Social distancing is reducing Covid-19 burden in King and Snohomish counties

There’s a plot that has been stuck in my brain for about 10 days:

Part of Figure 1. Scenarios for the possible cumulative burden of COVID-19 infection in King and Snohomish counties. (Klein et. al.. 2020)

The plot is based on an infection model that was published by a team of researchers in the Seattle area who projected future Covid-19 cumulative infections for King and Snohomish (I’ll use the term Sno-King) over a four week interval commencing on 11 March. (Klein et. al., 2020) [1] I wanted to understand how our communities are doing in the struggle to slow the rate of new infections.

We do not yet know which scenario best represents current conditions in King and Snohomish counties, but previous experience in the region with weather-related social distancing and in other countries suggests to us that current efforts will likely land between baseline and 25% reduction scenarios.

(Klein et. al., 2020) on 11 March 2020

I believe there’s enough data (as of 25 March 2020) to claim that the Sno-King population has achieved the 25% reduction level due to social distancing. That’s certainly an improvement over two weeks but there’s still more work to be done. I’ll present some results from a very simple model I made and then discuss how I made this model, what its limitations are and suggest some improvements.

In Figure 1 below, the blue curve is a projection using an exponential model of the baseline for new infections for 28 days ending on 7 April 2020. The red curve is a projection of a 25% reduction in infection rate. The intent of these curves was to reproduce the model curves of Klein et. al. Finally, the yellow curves plots the number of cases in Sno-King. The underlying data, model and plots are available on a Google Sheet I created.

Figure 1: Cumulative Covid-19 infections, Exponential model
King and Snohomish Counties, updated 25 March 2020

Now, I realize that it’s difficult to see much from this curve. I looked at the change in new daily infections, I believe that’s a better metric to visualize how we are improving. Figure 2 provides this visualization with the yellow data points show the daily increase in new cases compared to the baseline (blue) and 25% reduction (red) lines. I realize that there’s not very much data yet but we are seeing new data being published daily (and I will update this analysis sheet daily). Still, this made me realize that we are likely achieving 25% reduction level due to social distancing in Sno-King!

Figure 2: Daily increase in Covid-19 infections, Exponential model
King and Snohomish Counties, updated 25 March 2020

Building the Exponential Model

Since I’m an engineer, the first thing I did was build my own model and then start feeding in data to measure how we are doing.Of course, the devil is in the details, and I’m not an epidemiologist. What I did was reproduce the results of Klein et. al.. 2020 using the facts they provided: a doubling time for the epidemic of 6.2 days, one large transmission cluster, four week duration, and less than 1% (25,000 of the 3 million infected at the end of the four weeks.

Let me explain the simple, deterministic model I used. To follow along, you may find it helpful to look at the underlying Google Sheet I developed. I am including underlying cell references in parentheses. I used an exponential increasing model that starts with 267 infections (cell L2) at day zero. For a time series of 28 days (cells F2:F30), I calculated the total number of infections using a baseline doubling rate parameter of 6.2 days (cell L3). For the entire 28 days, the baseline I calculated was 24,425 cumulative cases (cell G30). For comparison, the multiple simulations performed by Klein et. al. estimated 25,000 cumulative cases. Thus, my baseline model estimate is about 2% lower than Klein et. al.

For the the social distancing intervention representing a 25% reduction, I increased the baseline doubling rate parameter by a factor of 1.25 to 7.8 days (cell L4) For the 25% reduction case, I calculated was 9,899 cumulative cases (cell H30). For comparison, the multiple simulations performed by Klein et. al. estimated 9,700 cumulative cases. Thus, my model estimate is about 2% higher than Klein et. al. in the the 25% reduction case.

