U. of Chicago COVID-19 interactive data visualization tool

[2G]

The U. of Chicago has taken my infection rate metric (confirmed cases per million population) to the next level: interactive county-by-county visualization. This shows hot spots that state level data miss. Hot spots are counties with high infection rate that are surrounded by counties with elevated infection rates (this filters outliers, isolated counties with a high infection rate). The U. of Chicago is using the same data source that I have been using in my personal data analysis (1point3acres.com).

https://news.uchicago.edu/story/state-level-data-misses-growing-coronavirus-hot-spots-us-including-south

The tool allows you to drill down to county level data that includes:
1. Confirmed case count.
2. COVID-19 deaths.
3. Licensed hospital beds
4. Daily new data (cases, deaths, infection rate, death rate)

https://geodacenter.github.io/covid/map.html

The country-wide view can select from 10 different metrics:
1. Confirmed count
2. Confirmed count per 10k population
3. Confirmed count per licensed bed (this is well above 1 for the NYC area)
4. Death count
5. Death count per 10k population
6. Death count per Confirmed count
7-10. Daily metrics

All of this data is available by date since the start of the crisis. You can also compare state-only data to country data to see the dramatic difference between the two.

[Dan Marotta]

Very nice!Â* Thanks for sharing.

On 4/6/2020 12:07 PM, 2G wrote:
> The U. of Chicago has taken my infection rate metric (confirmed cases per million population) to the next level: interactive county-by-county visualization. This shows hot spots that state level data miss. Hot spots are counties with high infection rate that are surrounded by counties with elevated infection rates (this filters outliers, isolated counties with a high infection rate). The U. of Chicago is using the same data source that I have been using in my personal data analysis (1point3acres.com).
>
> https://news.uchicago.edu/story/state-level-data-misses-growing-coronavirus-hot-spots-us-including-south
>
> The tool allows you to drill down to county level data that includes:
> 1. Confirmed case count.
> 2. COVID-19 deaths.
> 3. Licensed hospital beds
> 4. Daily new data (cases, deaths, infection rate, death rate)
>
> https://geodacenter.github.io/covid/map.html
>
> The country-wide view can select from 10 different metrics:
> 1. Confirmed count
> 2. Confirmed count per 10k population
> 3. Confirmed count per licensed bed (this is well above 1 for the NYC area)
> 4. Death count
> 5. Death count per 10k population
> 6. Death count per Confirmed count
> 7-10. Daily metrics
>
> All of this data is available by date since the start of the crisis. You can also compare state-only data to country data to see the dramatic difference between the two.

--
Dan, 5J

[Andy Blackburn[_3_]]

Nice site.

I've been looking at a lot of data. The problem with the confirmed case counts is that they seem to be substantially gated by availability of tests. The rates of confirmed cases by age bracket vary by 40x (older people get a lot more tests, because they get sicker - but I doubt millennia's are 1/40th as likely to get infected - they just don't get symptomatic - or sick enough to justify a test).

So, rates of infection based on under-testing alone are possibly 5x what's reported overall. Then there is the time lag from infection to test result which has averaged around 11 days (7 days to become symptomatic enough to go to the doctor and 4 days to get a test result and biome a confirmed case) , so the reported rates of infection are whatever the daily growth rate is to the 11th power. That can be up to 25x in the rapid growth phase, but probably more like 2-3x now. Once everything peaks the time lag effects are more manageable, but still the mortality rate is a highly confounded metric because the denominator is so uncertain.

Once we get broad, randomly distributed antibody tests we will know a lot better what's going on. In the mean time take a grain of salt on the reliability of the data - depending on which data you are looking at.

