1. Caveats and Comments
1
Overview:
This is my analysis, not Stanford’s. My goal is to understand the trajectory of COVID. It is not confidential and can be freely shared. The R program code is
available at https://github.com/StevenLShafer/COVID19/. The daily analysis are available at https://1drv.ms/u/s!AuOyHP_aTIy7rowrt2AjGpWm_frnEQ?e=KBcNbh.
You are welcome to use the R code on GitHub for any purpose.
I am attempting to keep the analysis and commentary apolitical. I am now including partisan lean as a metric to help understand the epidemic. I occasionally point
out misrepresentations by government officials. I occasionally point out where government recommendations have placed Americans at increasing risk.
I try to provide a daily update in the morning, except Sundays. My analysis my be delayed by my clinical responsibilities as a Stanford anesthesiologist.
There is a lot of information on the figures. If something isn’t clear, please see the explanation on slide 2.
Data sources:
• USA Case Data: https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv
• USA Death Data: https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_US.csv
• USA Testing and Hospitalization Data: https://raw.githubusercontent.com/COVID19Tracking/covid-tracking-data/master/data/states_daily_4pm_et.csv
• Global Case Data: https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv
• Global Death Data: https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv
• Global Testing Data: https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv
• Mobility Data: https://www.gstatic.com/covid19/mobility/Global_Mobility_Report.csv
• Partisan Lean: MIT Election Data and Science Lab: https://doi.org/10.7910/DVN/VOQCHQ/HEIJCQ
• Ensemble Model: https://github.com/reichlab/covid19-forecast-hub/raw/master/data-processed/COVIDhub-ensemble/2020-xx-xx-COVIDhub-ensemble.csv
Models:
1. Future projections of case numbers are based on the Gompertz function (https://en.wikipedia.org/wiki/Gompertz_function): log 𝑐𝑢𝑚𝑢𝑙𝑎𝑡𝑖𝑣𝑒 𝑐𝑎𝑠𝑒𝑠 =
𝑐𝑢𝑟𝑟𝑒𝑛𝑡 𝑐𝑎𝑠𝑒𝑠 + 𝑚𝑎𝑥𝑖𝑚𝑢𝑚 𝑐𝑎𝑠𝑒𝑠 − 𝑐𝑢𝑟𝑟𝑒𝑛𝑡 𝑐𝑎𝑠𝑒𝑠 1 − 𝑒−𝑘 𝑡 . This is a naïve asymptotic model. k is the rate constant, such that log(2) / k = time to 50%
rise. t is the number of days. Wikipedia The Gompertz function is estimated from the last 3 weeks of data for cumulative cases (red dots in the figures).
Deaths are predicted from a log linear regression of deaths over the past 21 days. For the US, and individual states, I am also including the 98% prediction
interval from the COVID-19 Forecast Hub (https://covid19forecasthub.org/).
2. The rate of change in daily cases and deaths is the slope of delta cases / day over the last 14 days, divided by the average number of cases.
Locations
The locations for the modeling are where Pamela and I have family and friends, locations of interest to friends and colleagues, or countries in the news (e.g.,
China, South Korea, Sweden, Brazil) or with significant economic impact on the United States (e.g., Japan, Canada, Mexico). Locations are easy to add.
Stay safe, well, resilient, and kind.
Steve Shafer
steven.shafer@Stanford.edu
2. 2,586,092
152,804
1
10
100
1,000
10,000
100,000
1,000,000
10,000,000
100,000,000
Actual(points)/Predicted(line)
Phase
Pre-Model
Modeled
Deaths
Tests
USA projection as of 2020-05-27
0
10,000
20,000
30,000
0
2,000
4,000
6,000
Cases/Day
Deaths/Day
Cases: 1,662,302 (32,123) -- Deaths: 98,220 (829) -- Case Mortality: 5.9% -- Daily Change in Cases: -0.5%
Explanation of the Figures
2
Brown dots:
cumulative tests
Red dots: cumulative cases
used to estimate Gompertz
function, presently set to last
3 weeks
Red line: predicted cumulative
cases based on the Gompertz
function estimated from the red
dots
Red number: total cases
on June 30th, based on
the Gompertz function
estimated from the red
dots
Black number: total
Deaths on July 31th,
based on log-linear
regression of the past
21 days
Black line: predicted
cumulative deaths, based
on a log linear regression
of deaths over past 21
days.