Next, I used the graphic “COVID-19 in Washington State” published daily by the Seattle Times to determine the cumulative number of cases in King (C3:C16) and Snohomish (D3:D16) county for each day and then computed the Sno-King total cases (E3:E16). I have included a tab labeled “DataSource” that lists the URL for each day’s data. Some days, the actual case data is suspect, for example, there was disagreement between King County and Washington State regarding cases on 17 March 2020. The cumulative infections are plotted for the baseline, 25% reduction, and actual cases in the chart labeled “Cumul25March”

I computed the first order difference in infections, the change in number of daily infections, for each condition: baseline (cells J3:J16), 25% reduction (cells K3:K16) and actual cases (cells I3:I16). The change in number of daily infections are plotted for the baseline, 25% reduction, and actual cases in the chart labeled “1stDiff25March”

Limitations and Utility of this Model

This is a very simple model of a complex epidemic. I don’t think it will have much validity beyond 7 April 2020. At that point, a more rigorous model that models the underlying epidemic using ordinary differential equations is in order. Also, the underlying parameters will be better understood. Finally, once more than 1% of the Sno-King population is infected, the simple exponential model will become less accurate.

I think this model will be a useful way for people to visualize the impact of social distancing efforts in the short-term. There’s enough data here to say that social distancing is making an impact. Also, in a small way, this simple model and analysis confirms that our current effort will result in 25% reduction due to social distancing. Maybe the next two weeks will show additional improvement?

Thanks to the Seattle Times and Klein et. al. making me think and look at the data. Also, hats are off to all the essential workers in government, grocery stores, pharmacies and the news media for keeping us safe, healthy and informed.

I welcome suggestions for improvement, corrections and any words of wisdom from anyone reading this. Stay safe.

Quantifying Hiking and Running Part 1

For the last eight years (2012-2019), I’ve been keeping tracking of my daily steps and miles using a pedometer.  I realize there are better gadgets to do this: Fitbits, watches, and phones that will do this job with more data and better graphics. I like to “roll my own” and I thought I would write up what I have been doing. I welcome constructive feedback; my goal is to maintain and improve my fitness as I age through data analysis.

I record my mileage data daily and analyze my results weekly, monthly and yearly.  Here is a link to my monthly and yearly mileage data in a Google Sheets file. In Table 1, I want to look at my mileage results on a yearly basis; I’ve also included my age. I can see that my mileage increased significantly after 2013, one reason for this is a greater emphasis on hiking and running. I can also see a drop in yearly mileage in 2016; this was due to some medical problems that required surgery, I had some months were I couldn’t exercise very much. In 2017 and 2018 I was training for ultra marathons and had increased my annual mileage. I find having yearly goals, such as races or long distance hikes, motivates me.

Table 1: Yearly Mileage
Year Miles Age
2019 3174 61
2018 3387 60
2017 3286 59
2016 2754 58
2015 3117 57
2014 3008 56
2013 2634 55
2012 2470 54

Here’s a summary of the mileage I’ve done month by month. Table 2 provides a monthly view of my mileage.

Table 2: Monthly Mileage
Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Year
2019 301 241 289 242 238 250 273 269 276 280 274 242 3174
2018 318 271 315 252 304 315 272 338 229 301 240 232 3387
2017 256 296 298 259 286 295 288 283 214 291 281 240 3286
2016 187 188 193 215 206 225 238 267 267 305 269 194 2754
2015 245 258 260 244 266 281 247 306 255 250 237 269 3117
2014 224 211 239 206 212 253 282 302 265 267 275 273 3008
2013 210 190 208 229 243 238 256 220 221 209 199 211 2634
2012 147 201 184 192 242 238 245 190 200 213 202 214 2470
Mean 236 232 248 230 249 262 263 272 241 264 247 234 2951

For example, in the first three months of 2016 my mileage was lower than usual, these were months when I was recovering from surgery. Looking at the monthly mileage data, a high mileage month for me has been greater than 300 miles. For each month, I have computed the mean monthly mileage. My mileage tends to be lower in the shorter winter and early spring (December through April); the most likely cause is the dreary Pacific Northwest winters I manage to slog through each year. There are some exceptions such as 2018 when I was training for a 100 miler in the winter and 2019 when I spent time in South America during the winter.