Andy Blackburn
9B


On Monday, April 6, 2020 at 11:07:16 AM UTC-7, 2G wrote:
> The U. of Chicago has taken my infection rate metric (confirmed cases per million population) to the next level: interactive county-by-county visualization. This shows hot spots that state level data miss. Hot spots are counties with high infection rate that are surrounded by counties with elevated infection rates (this filters outliers, isolated counties with a high infection rate). The U. of Chicago is using the same data source that I have been using in my personal data analysis (1point3acres.com).
>
> https://news.uchicago.edu/story/state-level-data-misses-growing-coronavirus-hot-spots-us-including-south
>
> The tool allows you to drill down to county level data that includes:
> 1. Confirmed case count.
> 2. COVID-19 deaths.
> 3. Licensed hospital beds
> 4. Daily new data (cases, deaths, infection rate, death rate)
>
> https://geodacenter.github.io/covid/map.html
>
> The country-wide view can select from 10 different metrics:
> 1. Confirmed count
> 2. Confirmed count per 10k population
> 3. Confirmed count per licensed bed (this is well above 1 for the NYC area)
> 4. Death count
> 5. Death count per 10k population
> 6. Death count per Confirmed count
> 7-10. Daily metrics
>
> All of this data is available by date since the start of the crisis. You can also compare state-only data to country data to see the dramatic difference between the two.

[2G]

On Monday, April 6, 2020 at 6:45:59 PM UTC-7, Andy Blackburn wrote:
> Nice site.
>
> I've been looking at a lot of data. The problem with the confirmed case counts is that they seem to be substantially gated by availability of tests. The rates of confirmed cases by age bracket vary by 40x (older people get a lot more tests, because they get sicker - but I doubt millennia's are 1/40th as likely to get infected - they just don't get symptomatic - or sick enough to justify a test).
>
> So, rates of infection based on under-testing alone are possibly 5x what's reported overall. Then there is the time lag from infection to test result which has averaged around 11 days (7 days to become symptomatic enough to go to the doctor and 4 days to get a test result and biome a confirmed case) , so the reported rates of infection are whatever the daily growth rate is to the 11th power. That can be up to 25x in the rapid growth phase, but probably more like 2-3x now. Once everything peaks the time lag effects are more manageable, but still the mortality rate is a highly confounded metric because the denominator is so uncertain.
>
> Once we get broad, randomly distributed antibody tests we will know a lot better what's going on. In the mean time take a grain of salt on the reliability of the data - depending on which data you are looking at.
>
> Andy Blackburn
> 9B
>
>
> On Monday, April 6, 2020 at 11:07:16 AM UTC-7, 2G wrote:
> > The U. of Chicago has taken my infection rate metric (confirmed cases per million population) to the next level: interactive county-by-county visualization. This shows hot spots that state level data miss. Hot spots are counties with high infection rate that are surrounded by counties with elevated infection rates (this filters outliers, isolated counties with a high infection rate). The U. of Chicago is using the same data source that I have been using in my personal data analysis (1point3acres.com).
> >
> > https://news.uchicago.edu/story/state-level-data-misses-growing-coronavirus-hot-spots-us-including-south
> >
> > The tool allows you to drill down to county level data that includes:
> > 1. Confirmed case count.
> > 2. COVID-19 deaths.
> > 3. Licensed hospital beds
> > 4. Daily new data (cases, deaths, infection rate, death rate)
> >
> > https://geodacenter.github.io/covid/map.html
> >
> > The country-wide view can select from 10 different metrics:
> > 1. Confirmed count
> > 2. Confirmed count per 10k population
> > 3. Confirmed count per licensed bed (this is well above 1 for the NYC area)
> > 4. Death count
> > 5. Death count per 10k population
> > 6. Death count per Confirmed count
> > 7-10. Daily metrics
> >
> > All of this data is available by date since the start of the crisis. You can also compare state-only data to country data to see the dramatic difference between the two.

Agreed that there is a major limitation on the confirmed cases data, but it is all we have to work with. I expected a quantum jump in this as testing became more available, but that didn't happen, just a very smooth exponential increase. This must be because "confirmed" must include doctor's diagnosis as well as positive test results. On the other hand, deaths are deaths, so you can rely on that data.