Axis for deaths / day, usually
1/10th of the axis for cases /
day on the left side of the
figure.
Green line: linear regression
over 8 days, used to calculate
percent increase / decrease
(see below)
Daily change in cases,
calculated as the slope of the
green line (above left) /
number of new cases
yesterday.
Case mortality:
cumulative deaths
/ cumulative cases.
Cases / day calculated
from cumulative cases
used to estimate the
Gompertz function
Cases / day calculated
from cumulative cases
not used to estimate the
Gompertz function
Deaths / day,
axis is on the left
Blue line: today
Blue dots: cumulative cases not
used to estimate Gompertz
function
Cumulative cases
(yesterday’s cases)
and cumulative deaths
(yesterday’s deaths)
Axis for cases / day.
Axis for deaths / day
appears to the right.
Geographic
location
Date of analysis,
also shown as
blue vertical line
below
Purple wedge: 98% ensemble
prediction interval from COVID-19
Forecast Hub (USA and US
States only)
9. Average new cases over past 7 days
Israel
Argentina
Spain
Peru
Colombia
Brazil
Iraq
France
Libya
Paraguay
USA
Chile
CzechRepublic
Bolivia
India
DominicanRepublic
Netherlands
Belgium
Ukraine
Romania
Morocco
Austria
Switzerland
Hungary
Mexico
Honduras
UnitedKingdom
Portugal
Guatemala
Denmark
Venezuela
Nepal
Russia
SouthAfrica
Iran
Philippines
SaudiArabia
Italy
Slovakia
Sweden
Tunisia
Turkey
Greece
Canada
Belarus
Bulgaria
Azerbaijan
Germany
Uzbekistan
Kyrgyzstan
Jordan
Indonesia
ElSalvador
Poland
Bangladesh
Ethiopia
Serbia
Zambia
Algeria
Zimbabwe
Finland
Guinea
Kazakhstan
Tajikistan
Angola
USA
None
1 in 10,000
1 in 5,000
1 in 3,333
1 in 2,500
1 in 2,000
1 6 11 16 21 26 31 36 41 46 51 56 61 66
Rank
Averagecases/day
Average new cases over past 7 days
Excludes countries with population < 5,000,000
2020-09-12 Summary: 9
12. Average daily deaths over past 7 days
Ecuador
Bolivia
Argentina
Peru
Colombia
Mexico
Brazil
Chile
Iraq
USA
Paraguay
SouthAfrica
Libya
Romania
Iran
Israel
DominicanRepublic
Honduras
Spain
Guatemala
Ukraine
SaudiArabia
Morocco
India
Bulgaria
Russia
Turkey
ElSalvador
Belarus
Philippines
Indonesia
Australia
Kazakhstan
France
Venezuela
Portugal
CzechRepublic
Nepal
Greece
Algeria
Poland
Azerbaijan
Belgium
Austria
Bangladesh
Tunisia
Uzbekistan
Serbia
Italy
Sweden
Egypt
Ethiopia
UnitedKingdom
Zimbabwe
Angola
Netherlands
Syria
Zambia
Hungary
Togo
Jordan
Switzerland
Kenya
Canada
Japan
USA
None
1 in 100,000
1 in 50,000
1 in 33,333
1 in 25,000
1 6 11 16 21 26 31 36 41 46 51 56 61 66
Rank
Averagedeaths/day
Average daily deaths over past 7 days
Excludes countries with population < 5,000,000
2020-09-12 Summary: 12
14. Change in New Cases per Day
New cases are:
Increasing > +3%
Increasing between +1% and +3%
No Change (-1% to +1%)
Decreasing between -1% and -3%
Decreasing > -3%