Another way I like to view the monthly mileage data is a cumulative view. Table 3 shows the cumulative monthly data over the course of a year.

Table 3: Cumulative Monthly Mileage
Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
2019 301 542 831 1073 1311 1561 1833 2102 2378 2658 2932 3174
2018 318 589 903 1155 1459 1774 2047 2385 2614 2915 3155 3387
2017 256 553 850 1109 1395 1690 1978 2261 2474 2765 3047 3286
2016 187 375 569 783 989 1214 1452 1719 1986 2291 2560 2754
2015 245 502 762 1006 1272 1553 1800 2106 2362 2612 2849 3117
2014 224 435 674 880 1092 1345 1627 1929 2194 2460 2735 3008
2013 210 400 607 837 1079 1317 1573 1793 2014 2223 2422 2634
2012 147 348 532 724 966 1205 1450 1640 1840 2053 2256 2470

The sum of all the yearly mileage is 23,831 miles over 96 months or 248 miles per month. Now, how does this compare to my goal performance?

In 2014, I decided to set a goal of 3000 miles in a year. A yearly goal of 3000 miles works out to an average of 250 miles per month or 8.22 miles per day. Before that, I had goals but they were haphazard. Here are my monthly goals for each year (adjusted for leap years.

Table 4: Cumulative Goal Monthly Mileage
Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
2019 255 485 740 986 1241 1488 1743 1997 2244 2499 2745 3000
2018 255 485 740 986 1241 1488 1743 1997 2244 2499 2745 3000
2017 255 485 740 986 1241 1488 1743 1997 2244 2499 2745 3000
2016 255 493 748 995 1249 1496 1751 2006 2252 2507 2754 3009
2015 255 485 740 986 1241 1488 1743 1997 2244 2499 2745 3000
2014 255 485 740 986 1241 1488 1743 1997 2244 2499 2745 3000
2013 255 485 740 986 1241 1488 1743 1997 2244 2499 2745 3000
2012 255 493 748 995 1249 1496 1751 2006 2252 2507 2754 3009

Once I had my goal and actual monthly mileage, I can compute the difference. A negative number indicates that I am less than my goal. Figure 1 shows the cumulative difference from goal over eight years.

Figure 1 shows five trends that are significant to me.

  1. January, 2012 to May, 2014 there is a negative slope: every month my actual monthly mileage was generally less than my goal of 250 miles per month./li>
  2. June, 2014 to December, 2015 the slope is mostly positive; my actual miles were greater than my goal of 250 miles per month.
  3. January to July, 2016 the slope is again negative; this is the period of time when I was recovering from surgery.
  4. mid-2016 until the end of 2018 I have been (mostly) exceeding my goal of 250 miles per month; the slope is positive with a few wintertime plateaus.
  5. For 2019, the slope is still positive but not as steep, I haven’t been traing for ultra marathons; only a trail marathon and lots of hiking

Keeping track of my monthly mileage difference from goal provides me some useful month to month feedback. Of course, I am motivated by numerical metrics; not everyone is. I have discovered there is a quantified self community; that discovery came just a few years ago. I welcome feedback from everyone. It’s good to learn from others!

I find that this feedback, along with yearly specific hiking or running goals such as run a 100 mile race or hike the Appalachian Trail (a 2020 goal) keep me on track and motivated.

In part 2, I will add my daily and weekly hiking and running goals and tracking methods.

Book Review Army of None: by Paul Scharre

Book Review Army of None: Autonomous Weapons and the Future of War by Paul Scharre (reviewed 8 July 2019)

We are witnessing the evolution of autonomous technologies in our world. As in much of technological evolution, military needs drive much of this development. Peter Scharre has done a remarkable job to explain autonomous technologies and how military establishment embrace autonomy: past, present and future. A critical question: “Would a robot know when it is lawful to kill, but wrong?”