Tom

[Andy Blackburn[_3_]]

Yup.

Only the mortality data offers reliable trending and it's lagged 2-3 weeks.

I think one of the reasons why we may be seeing the peak in cases a bit later than the initial models predicted is we are seeing a fairly smooth increase in testing availability - adding a bit of a false growth rate. At some point we will be able to test everyone who presents for medical attention - which ought to be a fairly steady proportion of overall cases and so okay as a (still lagged) view of new case trending.

As the testing lag/backlog closes we should have a reasonably decent sense of trending. It won't be until we get broad and randomized testing (antibody tests to look at all infections since the beginning and RNA tests to get rapid identification of current infections for contract tracing and rapid isolation). That we will have any detailed sense of what is really going on - or an ability to contain new outbreaks - which will likely be many.

Life is unlikely to return to normal until sometime in 2021 with (hopefully) a broadly available vaccine. Until then we will all be sitting in a tinder box with a bunch of lit candles and a handful of fly swatters.

Until then we play with Excel spreadsheets and hope.

Andy

On Monday, April 6, 2020 at 9:26:47 PM UTC-7, 2G wrote:
> Agreed that there is a major limitation on the confirmed cases data, but it is all we have to work with. I expected a quantum jump in this as testing became more available, but that didn't happen, just a very smooth exponential increase. This must be because "confirmed" must include doctor's diagnosis as well as positive test results. On the other hand, deaths are deaths, so you can rely on that data.
>
> Tom

[Tony[_5_]]

Hope is not a strategy ;)

[[email protected]]

>
> Only the mortality data offers reliable trending and it's lagged 2-3 weeks.
>

Excel's daily ratio between new and active cases seems useful as well. It has been going down from 35% to 10% as the testing ratios are going up. That seems a reliable indicator that the transmission rate is going down.

In other words, the tinder box with only the candles lit is looking good and trending possible.

If behavioral changes to lower R are more than just a fly swatter, then perhaps minimal risks to R like flying solo later in the summer or Fall.

[[email protected]]

We should about break even this year, pneumonia deaths have fallen to almost zero this winter.

[Craig Reinholt]

On Tuesday, April 7, 2020 at 12:05:53 AM UTC-7, Andy Blackburn wrote:
> Yup.
>
> Only the mortality data offers reliable trending and it's lagged 2-3 weeks.
>
> I think one of the reasons why we may be seeing the peak in cases a bit later than the initial models predicted is we are seeing a fairly smooth increase in testing availability - adding a bit of a false growth rate. At some point we will be able to test everyone who presents for medical attention - which ought to be a fairly steady proportion of overall cases and so okay as a (still lagged) view of new case trending.
>
> As the testing lag/backlog closes we should have a reasonably decent sense of trending. It won't be until we get broad and randomized testing (antibody tests to look at all infections since the beginning and RNA tests to get rapid identification of current infections for contract tracing and rapid isolation). That we will have any detailed sense of what is really going on - or an ability to contain new outbreaks - which will likely be many.
>
> Life is unlikely to return to normal until sometime in 2021 with (hopefully) a broadly available vaccine. Until then we will all be sitting in a tinder box with a bunch of lit candles and a handful of fly swatters.
>
> Until then we play with Excel spreadsheets and hope.
>
> Andy
>
> On Monday, April 6, 2020 at 9:26:47 PM UTC-7, 2G wrote:
> > Agreed that there is a major limitation on the confirmed cases data, but it is all we have to work with. I expected a quantum jump in this as testing became more available, but that didn't happen, just a very smooth exponential increase. This must be because "confirmed" must include doctor's diagnosis as well as positive test results. On the other hand, deaths are deaths, so you can rely on that data.
> >
> > Tom

One immediate problem is the accuracy of the current testing. One our club members has CV. Multiple doctors giving him medical care say he had all the symptoms. He was extremely sick in ICU (and feeling better now). However, 2 tests came back negative. After talking to his health care providers about the false negatives, their response was it appears to be at a rate of about 20-25%. As you say, better and broader testing down the road is needed, but the current numbers are "in the books".