New cases by state as of 2020-09-12
2020-09-12 Summary: 14
15. Cases as a Percent of Peak Cases
HI TX FL
OK LA MS AL GA
AZ NM KS AR TN NC SC DC
CA UT CO NE MO KY WV VA MD DE
OR NV WY SD IA IN OH PA NJ CT RI
WA ID MT ND MN IL MI NY MA
WI VT NH
AK ME
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
PercentofPeak
Daily Cases as a Percent of Peak Cases
2020-09-12 Summary: 15
16. Change in New Deaths per Day
New deaths are:
Increasing > +0.5%
Increasing between +0.1% and +0.5%
No Change (-0.1% to +0.1%)
Decreasing between -0.1% and -0.5%
Decreasing > -0.5%
New deaths by state as of 2020-09-12
2020-09-12 Summary: 16
17. Deaths as a Percent of Peak Deaths
HI TX FL
OK LA MS AL GA
AZ NM KS AR TN NC SC DC
CA UT CO NE MO KY WV VA MD DE
OR NV WY SD IA IN OH PA NJ CT RI
WA ID MT ND MN IL MI NY MA
WI VT NH
AK ME
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
0
25
50
75
100
PercentofPeak
Daily Deaths as a Percent of Peak Deaths
2020-09-12 Summary: 17
18. Change in cases vs change in deaths
AL
AK
AZ
AR
CA
CO
CTDE
DC
FL
GA
HI
ID
IL
INIA
KS
KY
LA
ME
MD
MA
MIMN
MS
MO
MT
NE
NV
NH
NJ
NM
NY
NC
ND
OH
OK
OR
PA
RI
SC
SD
TN
TX
UT
VT
VA
WA
WV
WI
WY-6
-3
0
3
6
-20 -10 0
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days as of 2020-09-12
2020-09-12 Summary: 18
19. Total US COVID-19 Cases
California
Texas
Florida
NewYork
Georgia
Illinois
Arizona
NewJersey
NorthCarolina
Tennessee
Louisiana
Pennsylvania
Alabama
Ohio
Virginia
Massachusetts
SouthCarolina
Michigan
Maryland
Indiana
Missouri
Mississippi
Wisconsin
Minnesota
Washington
Iowa
Nevada
Arkansas
Oklahoma
Colorado
Utah
Kentucky
Connecticut
Kansas
Nebraska
Idaho
Oregon
NewMexico
RhodeIsland
Delaware
SouthDakota
NorthDakota
DistrictofColumbia
WestVirginia
Hawaii
Montana
NewHampshire
Alaska
Maine
Wyoming
Vermont
0
200,000
400,000
600,000
800,000
1 6 11 16 21 26 31 36 41 46 51
Rank
Totalcases
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Cases
p masks as of July 20, 2020: 0.46, p governor: 0.82. NB: association != causation.
2020-09-12 Summary: 19
20. Total US COVID-19 Cases
Louisiana
Florida
Mississippi
Arizona
Alabama
Georgia
SouthCarolina
Tennessee
Nevada
Texas
Iowa
NewYork
Arkansas
NewJersey
RhodeIsland
DistrictofColumbia
Illinois
Nebraska
Idaho
NorthDakota
California
Delaware
Maryland
Massachusetts
SouthDakota
Utah
NorthCarolina
Oklahoma
Kansas
Missouri
Virginia
Indiana
Connecticut
Wisconsin
Minnesota
NewMexico
Kentucky
Michigan
Ohio
Pennsylvania
Colorado
Washington
Alaska
Montana
Hawaii
Wyoming
Oregon
WestVirginia
NewHampshire
Maine
Vermont
None
1 in 100
1 in 50
1 in 33
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalCases
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Cases
p masks as of July 20, 2020: 0.43, p governor: 0.063. NB: association != causation.
