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Re: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

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thompnickson2

Re: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

Friammers,

Jim Girard and I have been having a conversation about the period between the bent curve and the vaccine. His responses have been fascinating, but in some particulars, are more technical than this old rejected English major can parse. I therefore wanted you all to get the benefit of them and, perhaps, explain them to me. Jim gave me permission to forward the correspondence to you.

So right now I have contact with 5 other people, my “pod”. (Think whales) I walk a mile or so a day in the neighborhood, designating one “clean” hand (for adjusting my glasses, etc.) and one “dirty” hand for touching anything outside my own person, on those rare occasions that I have to. I scrub both hands when I get back. I go once to the store a week (at most). I put on a parka, hood, glasses, face mask, wear gloves, and I carry alcohol with me for rubbing down any surface I touch and sterilizing the gloves afterwards. I back off from any encounter with a human being closer from 6 feet. Assume that all members of my pod follow these same rules. Which of these rules do you see us relaxing after the bent curve?

I went to the SouthWest airlines website to see what comfort they might offer me for flying back to MA for the summer. Lots of talk of bottles of purel on every counter and in every waiting area. Apparently, some procedures have been altered concerning the verification of documents at check in to minimize actual exchange of physical objects. No snack service. They make a big deal about how they hose down the airplanes every night, but there is no attempt to screen passengers either at checkin or at boarding. Is this sufficient? Are flight attendants getting sick? Does anybody know?

Any way. Sorry to run on. Look at what Jim has to say, and help me to understand it.

NIck

Nicholas Thompson

Emeritus Professor of Ethology and Psychology

Clark University

[hidden email]

https://wordpress.clarku.edu/nthompson/

From: [hidden email] <[hidden email]>
Sent: Wednesday, April 8, 2020 1:44 PM
To: [hidden email]
Subject: RE: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

Nick,

Can't find the harvard study now, it was brought up at Friam 2(?) weeks ago. The upshot I think was more than just avoiding overloading the medical system - it was amplifying herd immunity via quite selective quarantining/distancing and reducing the overall number of cases, not just spreading them out.

Consider: Let's say we develop an antibody test that is widely available. And we determine the contagion is dependent on asymptomatic carriers, and we can roughtly guess based on priors (age, health, etc.). A selective drawdown and reimposal of restrictions at different times & places could effectively amplify the herd immunity such that the R-effective for the virus is below 1, so it dies out and total cases over time is reduced. I'm not even sure the antibody test is necessary.

Separately, thinking about it more, the prior system I described would result in a true sin/cosine wave. There is the added effect of the delay between the forcing function (quarantining/distancing) and the resulting cases.

I'm thinking that any kind of feedback of the forcing function being monotonically increasing and negative to the resulting cases will cause some kind of oscillation, FWIW.

In engineering systems theory, this would be an underdamped system. An overdamped system would result in an asymptote. Not sure what in the real contagion world would correspond to overdamped, but some kind of asymptotic behavior is what seems to happen with most contagion.

Thinking more, it really it should be a complex/agent-based analysis, with the tension in the model similarly between the quarantining/distancing and the delayed results of cases/deaths. Various levels and accuracy of testing could be programmed in as well. Who needs a thesis?

And anyway, where is episims/transims or their progeny in all this?

Feel free to share this. My new position will overwhelm me for a while - unfortunately no real time to spend congitating on this.

be well Nick.

-Jim

-------- Original Message --------
Subject: RE: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data
From: <[hidden email]>
Date: Tue, April 07, 2020 9:03 pm
To: <[hidden email]>
Jim

Well, I think the state will be unsteady in any case, rather like Steve G;s spot fire analogy. Every once in a while a spark will land from TX of CA. We have to be able jump on it and surround it As long as the capacity to identify and contain is robust, most people in nm can go about their business most of the time. But do we even have such a robust strategy and would our society tolerate it.

Is the Harvard strategy what I think of as the “leak” strategy. You leak new cases into the community at a steady low rate until heard immunity is established? People die, but relatively few because the hospitals are ready for them. I think such a strategy might make sense in a world in which no vaccine is coming. But let’s say a million people die of this thing which means, presumably, that a hundred million caught it. That still leaves 200 million for the virus to eat. Think how few people it took to sustain the recent measles epidemic.

Jim, can I forward this correspondence to the list? I think it’s fruitful and I would like to know that others think.

