range of 15-20%, just the threshold we could perhaps tolerate with the higher herd immunity range.

So what about the chart?

As we begin vaccinations, some states are reporting the numbers of people in their state that have been fully vaccinated against the coronavirus. I plot those numbers here. Pennsylvania, Virginia, and Illinois do so. Unfortunately, neither New Jersey nor Delaware does. I only have one data point recorded for Virginia and Illinois, and so they are not plotted yet, but both fall below the level of Pennsylvania, which has reported 0.50% of its population fully vaccinated. I have added a bar to show the range of estimated herd immunity we need.

And that gets us to the second new chart, the number of total doses administered per day.

Functionally this resembles the usual two charts. We track the number of doses administered daily and then plot their seven-day average to smooth out any day-to-day blips. Of course this means almost the opposite of those two charts as we are tracking the progress of people who will be immune from the virus.

The catch is that with the current vaccines we need two shots for a full course of treatment and not all states break the data down with that level of granularity. Again, we are looking at Delaware and New Jersey as they provide only the total number of doses administered. Now that’s still helpful, but it doesn’t give us the most accurate picture of what is happening with vaccinations.

But in order to make things comparable across five states, I have decided to use that broader, total doses administered metric for Pennsylvania, Virginia, and Illinois. (Virginia and Illinois provide another headache in that it reports the daily number of people fully vaccinated, but does not break down the number of full vaccination doses.)

So what is this second chart showing us?

Well, we are seeing a slow, nearly steady growth in the number of vaccines administered. The problem is that we need to see steep, nearly exponential line charts here if we want to have any hope of returning to “normal” anytime soon. Reporting tells us that the federal government’s approach to the logistics of vaccine distribution has been…not great. (Although at this point, perhaps that should not surprise us.)

Until we see these second charts begin to show more exponential growth, the first charts of the number of people fully vaccinated will be far below that herd immunity threshold we need to see.

Covering the vaccines in addition to the virus is a bit more work, but I’m going to try and cover them both over the next several months as I have with the outbreak itself.

Credit for the piece is mine.

Covid-19 Update: 10 January

The last time we checked in on Covid-19 in the states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois, things were peaking across the five states. As I said then:

If you look at the very tippy tip top of the curves in the other four states, we might just be seeing an inflection point.

And in the month since, my highly scientific term of “tippy point” appears to have been correct. New cases did begin to drop and by the start of the Christmas holiday we began to see real improvement. I should point out that deaths continued to rise, however, but we should expect that because deaths lag new cases by sometimes as many as four to six weeks.

So how are things now, a month hence?

The new case curves for PA, NJ, DE, VA, & IL.

Well as you can see with new cases, not great and getting worse. Pennsylvania, New Jersey, Delaware, and Illinois all bottomed out prior to the holidays, and since then have been rising. It speaks to a surge in new cases likely caused by gatherings centred on the holidays.

The good news—if you can call it that—is that in Pennsylvania and Illinois, whilst cases rebound, they have not yet reached their mid-December peak in Pennsylvania and mid-November peak in Illinois. It’s worth pointing out that Chicago and separately Illinois instituted lockdowns earlier than the other four states prior to the holidays. That may account for the more dramatic reduction in those states.

The bad news is that in New Jersey and Delaware, the rebounds have now surpassed the peaks we saw in mid-December and cases continue to climb with new daily records pointing towards escalation of new cases in those states.

But the really bad news is in Virginia, where the inflection point was there—note the little mini “W” at the top of the chart—but that new cases declined neither significantly long nor in significant numbers such that there was no real holiday decline. Instead, at best we could describe it as numbers paused for two weeks before resuming their upward trends.

How about deaths?

Death curves in PA, NJ, DE, VA, & IL.

Again, fairly grim news here. A month ago we were talking about rising rates of deaths in all but Illinois. And in fact, Illinois is the only state where the death rate is significantly lower than what it was in mid-December.

In New Jersey and Virginia, we see two states where the rising death rate perhaps slowed, but it never really entered into decline. Pennsylvania and Delaware offer perhaps static death rates. In fact, Pennsylvania just yesterday surpassed its mid-December peak level.

But keep in mind that deaths lag new cases by somewhere between two to four weeks, sometimes longer. What this means is that with new cases now rebounding and in fact surpassing their peaks from a month ago, we can expect that the end of January and beginning of February could be particularly deadly.

The situation is dire in the United States and things are going to get worse before they get better.

Credit for the piece is mine.