[[email protected]]

On Tuesday, April 7, 2020 at 9:18:38 AM UTC-5, wrote:
> We should about break even this year, pneumonia deaths have fallen to almost zero this winter.

gregg..., Where did you get your information from, or are you just messing with us? What do you think people are dying from during these influenza and SARS-related pandemics? Victims are put on ventilators because of....? Really, give us a few citations to support your claim please. Here's one from me.

https://www.rochesterregional.org/news/2020/01/flu-season-2020

[[email protected]]

On Tuesday, April 7, 2020 at 9:54:43 AM UTC-5, Craig Reinholt wrote:
> On Tuesday, April 7, 2020 at 12:05:53 AM UTC-7, Andy Blackburn wrote:
> > Yup.
> >
> > Only the mortality data offers reliable trending and it's lagged 2-3 weeks.
> >
> > I think one of the reasons why we may be seeing the peak in cases a bit later than the initial models predicted is we are seeing a fairly smooth increase in testing availability - adding a bit of a false growth rate. At some point we will be able to test everyone who presents for medical attention - which ought to be a fairly steady proportion of overall cases and so okay as a (still lagged) view of new case trending.
> >
> > As the testing lag/backlog closes we should have a reasonably decent sense of trending. It won't be until we get broad and randomized testing (antibody tests to look at all infections since the beginning and RNA tests to get rapid identification of current infections for contract tracing and rapid isolation). That we will have any detailed sense of what is really going on - or an ability to contain new outbreaks - which will likely be many.
> >
> > Life is unlikely to return to normal until sometime in 2021 with (hopefully) a broadly available vaccine. Until then we will all be sitting in a tinder box with a bunch of lit candles and a handful of fly swatters.
> >
> > Until then we play with Excel spreadsheets and hope.
> >
> > Andy
> >
> > On Monday, April 6, 2020 at 9:26:47 PM UTC-7, 2G wrote:
> > > Agreed that there is a major limitation on the confirmed cases data, but it is all we have to work with. I expected a quantum jump in this as testing became more available, but that didn't happen, just a very smooth exponential increase. This must be because "confirmed" must include doctor's diagnosis as well as positive test results. On the other hand, deaths are deaths, so you can rely on that data.
> > >
> > > Tom
>
> One immediate problem is the accuracy of the current testing. One our club members has CV. Multiple doctors giving him medical care say he had all the symptoms. He was extremely sick in ICU (and feeling better now). However, 2 tests came back negative. After talking to his health care providers about the false negatives, their response was it appears to be at a rate of about 20-25%. As you say, better and broader testing down the road is needed, but the current numbers are "in the books".

Glad to hear he's on the mend. Curious as to what makes them think he had COVID beside symptoms that could arise from other infections? There are indeed both false negatives (potentially more deadly) than false positives, but it isn't the oft-referred to litmus diagnostic test that will add most value, it's the serologic blood test that shows someone had the infection, but is asymptomatic. The swab test is just a snapshot, one timepoint, that indicates current infection (one would have to be tested every few days for the data to be more valuable). IMO

[Nick Kennedy[_3_]]

Interesting, with data, Article:

https://www.nytimes.com/interactive/2020/04/03/us/coronavirus-stay-home-rich-poor.html?utm_source=pocket-newtab

If you have money its much easier to stay home, If your in the lower income brackets your going to work.