N

Nicholas Thompson
Emeritus Professor of Ethology and Psychology
Clark University
[hidden email]
https://wordpress.clarku.edu/nthompson/

From: [hidden email] <[hidden email]>
Sent: Tuesday, April 7, 2020 8:45 PM
To: [hidden email]
Cc: [hidden email]
Subject: RE: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

All good questions Nick

I tend to believe there's usually more than one way to handle these things (well, there are at least two: shutdown and tracing/quarantine) The harvard study to manage herd immunity is another, but that may qualify as your "unsteady state"

From an engineering systems standpoint, the unsteady state could be caused by a system that accelerates proportional to the negative of position. If position is the number of positive cases being found, and acceleration would be the second derivitive of that. Does lockdown correspond to the 2nd derivitive of cases? Have to think about that.

-Jim
-------- Original Message --------
Subject: RE: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data
From: <[hidden email]>
Date: Tue, April 07, 2020 6:06 pm
To: <[hidden email]>
Cc: <[hidden email]>
Jim,

Can I get you to ponder a bit on the unsteady state that will obtain between curve flattening and vaccine/herd immunity? Do agree that that state cannot be reached until we can get the number of new cases a day down to that number that can be contact-traced and contact isolated. So using santa fe as an example, how many contact tracings and contact isolations do you think the City public health system can handle in a day, week, etc. So let’s say I get the disease tomorrow but don’t get tested for three day. So in that time I am within six feet of three people and I so tell the public health department. Do the police go and “arrest” those three people and stick them in a motel somewhere? And where do they take me?

I really don’t see the conditions under which social distancing could be eased UNTIL there is a vaccine.

Those two new cases in China, today. What happened to the patients and what happened to the n people they happened to have run into since they themselves became infectious?

Nick

Nicholas Thompson
Emeritus Professor of Ethology and Psychology
Clark University
[hidden email]
https://wordpress.clarku.edu/nthompson/

From: [hidden email] <[hidden email]>
Sent: Tuesday, April 7, 2020 5:44 PM
To: Tom Johnson <[hidden email]>; Steve Smith <[hidden email]>; Nick Thompson <[hidden email]>
Subject: RE: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

In the 20 days or so I've been using it, I've noticed a single problem, which was fixed within a couple of hours.

Of course, I'm only looking at a handful of countries in the daily reports.

-Jim
-------- Original Message --------
Subject: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data
From: Tom Johnson <[hidden email]>
Date: Tue, April 07, 2020 4:34 pm
To: Jim Girard <[hidden email]>, Steve Smith
<[hidden email]>, Nick Thompson <[hidden email]>

============================================
Tom Johnson - [hidden email]
Institute for Analytic Journalism   --     Santa Fe, NM USA
505.577.6482(c)               505.473.9646(h)
NM Foundation for Open Government
Check out It's The People's Data
============================================

---------- Forwarded message ---------
From: Thomas Wilburn <[hidden email]>
Date: Tue, Apr 7, 2020 at 4:25 PM
Subject: Re: [NICAR-L] AP/Johns Hopkins COVID-19 data
To: <[hidden email]>

Yeah, I have to say that we've been working with the JHU data for a few weeks now and it has just been a total nightmare in terms of consistency and organization. All due respect to that team but it's clear that they were not really expecting the attention and have been scrambling to keep up. If you can use a dataset that has been better normalized and organized, you should.

Thomas

-----Original Message-----
From: Dan Nguyen <[hidden email]>
To: [hidden email]
Sent: Tue, 07 Apr 2020 4:57 PM
Subject: Re: [NICAR-L] AP/Johns Hopkins COVID-19 data

You mean the timeseries/daily counts found here?
https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data

I think every covid-19 dataset is subject to the same real-world
limitations of testing availability (nevermind accuracy/timeliness of
bureaucratic reporting). That said, for my own U.S. analysis, I've switched
to the NYT repo for now, which has daily counts at the state and county
level: https://github.com/nytimes/covid-19-data/

I did do a spotcheck of a couple NYC counts, and in at least one instance,
NYT did a better job of reflecting a completed day's count, i.e. recording
the afternoon city report for a day, rather than an early morning. But
overall, I wouldn't be surprised if both datasets were accurate enough,
when averaged over several weeks of data points. For me, the thing I like
about the NYT's data is that it's already normalized and tidied by standard
conventions.