Let me jump to Scharre’s conclusion first: “Machines can do many things, but they cannot create meaning. They cannot answer these questions for us. Machines cannot tell us what we value, what choices we should make. The world we are creating is one that will have intelligent machines in it, but it is not for them. It is a world for us.” The author has done a remarkable job to explain what an autonomous world might look like.

Scharre spends considerable time to define and explain autonomy, here’s a cogent summary:

  • “Autonomy encompasses three distinct concepts: the type of task the machine is performing; the relationship of the human to the machine when performing that task; and the sophistication of the machine’s decision-making when performing the task. This means there are three different dimensions of autonomy. These dimensions are independent, and a machine can be “more autonomous” by increasing the amount of autonomy along any of these spectrums.”

These two quotes summarize some concerns about make autonomous systems fail-safe. (Spoiler alert: it can’t be done…)

  • “Failures may be unlikely, but over a long enough timeline they are inevitable. Engineers refer to these incidents as “normal accidents” because their occurrence is inevitable, even normal, in complex systems. “Why would autonomous systems be any different?” Borrie asked. The textbook example of a normal accident is the Three Mile Island nuclear power plant meltdown in 1979.”
  • “In 2017, a group of scientific experts called JASON tasked with studying the implications of AI for the Defense Department came to a similar conclusion. After an exhaustive analysis of the current state of the art in AI, they concluded: [T]he sheer magnitude, millions or billions of parameters (i.e. weights/biases/etc.), which are learned as part of the training of the net . . . makes it impossible to really understand exactly how the network does what it does. Thus the response of the network to all possible inputs is unknowable.”

Here are several passages capturing the future of autnomy. I’m trying to summarize a lot of the author’s work into just a few quotes:

  • “Artificial general intelligence (AGI) is a hypothetical future AI that would exhibit human-level intelligence across the full range of cognitive tasks. AGI could be applied to solving humanity’s toughest problems, including those that involve nuance, ambiguity, and uncertainty.”
  • ““intelligence explosion.” The concept was first outlined by I. J. Good in 1964: Let an ultraintelligent machine be defined as a machine that can far surpass all the intellectual activities of any man however clever. Since the design of machines is one of these intellectual activities, an ultraintelligent machine could design even better machines; there would then unquestionably be an “intelligence explosion,” and the intelligence of man would be left far behind. Thus the first ultraintelligent machine is the last invention that man need ever make, provided that the machine is docile enough to tell us how to keep it under control.” (This is also known as the Technological Singularity)
  • “Hybrid human-machine cognitive systems, often called “centaur warfighters” after the classic Greek myth of the half-human, half-horse creature, can leverage the precision and reliability of automation without sacrificing the robustness and flexibility of human intelligence.”

In summary, “Army of None” is well worth reading to gain an understanding of how autonomous technologies impact our world, now and in the future.

Bryce Canyon 100 – Fail forward

“Focus on how far you’ve come from the starting line;
not the distance to the finish.”

I ran the Bryce Canyon 100 race on 1-2 June 2018.   My reason for trying this are to overcome the physical and mental challenges of a 100 mile run… while enjoying the journey.  I’m a 60 year old runner; quite content to run slow and steady at the back of the pack. My goal for this race was to be DFL (Dead Flipping Last) but finish. This was my second attempt at covering 100 miles; I ended up running 81 miles.  I learned a lot about myself and running, here’s my story.