[[email protected]]

On Tuesday, April 7, 2020 at 11:02:15 AM UTC-4, wrote:
> On Tuesday, April 7, 2020 at 9:18:38 AM UTC-5, wrote:
> > We should about break even this year, pneumonia deaths have fallen to almost zero this winter.
>
> gregg..., Where did you get your information from, or are you just messing with us? What do you think people are dying from during these influenza and SARS-related pandemics? Victims are put on ventilators because of....? Really, give us a few citations to support your claim please. Here's one from me.
>
> https://www.rochesterregional.org/news/2020/01/flu-season-2020
Corona virus cures pneumonia. Look people around and think for yourselves.
https://www.barnhardt.biz/2020/04/06/textbook-book-cooking-or-do-we-actually-believe-that-coronacold-magically-eradicates-pneumonia/

[[email protected]]

> Corona virus cures pneumonia. Look people around and think for yourselves..
> https://www.barnhardt.biz/2020/04/06/textbook-book-cooking-or-do-we-actually-believe-that-coronacold-magically-eradicates-pneumonia/

Apples and oranges. Pneumonia on a death certificate is a clinical diagnosis that doesn't specify the pathogen whereas Coronavirus pneumonia gives more specific information - they are still dying from pneumonia and the specific complications thereof associated with Covid-19.

[Andy Blackburn[_3_]]

Dude,

People almost certainly are catching fewer communicable diseases of all kinds due to the lockdown (look no further than the Kinsa dataset on seasonally adjusted fever instances) so that's not especially new news. I assume you were just joking when you called it a "cure" for C19.

I can't speak to the source of the pneumonia data. It comes from a blogger who has some pretty bizarre views, including refusing to pay taxes for years (leading to her bankruptcy after getting caught), and a belief that there is some sort of conspiracy to underreport being a "sodomite" as a COVID-19 co-morbidity. Her self-written bio is a sort of Unabomber manifesto of jumbled thoughts. Sort of comical and ominous at the same time.

https://www.barnhardt.biz/about/

Be careful about your reading materials while sheltered at home - it can make you paranoid. :-)

Be safe,

Andy


On Tuesday, April 7, 2020 at 8:47:45 AM UTC-7, wrote
> >
> > https://www.rochesterregional.org/news/2020/01/flu-season-2020
> Corona virus cures pneumonia. Look people around and think for yourselves..
> https://www.barnhardt.biz/2020/04/06/textbook-book-cooking-or-do-we-actually-believe-that-coronacold-magically-eradicates-pneumonia/

[jfitch]

On Tuesday, April 7, 2020 at 7:18:38 AM UTC-7, wrote:
> We should about break even this year, pneumonia deaths have fallen to almost zero this winter.

I only recently discovered that 5G cell towers cause corona virus. It was on the internet so it must be true.

The conflation of discovery rate with infection rate has been pandemic in this pandemic, among the media, health, and government officials alike. Only widespread antibody testing will reveal what has happened and is happening.. Beyond immediate care, that should be top priority. Basically we are flying in fog with bad instruments.

[[email protected]]

On Tuesday, April 7, 2020 at 12:32:08 PM UTC-4, wrote:
> > Corona virus cures pneumonia. Look people around and think for yourselves.
> > https://www.barnhardt.biz/2020/04/06/textbook-book-cooking-or-do-we-actually-believe-that-coronacold-magically-eradicates-pneumonia/
>
> Apples and oranges. Pneumonia on a death certificate is a clinical diagnosis that doesn't specify the pathogen whereas Coronavirus pneumonia gives more specific information - they are still dying from pneumonia and the specific complications thereof associated with Covid-19.

The baseline pneumonia deaths would still be there if they weren't reclassified as chinkiepox kills.

[[email protected]]

Here is the guidance we've been given by the CDC on death certificates when reporting COVID-related fatalities.[e.g., "Acute respiratory distress syndrome due to or as a consequence of Pneumonia due to or as a consequence of COVID-19."

https://www.cdc.gov/nchs/data/nvss/vsrg/vsrg03-508.pdf

https://health.hawaii.gov/vitalrecords/guidance-for-certifying-covid-19-deaths/

We spend too much time correcting misinformation than informing.