2020-09-12 Summary: 20
21. Average US COVID-19 cases over the past
7 days
NorthDakota
SouthDakota
Iowa
Missouri
Oklahoma
Arkansas
Alabama
Tennessee
Wisconsin
Illinois
SouthCarolina
Kansas
Mississippi
Georgia
Nebraska
Louisiana
Idaho
Kentucky
Utah
Texas
Florida
Indiana
NorthCarolina
Delaware
Virginia
Hawaii
Alaska
Montana
Nevada
Minnesota
Maryland
WestVirginia
California
RhodeIsland
Ohio
Michigan
Wyoming
DistrictofColumbia
Arizona
Pennsylvania
Washington
Colorado
Oregon
NewMexico
NewJersey
Connecticut
NewYork
NewHampshire
Maine
Vermont
Massachusetts
None
1 in 10,000
1 in 5,000
1 in 3,333
1 6 11 16 21 26 31 36 41 46 51
Rank
NewCases/Day
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 cases over the past 7 days
p masks as of July 20, 2020: 0.002, p governor: 0.0051. NB: association != causation.
2020-09-12 Summary: 21
22. Total US COVID-19 Deaths
NewYork
NewJersey
California
Texas
Florida
Massachusetts
Illinois
Pennsylvania
Michigan
Georgia
Arizona
Louisiana
Connecticut
Ohio
Maryland
Indiana
SouthCarolina
NorthCarolina
Virginia
Mississippi
Alabama
Tennessee
Washington
Colorado
Minnesota
Missouri
Nevada
Iowa
Wisconsin
RhodeIsland
Kentucky
Arkansas
Oklahoma
NewMexico
DistrictofColumbia
Delaware
Kansas
Oregon
Nebraska
NewHampshire
Utah
Idaho
WestVirginia
SouthDakota
NorthDakota
Maine
Montana
Hawaii
Vermont
Alaska
Wyoming
0
10,000
20,000
30,000
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalDeaths
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Deaths
p masks as of July 20, 2020: 0.066, p governor: 0.26. NB: association != causation.
2020-09-12 Summary: 22
23. Total US COVID-19 Deaths
NewJersey
NewYork
Massachusetts
Connecticut
Louisiana
RhodeIsland
Mississippi
DistrictofColumbia
Arizona
Michigan
Illinois
Maryland
Delaware
Pennsylvania
Georgia
SouthCarolina
Florida
Indiana
Texas
Alabama
Nevada
NewMexico
Iowa
Ohio
California
Minnesota
Colorado
NewHampshire
Virginia
Arkansas
Tennessee
NorthCarolina
Missouri
Washington
Idaho
Kentucky
Nebraska
Oklahoma
NorthDakota
Wisconsin
SouthDakota
Kansas
WestVirginia
Utah
Montana
Oregon
Maine
Vermont
Wyoming
Hawaii
Alaska
None
1 in 2,000
1 in 1,000
1 in 667
1 in 500
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalDeaths
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Deaths
p masks as of July 20, 2020: 0.032, p governor: 0.3. NB: association != causation.
2020-09-12 Summary: 23
24. Average US COVID-19 deaths over the past
7 days
Mississippi
SouthCarolina
Florida
Louisiana
Georgia
Texas
Tennessee
Arkansas
Idaho
Iowa
Nevada
Missouri
Arizona
NorthCarolina
Alabama
Montana
California
NorthDakota
Nebraska
Kansas
Kentucky
RhodeIsland
Massachusetts
Illinois
Oklahoma
WestVirginia
Indiana
Ohio
NewMexico
Hawaii
Michigan
Minnesota
DistrictofColumbia
SouthDakota
Wisconsin
Maryland
Pennsylvania
Delaware
Virginia
Oregon
Washington
NewJersey
Utah
Colorado
Alaska
Connecticut
NewYork
Wyoming
NewHampshire
Maine
Vermont
None
1 in 1,000,000
1 in 500,000
1 in 333,333
1 in 250,000
1 in 200,000
1 in 166,667
1 6 11 16 21 26 31 36 41 46 51
Rank
Deaths/Day
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 deaths over the past 7 days
p masks as of July 20, 2020: 0.2, p governor: 0.03. NB: association != causation.