Preparation
I’ve been doing trail running since 2016. I have previously done 50 km and 50 mile mountain runs along with a lot of hiking experience. My previous 100 mile shot had been to run 69 miles at the Badger Mountain Challenge in March, 2018. Coming into Bryce 100, I had learned a number of lessons from my Badger Mountain 100 experience:

  1.  Importance of electrolytes – used a 1/2 electrolyte, 1/2 water mixture
  2.  Dealing with blisters early – pre-taped my heels
  3. Keeping up with nutrition – especially after 50 miles
  4. Increase my vertical training – more mountain runs

For the Bryce Canyon race, at every aid station I used a 1/2 electrolyte, 1/2 water mixture to fill my 1.5 liter bladder in my pack. Also, I would eat a little solid food at each stop.  I should mention that I have achalasia; this disease makes it challenging for me to swallow.  I need to take extra time eating and drinking.

Since the Bryce 100 is at high altitude (7000 to 9500 feet) I knew that acclimation was important. In addition, I wanted to acclimate to the dry heat and cold nights. I spent five days prior to the race at the North Rim of the Grand canyon, camping and hiking at 8900 feet.  Since I had rolled an ankle about 3 weeks before the race on one of my mountain runs, I wanted to do a shakedown, so my friend Brenda and I hiked the Grand Canyon rim to rim four days before the race. (Yes, I know that’s a strange way to taper….)

Race Day
I started the Bryce 100 with my friend Roger. We were up at 0345, had some coffee and a little food.start

The race started in the dark at 0500. It was nice and cool, Roger and I joined the back of the pack. We ran slow on the downhills and walked the uphill sections. We reached the Blubber Creek aid station, 12 miles out,  at mid-morning. Here we earned a bonus mile, since we both walked past the well-signed turn while sending out text messages to update our status. We realized our error after about 10 minutes. We backtracked to the correct turn and got back on the course.

 

We were running along the Paunsaugunt Plateau, with lots of beautiful geology to see. This was one of the most scenic runs I’d ever done. Roger and I went through several more aid stations together as we climbed higher in the heat of the day.

2018-06-01 11.52.33
Roger running south on Paunsaugunt Plateau

We reached the Pink Cliffs aid station at mile 29.5 (9400 feet) in the early afternoon. This was a great aid station: enthusiastic volunteers, good food, and a phenomenal view of southern Utah and northern Arizona. This was ourturnaround point on the course, now we would head north again.

2018-06-01 14.56.54
View from Pink Cliffs, I’m ready to tackle some more miles.

I did a rest and refuel. Roger showed up and was feeling dismal; he was being affected by a cold. We decided to split up at this point and I continued on the pleasant downhill sections.

As I ran and walked uphills, I had an interesting conversation with Paul, a fellow engineer from the Bay area. I felt pretty decent as I arrived at the Mile 39 aid station, although I did have to force myself to have some electrolytes and food.  I headed north in the late afternoon; along the way chatting with Marcelo from Florida. I reached the Blubber Creek aid station (mile 47) near dusk. I had a problem with my headlamp, couldn’t seem to get it to provide white light; only green or blue.  I switched to my backup headlamp and trudged on into the growing darkness.

The next few sections were lots of uphill slogging in the dark alternating with some roads. I did run into a couple of runners in this section who were stopped but said they were OK. The trail was very well-marked. I was behind schedule a bit, there was a cutoff at mile 53 (Grim Reaper) which I made with an hour to spare. On the road before the Blue Fly aid station, I ran and walked with Justin from North Carolina.  The last section up to the Blue Fly aid station felt brutal. I was surprised to pass a few people.

Reached the Blue Fly aid station (mile 57) at 1 AM. I changed my clothes here and refueled. I was ahead of the cutoff and feeling a bit down. It was very tempting to stop here BUT the aid station workers were very positive and encouraging.   I left Blue Fly moving slow and steady.

On the road, it was getting cold and I was glad I had some warm gloves. I felt pretty decent although I was occasionally having some double vision. This seems to happen to me after about 20 hours of exercise. I’d experienced it before. I also had a few mild hallucinations, for example, what I thought was an owl on the ground turned out to be a reflective marker. Around mile 61, a volunteer riding on an ATV checked on me. I told him I was OK and would just keep going. He had another runner on the back who must have dropped on the road.