[2G]

On Tuesday, April 7, 2020 at 12:05:53 AM UTC-7, Andy Blackburn wrote:
> Yup.
>
> Only the mortality data offers reliable trending and it's lagged 2-3 weeks.
>
> I think one of the reasons why we may be seeing the peak in cases a bit later than the initial models predicted is we are seeing a fairly smooth increase in testing availability - adding a bit of a false growth rate. At some point we will be able to test everyone who presents for medical attention - which ought to be a fairly steady proportion of overall cases and so okay as a (still lagged) view of new case trending.
>
> As the testing lag/backlog closes we should have a reasonably decent sense of trending. It won't be until we get broad and randomized testing (antibody tests to look at all infections since the beginning and RNA tests to get rapid identification of current infections for contract tracing and rapid isolation). That we will have any detailed sense of what is really going on - or an ability to contain new outbreaks - which will likely be many.
>
> Life is unlikely to return to normal until sometime in 2021 with (hopefully) a broadly available vaccine. Until then we will all be sitting in a tinder box with a bunch of lit candles and a handful of fly swatters.
>
> Until then we play with Excel spreadsheets and hope.
>
> Andy
>
> On Monday, April 6, 2020 at 9:26:47 PM UTC-7, 2G wrote:
> > Agreed that there is a major limitation on the confirmed cases data, but it is all we have to work with. I expected a quantum jump in this as testing became more available, but that didn't happen, just a very smooth exponential increase. This must be because "confirmed" must include doctor's diagnosis as well as positive test results. On the other hand, deaths are deaths, so you can rely on that data.
> >
> > Tom

Actually mortality data is skewed, too. I listened to Dr. Deborah Birx today explain that many deaths are being attributed to COVID-19 when they may be another cause such as ordinary flu. Seasonal flu deaths are way down year-over-year which makes you wonder about this.

Tom

[2G]

On Tuesday, April 7, 2020 at 5:13:30 AM UTC-7, Tony wrote:
> Hope is not a strategy ;)

No, but it is a stress reliever.

Tom

[2G]

On Tuesday, April 7, 2020 at 9:33:11 AM UTC-7, jfitch wrote:
> On Tuesday, April 7, 2020 at 7:18:38 AM UTC-7, wrote:
> > We should about break even this year, pneumonia deaths have fallen to almost zero this winter.
>
> I only recently discovered that 5G cell towers cause corona virus. It was on the internet so it must be true.
>
> The conflation of discovery rate with infection rate has been pandemic in this pandemic, among the media, health, and government officials alike. Only widespread antibody testing will reveal what has happened and is happening. Beyond immediate care, that should be top priority. Basically we are flying in fog with bad instruments.

THANK GOD! I heard that they cause sterility.

[Martin Gregorie[_6_]]

On Tue, 07 Apr 2020 21:26:18 -0700, 2G wrote:

> Actually mortality data is skewed, too. I listened to Dr. Deborah Birx
> today explain that many deaths are being attributed to COVID-19 when
> they may be another cause such as ordinary flu. Seasonal flu deaths are
> way down year-over-year which makes you wonder about this.
>
There's another cause of mortality skew as well: during a pandemic
hospital staff can be busy enough that actually recording/reporting
deaths can be delayed by more than a day: its simply seen as not so
important as looking after patients. This is happening here (UK) so
probably happens in others countries as well.

Source: it was mentioned in a discussion about COVID-19 statistics on Tim
Harford's "More or Less" program on BBC Radio 4 this morning.

This repeats tomorrow night at 21:00 BST or can be downloaded:
https://www.bbc.co.uk/programmes/p02nrss1/episodes/downloads

Tim Harford is an economist. His programs look at the statistics of real-
life events and what can skew them, so this program, which covers CV
statistics and the probability of other solar systems to ours existing in
our galaxy, is fairly typical in content and analysis.


--
Martin | martin at
Gregorie | gregorie dot org