2020-09-12 Summary: 24
25. Daily testing trends
HI TX FL
OK LA MS AL GA
AZ NM KS AR TN NC SC DC
CA UT CO NE MO KY WV VA MD DE
OR NV WY SD IA IN OH PA NJ CT RI
WA ID MT ND MN IL MI NY MA
WI VT NH
AK ME
min
max
min
max
min
max
min
max
min
max
min
max
min
max
min
max
Dailytestingfrommintomax
Daily testing trends from min to max
Line = Friedman's supersmoother
2020-09-12 Summary: 25
26. Change in daily tests over past 14 days
Maine
Hawaii
Michigan
Illinois
Wyoming
Connecticut
Washington
Oklahoma
Massachusetts
SouthCarolina
Arkansas
Minnesota
RhodeIsland
NorthCarolina
Kentucky
Kansas
NewYork
Delaware
Mississippi
NewJersey
Indiana
SouthDakota
Nebraska
Iowa
Ohio
Missouri
NewHampshire
Utah
Texas
Virginia
Oregon
Montana
Tennessee
DistrictofColumbia
WestVirginia
Pennsylvania
Colorado
Georgia
Maryland
NewMexico
Louisiana
Idaho
Alabama
Florida
Wisconsin
Arizona
California
NorthDakota
Nevada
Alaska
Vermont
-4.0
-2.0
0.0
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeindailytests(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in daily tests over past 14 days
p masks as of July 20, 2020: 0.14, p governor: 0.13. NB: association != causation.
2020-09-12 Summary: 26
28. Percent of Positive COVID Tests
Arizona
Mississippi
Alabama
Florida
Idaho
SouthCarolina
Texas
Nevada
Georgia
Kansas
Iowa
SouthDakota
Nebraska
Missouri
Indiana
Arkansas
Utah
Maryland
Pennsylvania
Colorado
Louisiana
Virginia
RhodeIsland
Delaware
NorthCarolina
Tennessee
Oklahoma
NorthDakota
Minnesota
Wisconsin
Massachusetts
NewJersey
Kentucky
California
Illinois
Ohio
Wyoming
Washington
NewYork
Oregon
DistrictofColumbia
Hawaii
Connecticut
Michigan
NewHampshire
NewMexico
Montana
WestVirginia
Alaska
Maine
Vermont
0.0
5.0
10.0
15.0
1 6 11 16 21 26 31 36 41 46 51
Rank
PercentofPositiveTests
Masks
No
Yes
Governor
aa
Democratic
Republican
Percent of Positive COVID Tests
p masks as of July 20, 2020: 0.018, p governor: 0.003. NB: association != causation.
2020-09-12 Summary: 28
29. Positive fraction trends
HI TX FL
OK LA MS AL GA
AZ NM KS AR TN NC SC DC
CA UT CO NE MO KY WV VA MD DE
OR NV WY SD IA IN OH PA NJ CT RI
WA ID MT ND MN IL MI NY MA
WI VT NH
AK ME
min
max
min
max
min
max
min
max
min
max
min
max
min
max
min
max
Fractionpositivefrommintomax
Positive fraction trends from min to max
2020-09-12 Summary: 29
30. Change in positive tests over past 14 days
NorthDakota
WestVirginia
SouthDakota
Montana
Kansas
Missouri
Wisconsin
Kentucky
Alabama
Oklahoma
Iowa
Alaska
Minnesota
Idaho
Utah
Arkansas
Nebraska
Tennessee
Indiana
Florida
Hawaii
Oregon
Virginia
Nevada
Mississippi
Pennsylvania
SouthCarolina
Georgia
Wyoming
Maryland
NewMexico
Louisiana
Colorado
Delaware
Ohio
Texas
Michigan
NorthCarolina
NewHampshire
Arizona
California
Illinois
Washington
RhodeIsland
DistrictofColumbia
Vermont
NewJersey
NewYork
Connecticut
Maine
Massachusetts
-1.0
0.0
1.0
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeinpositivetests(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in positive tests over past 14 days
p masks as of July 20, 2020: 0.0053, p governor: 0.017. NB: association != causation.