-Dan

On Tue, Apr 7, 2020 at 4:23 PM Anthony Cave <[hidden email]> wrote:

> Just curious, how are y'all using the AP Johns Hopkins COVID-19 data, if
> at all?
>
> It seems like you'd need an editor's note/margin of error, given that it's
> noted that the data relies on testing availability as opposed to true
> infection rates.
>
> Was just curious what others thought about it.
>
> Thanks,
>
> Anthony Cave
> Investigative Producer/Reporter, KXAN News
> 305-467-7121 (cell)
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gepr

Re: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

My guess would be parka, hood, glasses, 6' distance, and limited trips will go first because they have very limited effect. If you doubt masks have an effect, then these should be so doubtful as to be silly. But sanitation and aerosol/spittle measures have clear support.

The conversation you forwarded seems to reduce the complex vector space of transmission into some kind of coarse, unidimensional forcing function. (Isolation and quarantine are anything but unidimensional. So, the analogy between them and dampening is stretched.) But if we were to do that, then limited trips would be the most salient, I think. My guess is an periodic driver (and measurement) of stay-at-home orders would be reasonably effective. What we've done so far with "essential businesses" is too coarse. E.g. I can go to the liquor store, but my arborist can't come prune my trees ... way more than 6' away from any other human. I can go to a restaurant and order a tossed salad to take home, but can't go play frisbee with a dog in a public park.

Many businesses already have particular days of the week they're open. It seems reasonable to relax the closures periodically, say everything's open on Fri and Sat, but closed every other day. That driving signal would surely show up in the number of confirmed cases.

On 4/8/20 2:21 PM, [hidden email] wrote:
> I walk a mile or so a day in the neighborhood, designating one “clean” hand (for adjusting my glasses, etc.) and one “dirty” hand for touching anything outside my own person, on those rare occasions that I have to. I scrub both hands when I get back. I go once to the store a week (at most). I put on a parka, hood, glasses, face mask, wear gloves, and I carry alcohol with me for rubbing down any surface I touch and sterilizing the gloves afterwards. I back off from any encounter with a human being closer from 6 feet. Assume that all members of my pod follow these same rules. Which of these rules do you see us relaxing after the bent curve?

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Steve Smith

Re: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

I think there are two issues... what your risk of becoming infected and
what is your contribution to the larger risk of infecting others. The
first is linear with the number of people you encounter, the percentage
of the population currently infected and the amount of de-coupling your
various measures provide.
> My guess would be parka, hood, glasses, 6' distance, and limited trips will go first because they have very limited effect. If you doubt masks have an effect, then these should be so doubtful as to be silly. But sanitation and aerosol/spittle measures have clear support.

I agree that parka and hood are much lower on the list than even glasses
which is lower on the list than 6' distances. Limited trips are pretty
much linear with the number of trips, dwell time and how congested your
destinations are.

An observant person will notice that in the right light (my favorite is
early morning and late afternoon sunshine coming through a window into a
dark room) how much we all "Spray it when we Say it".   Just today I
tried working on my laptop on my outdoor deck and as the sun began to
*hit* my screen I realized acutely how many thousand of microdroplets
had hit my screen... *probably* many of them while I was "spraying it"
into my Skype/Zoom chat sessions this last few weeks. So I *do* think
6' distance (especially while talking animatedly to one another) is a
good idea...   unless the speaker has some kind of mouth covering.

> The conversation you forwarded seems to reduce the complex vector space of transmission into some kind of coarse, unidimensional forcing function. (Isolation and quarantine are anything but unidimensional. So, the analogy between them and dampening is stretched.) But if we were to do that, then limited trips would be the most salient, I think. My guess is an periodic driver (and measurement) of stay-at-home orders would be reasonably effective. What we've done so far with "essential businesses" is too coarse. E.g. I can go to the liquor store, but my arborist can't come prune my trees ... way more than 6' away from any other human. I can go to a restaurant and order a tossed salad to take home, but can't go play frisbee with a dog in a public park.
Our Governor just closed liquor stores (but you can still buy liquor at
the grocery)... and I was left wondering if she couldn't have re-opened
drive-through windows.   We shut ours down recently enough (<20 years?)
that many still have the windows, though probably currently stacked over
with cases of liquor.     I'm not sure if "coarse" is as relevant as
improper dimension for binning?
> Many businesses already have particular days of the week they're open. It seems reasonable to relax the closures periodically, say everything's open on Fri and Sat, but closed every other day. That driving signal would surely show up in the number of confirmed cases.
I'm not sure why you imply reducing the number of days would reduce
infections?   I wondered if maybe opening grocery stores 24 hours a day
might reduce the average number of encounters between customers and give
those with a low risk-tolerance better times to shop (e.g. 6AM) I do
know that some big-box stores reserve the first couple of hours of
opening for the elderly++ which makes sense to me... overnight
sanitizing cleaning and a more homogenous population more likely to be
careful and less likely to be asymptomatic?
>> I walk a mile or so a day in the neighborhood, designating one “clean” hand (for adjusting my glasses, etc.) and one “dirty” hand for touching anything outside my own person, on those rare occasions that I have to. I scrub both hands when I get back. I go once to the store a week (at most). I put on a parka, hood, glasses, face mask, wear gloves, and I carry alcohol with me for rubbing down any surface I touch and sterilizing the gloves afterwards. I back off from any encounter with a human being closer from 6 feet. Assume that all members of my pod follow these same rules. Which of these rules do you see us relaxing after the bent curve?

