Team Toad Data Groupies - Skew-Normal Epidemic Modeling

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New model run, January 16, 2020, US cases and deaths

Daily new cases 7-day average 1/15/21

  I updated the US cases and US deaths using data posted today for 1/15/2021, and ran new curve fits for both.

The new case model (left, red) is 11% higher than the pre-Christmas model (left, green), with a peak about one week later (Jan 1 at 223,655 before and Jan 8 at 247,792 in the new model).

The new death model (right, red) is actually 4% lower than the pre-Christmas model (right, green), with a peak one day earlier (Jan 16 at 3,404 before and Jan 15 at 3,269 in the new model).
 
Daily deaths 7-day average 1/15/21


I note that the pre-Christmas model nailed both the timing and height of the third wave peak. The trailing 7-day average of deaths has been dropping for three days, now.

Because of the likelihood of underreporting cases during the Christmas and New Year's holidays, I used an upper-bound least-squares scoring function for today's curve fitting run. Basically the actual squared error was used if the model under-predicted the data point, but only 25% of the distance was used if the model over-predicted the data point. This modification was only used for data after November 16th, to allow for missing data from Thanksgiving on.

This change in scoring causes the fitted curve to skim the top of the data points, and to ignore the valleys.

The R-squared measures are still reported using standard least-squares (in this case 0.9682 for cases and 0.9633 for deaths).

The CDC is reporting that 10,595,866 people have received their first dose of the vaccine and 1,610,524 people have received two doses (CDC vaccine tracker).

My hope is that as more people are vaccinated, the model curves will start to over-predict and the skew will reduce in future model runs.

As always, please note that this is a retrospective data model, and can neither predict nor prohibit any future waves of virus outbreak. See the about page for data sources, disclosures, and disclaimers.

Graph update, January 13, 2020, US cases and deaths

Daily new cases 7-day average 1/12/21

  Added US cases and US deaths using data posted today for 1/12/2021.

Cases (left) are above the trend line from the pre-Christmas model run, but they are steady for the last 5 days (using a 7-day trailing average).

Deaths (right) are higher, but are also growing less rapidly, and have just reached the pre-Christmas model trend line.
 
Daily deaths 7-day average 1/12/21



Graph update, January 9, 2020, US cases and deaths, vaccinations

Daily new cases 7-day average 1/08/21

  Added US cases and US deaths using data posted today for 1/08/2021.

Cases (left) are above the trend line from the pre-Christmas model run. That probably indicates a new acceleration in the spread of the virus.

Deaths (right) are higher, but are not yet above the pre-Christmas model trend line.
 
Daily deaths 7-day average 1/08/21



I will run a new model at the end of next week, but there's still not enough good data to offset the numbers that were clearly depressed by the Christmas and New Year's holidays.

The CDC reports that 6,688,231 have received at least one dose of the vaccine so far (CDC Covid Data Tracker > vaccines).

I will be curious to see how vaccinating the population will affect these curves. My expectation is that we'll start to see decreasing skew for the third wave, and a much smaller or non-existant fourth wave.

As always, nothing predicts or prevents a new wave.

Graph update, January 7, 2020, US cases and deaths, CFR

Added US cases and US deaths using data posted today for 1/06/2021.

Cases are back to the trend line established before the Christmas holiday. The public expectation is that cases will climb sharply from here, assuming lots of family interaction over Christmas. Remember this model just fits the historical data, and has no knowledge of social interaction rates per se.

As always, nothing predicts or prevents a new wave.

Also added a new estimate for Case Fatality Rate (CFR) showing 1.224% for the last 21 days (shown at right). That corresponds to one death per 81 cases, an improvement over 1 death in 70 cases last month.
 
Estimated US Case Fatality Rate (CFR)

Also added charts showing the top six (6) states compared by daily deaths per million, and a heat map showing new confirmed cases by state the last 21 days. See the graphs page for explanation.

Deaths per million per day, top 6 states
Detail chart showing Fall 2020
Deaths per million per day, top 6 states
Same chart but showing the whole year 2020
New cases last 21 days, by state
not normalized by population
US CFR

Graph update, December 31, 2020, new outlier in Turkey

Update the case and death charts for the United States, the World ex-China, and I added a new pair of charts for the World ex-China ex-USA. See the Graphs Page

Notes: the World charts now have an outlier on 12/10/2020 from Turkey.

"Turkey has recorded nearly 1.75 million cases since the start of the pandemic, the health ministry said on Thursday, after releasing a significantly lower toll including only patients requiring medical care.

Officials had previously only published the number of coronavirus "patients" but last month returned to publishing the total number of cases." (Medical xPress, 12/10/2020).

Graph Update, December 26, 2020

The first version of the Data Groupies web site is up. The first thing to check out is the Theory page, which describes how I use the skew-normal distribution to model the cases and deaths in the coronavirus epidemic.
 

Facebook Posts

Before Christmas all the Data Groupies content was on Facebook. Here are all the links about coronavirus to all the posts I've made since January 29th.

January 29, 2020


February 14, 2020
February 24, 2020
February 26, 2020


March 4, 2020
March 14, 2020
March 17, 2020
March 17, 2020
March 22, 2020
March 28, 2020


April 3, 2020
April 8, 2020
April 14, 2020
April 22, 2020
April 22, 2020


May 2, 2020
May 5, 2020
May 9, 2020
May 14, 2020
May 16, 2020, part 1 of 3
May 16, 2020, part 2 of 3
May 16, 2020, part 3 of 3
May 17, 2020
May 19, 2020
May 22, 2020
May 22, 2020
May 29, 2020


June 6, 2020
June 13, 2020
June 22, 2020
June 27, 2020


July 4, 2020
July 11, 2020
July 18, 2020
July 25, 2020


August 1, 2020
August 8, 2020
August 9, 2020
August 29, 2020
August 30, 2020
August 31, 2020


September 5, 2020
September 10, 2020
September 14, 2020, fitting double wave
September 19, 2020
September 27, 2020
September 28, 2020
September 28, 2020


October 3, 2020
October 3, 2020
October 4, 2020
October 4, 2020
October 7, 2020
October 12, 2020
October 17, 2020
October 18, 2020
October 18, 2020
October 25, 2020
October 27, 2020
October 31, 2020
October 31, 2020


November 4, 2020
November 8, 2020
November 14, 2020
November 28, 2020


December 9, 2020
December 11, 2020
December 12, 2020
December 13, 2020
December 19, 2020
December 24, 2020



Last updated 16-Jan-2021 by fuzzy@lazytoad.com, from Lazy Toad Ranch
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