2020-09-12 Summary: 30
31. Change in tests vs change in positive tests
AL
AK
AZ
AR
CA
CO
CT
DE
DC
FL
GA
HI
ID
IL
IN
IA
KSKY
LA
ME
MD
MA
MI
MN
MS
MO
MT
NE
NV
NH
NJ
NM
NY
NC
ND
OH
OK
OR
PA
RI
SC
SD
TN
TX
UT
VT
VA
WA
WV
WI
WY
-1.0
-0.5
0.0
0.5
1.0
-4 -2 0
Change in tests (%/day)
Changeinpositivetests(%/day)
Change in tests vs change in positive tests last 14 days as of 2020-09-12
Size of the state font reflects the number of deaths over the past 7 days.
2020-09-12 Summary: 31
32. Current hospitalizations as a percent of peak
since FebruaryKansas
Montana
WestVirginia
Missouri
NorthDakota
Hawaii
SouthDakota
Alaska
Nebraska
Kentucky
Wyoming
Oklahoma
Iowa
Arkansas
Tennessee
NorthCarolina
Idaho
Virginia
Georgia
Utah
Ohio
Mississippi
Indiana
Oregon
Alabama
Wisconsin
Washington
SouthCarolina
California
Minnesota
Nevada
Louisiana
NewMexico
Texas
Illinois
Florida
RhodeIsland
Colorado
Maryland
DistrictofColumbia
Delaware
Michigan
Pennsylvania
Arizona
Maine
Massachusetts
NewHampshire
NewJersey
Vermont
Connecticut
NewYork
0
30
60
90
1 6 11 16 21 26 31 36 41 46 51
Rank
Hospitalizations(%ofpeak)
Masks
No
Yes
Governor
aa
Democratic
Republican
Current hospitalizations as a percent of peak since February
p masks as of July 20, 2020: 0.0097, p governor: 0.06. NB: association != causation.
2020-09-12 Summary: 32
34. Change in hospitalizations over past 14
days
Montana
SouthDakota
DistrictofColumbia
Maine
Delaware
Kansas
Utah
Nebraska
NewMexico
WestVirginia
Massachusetts
NorthDakota
Iowa
Missouri
Oregon
NewYork
RhodeIsland
Tennessee
Illinois
Wisconsin
Hawaii
Michigan
Alaska
Kentucky
Pennsylvania
NewJersey
Virginia
Connecticut
Arkansas
Oklahoma
Indiana
NorthCarolina
Wyoming
Georgia
NewHampshire
Idaho
Maryland
Colorado
Ohio
Minnesota
Mississippi
Washington
Louisiana
SouthCarolina
Texas
Alabama
California
Nevada
Arizona
Florida
Vermont
-8.0
-4.0
0.0
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeinhospitalizations(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in hospitalizations over past 14 days
p masks as of July 20, 2020: 0.66, p governor: 0.27. NB: association != causation.
2020-09-12 Summary: 34
35. Change in New Cases per Day
Direction
Increasing > +2%
Increasing between +0.5% and +2%
No Change (-0.5% to +0.5%)
Decreasing between -0.5% and -2%
Decreasing > -2%
NA
Trends by county as of 2020-09-12
NA = Inadequate data
2020-09-12 Summary: 35