Nick - I like your use of Pod vs Herd or Pack...

I think you will find that as time goes on there will be more
confidence in what to do to fly safely. Masks and hand hygiene (gloves
and/or washing) would go a long way.

I think waiting for two things is key: 1) wait until the numbers on
this end go down... until the peak of new infections has passed... but
maybe not until the general restrictions have relaxed...   2) waiting
until your destination is ready to recieve your pod IF you get infected
in the process.... don't be showing up just as they are trying to figure
out which parking lot or church to put new cases into.
https://covid19.healthdata.org/united-states-of-america/new-mexico   is
a good resource for seeing when the "estimated peak resource-use" is
which correlates with "acute infection"...   two gestation-periods (2
weeks?) after a peak might be a safeish time to travel (unless everyone
else uses the same calculus)?   Symptomatics will be isolated or under
care (still) and it might still be too soon for relaxed isolation to be
yielding a fresh peak?   Don't take my (specific) word for it, but maybe
you get the gist?

You might also consider driving as an option? If your Pod can "graze
on groceries" for the few days and trust the limited open motel rooms
you will need (2-3 nights?) to be sanitized, that *might* be less
exposure than a couple three airports/planes with hundreds of travelers
from all-over the place?   I suspect fuel nozzles contaminated with
gasoline and in the air/sun are more "safe" than most things you could
touch... bathroom stops include access to soap/water, backed up with
alcohol wipes in the car?    One way car rentals may be available...
there are even one-way RV (relocation) rentals (still?!) afoot, though
they won't get you all the way to your destination... just the longer
part of the haul...

I'm not sure when you normally try to migrate, but my estimates above
imply early May may be a "dip"?   Again, I'm just winging it here for
example, not as a strong recommendation.

- Steve

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thompnickson2

Re: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

Steve?

I like the very specific reflections on travel timing at the bottom of what is below.

I've lost track entirely of whose reflections they were, but I am grateful for them.

Nick

Nicholas Thompson
Emeritus Professor of Ethology and Psychology
Clark University
[hidden email]
https://wordpress.clarku.edu/nthompson/

-----Original Message-----
From: Friam <[hidden email]> On Behalf Of Steven A Smith
Sent: Wednesday, April 8, 2020 7:12 PM
To: [hidden email]
Subject: Re: [FRIAM] Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

I think there are two issues... what your risk of becoming infected and what is your contribution to the larger risk of infecting others. The first is linear with the number of people you encounter, the percentage of the population currently infected and the amount of de-coupling your various measures provide.
> My guess would be parka, hood, glasses, 6' distance, and limited trips will go first because they have very limited effect. If you doubt masks have an effect, then these should be so doubtful as to be silly. But sanitation and aerosol/spittle measures have clear support.

I agree that parka and hood are much lower on the list than even glasses which is lower on the list than 6' distances. Limited trips are pretty much linear with the number of trips, dwell time and how congested your destinations are.

An observant person will notice that in the right light (my favorite is early morning and late afternoon sunshine coming through a window into a dark room) how much we all "Spray it when we Say it". Just today I tried working on my laptop on my outdoor deck and as the sun began to
*hit* my screen I realized acutely how many thousand of microdroplets had hit my screen... *probably* many of them while I was "spraying it"
into my Skype/Zoom chat sessions this last few weeks. So I *do* think 6' distance (especially while talking animatedly to one another) is a good idea... unless the speaker has some kind of mouth covering.