Came into the mile 65 aid station at 4 AM. There were four volunteers here from the Gnarly Hydrate product. They fed me broth and electrolyte. I warmed up here and recharged from the positive energy of these aid station volunteers. When I was leaving, another runner came in; she was very cold and said she might drop. I decided it was time to leave and push on towards mile 73.  Started out on more roads, through a ranch road as the sun came up. I had to stop to deal with chafing and take my blood pressure medication. I still had a bit of double vision but kept moving. I crossed into a burned forest and was feeling pretty terrible about mile 71. At that point I came across Marcelo and we walked into the mile 73 aid station together. Marcelo gave me a good lift in spirits along with some nice encouragement from the aid station captain.

Departed about 0745 for the Thunder Mountain section of the race. It was beautiful, with lots of the characteristic geology of Bryce Canyon.  This was a gradual climb up followed by a long descent. At around mile 75, I had a bout of diarrhea and was feeling blah. I forced myself to drink electrolytes. At this point, some of the 50 mile runners were passing me; many had encouraging remarks. Also, began to hallucinate a bit more. I would see people that looking like they were working near the trail. When I got closer the people turned into tree stumps! Had one more bout of diarrhea and decided I better ask my friends to meet me at mile 80. Slowly slogged down beautiful Thunder Mountain, my thought was: “Just keep moving.”

My friend Linda hiked up to mile 79 and walked with me into the Mile 80 aid station. I was abit out of it, for example, forgot to use my sunscreen but luckily Linda caught that. I started seeing some other 100 milers on the trail heading back to the finish.  I hit the chair and thought about whether to continue.  Discussed my options with my friends Brenda, Linda, and Roger. I still had some “gas in the tank” but the bouts of diarrhea were dismal. I decided I was done.  Could I have gone on? Yes, I think I had at least 5 more miles left in me. Do I regret stopping? Nope, I learned much and have decided I’ll try another 100 next year with some better preparation.

 

Recovery
After the run, had a nice shower at the Bryce Canyon general store, followed by some salad, coffee, and ice cream. After that, we went to the Best Western in Cedar City, Utah for a couple of days. The highlight was the hot tub and free breakfast… each day I had first and second breakfast. I recovered very well, I was able to go hike at Cedar Breaks with the gang the next day.

2018-06-03 11.31.10
Brenda, me, Linda and Roger at Cedar Breaks the day after the Bryce 100

  • What Went Well
    • Help form my friends
    • Acclimation to altitude, cold, and heat
    • Hill work to get ready
    • Pretape known blister areas
    • Use of electrolyte (Tailwind and Gnarly)
    • Ankle recovery – glad I did Rim to Rim Grand Canyon shakedown
    • Use of Avenza map software especially at night
    • Controlled most chafing
    • Sun protection (long sleeve shirt, hat with drape, gloves)
    • Attitude – mostly positive
    • Great aid stations (especially miles 29.5, 57, 65, and 73)
  • Things to Improve
    • Too slow, need to train to go a little faster
    • Sometimes attitude was down
    • Better head lamp
    • Diarrhea
    • Pacer plan

Acknowledgements
While we run a race like this alone; we don’t get to the starting line alone. First, my wife Mary Ellen put up with my crazy training for this race, never would have got there without her. My friend Roger had the inspiration to propose the Bryce 100; I was glad I said yes.  I did lots of training and adventures with Roger and Linda. Learned a lot about ultrarunning from my friend Jeff; he provided both basic knowledge and inspiration the last few years. My friend Mark provided me some valuable advice after the Badger 100, especially about nutrition and electrolytes. Brenda joined me in acclimating before the run and some post-race adventures; she was crazy enough to take off for 17 days in the Southwest.  Finally, my inspiring brother Gerard who said: “Focus on how far you’ve come from the starting line – not the distance to the finish.”