> The conversation you forwarded seems to reduce the complex vector space of transmission into some kind of coarse, unidimensional forcing function. (Isolation and quarantine are anything but unidimensional. So, the analogy between them and dampening is stretched.) But if we were to do that, then limited trips would be the most salient, I think. My guess is an periodic driver (and measurement) of stay-at-home orders would be reasonably effective. What we've done so far with "essential businesses" is too coarse. E.g. I can go to the liquor store, but my arborist can't come prune my trees ... way more than 6' away from any other human. I can go to a restaurant and order a tossed salad to take home, but can't go play frisbee with a dog in a public park.
Our Governor just closed liquor stores (but you can still buy liquor at the grocery)... and I was left wondering if she couldn't have re-opened drive-through windows. We shut ours down recently enough (<20 years?) that many still have the windows, though probably currently stacked over with cases of liquor. I'm not sure if "coarse" is as relevant as improper dimension for binning?
> Many businesses already have particular days of the week they're open. It seems reasonable to relax the closures periodically, say everything's open on Fri and Sat, but closed every other day. That driving signal would surely show up in the number of confirmed cases.
I'm not sure why you imply reducing the number of days would reduce infections? I wondered if maybe opening grocery stores 24 hours a day might reduce the average number of encounters between customers and give those with a low risk-tolerance better times to shop (e.g. 6AM) I do know that some big-box stores reserve the first couple of hours of opening for the elderly++ which makes sense to me... overnight sanitizing cleaning and a more homogenous population more likely to be careful and less likely to be asymptomatic?
>> I walk a mile or so a day in the neighborhood, designating one
>> “clean” hand (for adjusting my glasses, etc.) and one “dirty” hand for touching anything outside my own person, on those rare occasions that I have to. I scrub both hands when I get back. I go once to the store a week (at most). I put on a parka, hood, glasses, face mask, wear gloves, and I carry alcohol with me for rubbing down any surface I touch and sterilizing the gloves afterwards. I back off from any encounter with a human being closer from 6 feet. Assume that all members of my pod follow these same rules. Which of these rules do you see us relaxing after the bent curve?

Nick - I like your use of Pod vs Herd or Pack...

I think you will find that as time goes on there will be more confidence in what to do to fly safely. Masks and hand hygiene (gloves and/or washing) would go a long way.

I think waiting for two things is key: 1) wait until the numbers on this end go down... until the peak of new infections has passed... but maybe not until the general restrictions have relaxed... 2) waiting until your destination is ready to recieve your pod IF you get infected in the process.... don't be showing up just as they are trying to figure out which parking lot or church to put new cases into. https://covid19.healthdata.org/united-states-of-america/new-mexico is a good resource for seeing when the "estimated peak resource-use" is which correlates with "acute infection"... two gestation-periods (2
weeks?) after a peak might be a safeish time to travel (unless everyone else uses the same calculus)? Symptomatics will be isolated or under care (still) and it might still be too soon for relaxed isolation to be yielding a fresh peak? Don't take my (specific) word for it, but maybe you get the gist?

You might also consider driving as an option? If your Pod can "graze on groceries" for the few days and trust the limited open motel rooms you will need (2-3 nights?) to be sanitized, that *might* be less exposure than a couple three airports/planes with hundreds of travelers from all-over the place? I suspect fuel nozzles contaminated with gasoline and in the air/sun are more "safe" than most things you could touch... bathroom stops include access to soap/water, backed up with alcohol wipes in the car? One way car rentals may be available... there are even one-way RV (relocation) rentals (still?!) afoot, though they won't get you all the way to your destination... just the longer part of the haul...

I'm not sure when you normally try to migrate, but my estimates above imply early May may be a "dip"? Again, I'm just winging it here for example, not as a strong recommendation.

- Steve

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gepr

Re: Fwd: [NICAR-L] AP/Johns Hopkins COVID-19 data

In reply to this post by Steve Smith

Sorry. I didn't imply that _reopening_ businesses for a couple of days/week would reduce infections. I was talking in the context of Jim's comments about underdampening. I feel like reopening businesses for 2 fixed days per week (and only those 2 days, same days for every business) would *drive* infections in a way that we could then distinguish from the noise.

I haven't seen any more data since they first started saying median 5.1 days from infection to symptoms. But 7-2 = 5. 8^) It might produce a cleaner signal to do it every 2 weeks. But that might be too difficult for us plebes. Our recycling and garbage services are on alternating 2 week schedules. So, here, we could simply add the alerts to our app ("RecycleCoach", I think it's called). But back in Portland, both garbage and recycling came every week.

On 4/8/20 6:11 PM, Steven A Smith wrote:
> I'm not sure why you imply reducing the number of days would reduce
> infections?

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