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)
6. Comparison of COVID-19 Cases & Deaths
between US & Europe
Cases
Deaths
50,341
56,727
915
321
3
10
30
100
300
1,000
3,000
10,000
30,000
100,000
Date
DailyCasesandDeaths
Location
USA (318MM)
Western Europe (344MM)
Log plot of 7 day average
Comparison of COVID-19 Cases & Deaths between US & Europe
The numbers on the right are yesterday's figures, and will differ a bit from the plotted rolling mean
2020-10-08 Summary: 6
10. Average new cases over past 7 days
Israel
CzechRepublic
Argentina
Spain
Netherlands
Belgium
France
UnitedKingdom
Jordan
Colombia
USA
Brazil
Iraq
Slovakia
Paraguay
Libya
Austria
Peru
Chile
Ukraine
Romania
Hungary
Tunisia
Switzerland
Honduras
Nepal
Portugal
Denmark
Russia
Mexico
Morocco
Ecuador
India
Canada
Sweden
Iran
Poland
DominicanRepublic
Italy
Guatemala
Belarus
Bolivia
Bulgaria
Kyrgyzstan
Greece
SouthAfrica
Germany
Venezuela
Finland
Philippines
Myanmar
Turkey
Indonesia
SaudiArabia
Azerbaijan
Uzbekistan
Malaysia
ElSalvador
Serbia
Ethiopia
Bangladesh
Angola
SriLanka
Tajikistan
Mozambique
USA
None
1 in 5,000
1 in 2,500
1 in 1,667
1 in 1,250
1 in 1,000
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
2020-10-08 Summary: 10
13. Average daily deaths over past 7 days
Argentina
Mexico
Israel
Colombia
Ecuador
Spain
Brazil
Bolivia
Iran
Chile
Paraguay
Peru
CzechRepublic
Romania
Honduras
USA
Iraq
Hungary
Ukraine
SouthAfrica
Jordan
Tunisia
Libya
Belgium
Russia
France
Bulgaria
Morocco
Poland
Netherlands
Canada
UnitedKingdom
Guatemala
SaudiArabia
Portugal
India
Turkey
DominicanRepublic
Philippines
Belarus
ElSalvador
Myanmar
Austria
Indonesia
Greece
Italy
Nepal
Angola
Denmark
Venezuela
Slovakia
Switzerland
Azerbaijan
Bangladesh
Kazakhstan
Algeria
Serbia
Germany
Egypt
Kenya
Kyrgyzstan
Uzbekistan
Ethiopia
Syria
Australia
USA
None
1 in 200,000
1 in 100,000
1 in 66,667
1 in 50,000
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
2020-10-08 Summary: 13
15. Change in New Cases per Day
Daily cases are:
Increasing > +3%
Increasing between +1% and +3%
No Change (-1% to +1%)
Decreasing between -1% and -3%
Decreasing > -3%
Daily cases by state as of 2020-10-08
2020-10-08 Summary: 15
16. 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
2020-10-08 Summary: 16
17. Change in Deaths per Day
Daily deaths are:
Increasing > +3%
Increasing between +1% and +3%
No Change (-1% to +1%)
Decreasing between -1% and -3%
Decreasing > -3%
Daily deaths by state as of 2020-10-08
2020-10-08 Summary: 17
18. 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
2020-10-08 Summary: 18
19. cases vs. change in deaths over last 14
days
AL
AKAZ
AR
CA
CO CT
DE
DC
FL
GA
HI ID
IL
IN
IA
KS
KY
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
-6
-3
0
3
6
-6 -3 0 3 6
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs. change in deaths over last 14 days as of 2020-10-08
Size is proportional total cases per capita
2020-10-08 Summary: 19
20. Total US COVID-19 Cases
California
Texas
Florida
NewYork
Georgia
Illinois
NorthCarolina
Arizona
NewJersey
Tennessee
Pennsylvania
Louisiana
Ohio
Alabama
SouthCarolina
Virginia
Michigan
Wisconsin
Missouri
Massachusetts
Maryland
Indiana
Minnesota
Mississippi
Iowa
Oklahoma
Washington
Arkansas
Nevada
Utah
Kentucky
Colorado
Kansas
Connecticut
Nebraska
Idaho
Oregon
NewMexico
SouthDakota
RhodeIsland
NorthDakota
Delaware
WestVirginia
Montana
DistrictofColumbia
Hawaii
Alaska
NewHampshire
Wyoming
Maine
Vermont
0
250,000
500,000
750,000
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: 0.64, p governor: 0.98. NB: association != causation.
2020-10-08 Summary: 20
21. Total US COVID-19 Cases
Louisiana
Mississippi
Florida
Alabama
NorthDakota
Georgia
Arizona
Tennessee
Iowa
SouthCarolina
Arkansas
SouthDakota
Texas
Nevada
Idaho
Nebraska
Utah
Illinois
RhodeIsland
NewYork
Oklahoma
Wisconsin
NewJersey
Missouri
DistrictofColumbia
Delaware
Kansas
California
Maryland
NorthCarolina
Massachusetts
Indiana
Minnesota
Virginia
Kentucky
Connecticut
Montana
NewMexico
Michigan
Ohio
Pennsylvania
Colorado
Alaska
Washington
Wyoming
WestVirginia
Hawaii
Oregon
NewHampshire
Maine
Vermont
None
1 in 100
1 in 50
1 in 33
1 in 25
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: 0.04, p governor: 0.016. NB: association != causation.
2020-10-08 Summary: 21
22. Average US COVID-19 cases over the past
7 days
NorthDakota
SouthDakota
Wisconsin
Montana
Utah
Idaho
Nebraska
Iowa
Oklahoma
Arkansas
Kentucky
Tennessee
Wyoming
Missouri
Alabama
Alaska
Kansas
Mississippi
Minnesota
Indiana
Illinois
Texas
Nevada
NorthCarolina
SouthCarolina
RhodeIsland
NewMexico
Delaware
Louisiana
Georgia
Colorado
Florida
Ohio
Michigan
WestVirginia
Maryland
Virginia
Massachusetts
California
Pennsylvania
Arizona
NewJersey
Connecticut
Oregon
Washington
NewYork
Hawaii
DistrictofColumbia
NewHampshire
Maine
Vermont
None
1 in 10,000
1 in 5,000
1 in 3,333
1 in 2,500
1 in 2,000
1 in 1,667
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: 0.015. NB: association != causation.
2020-10-08 Summary: 22
23. Total US COVID-19 Deaths
NewYork
Texas
California
NewJersey
Florida
Massachusetts
Illinois
Pennsylvania
Georgia
Michigan
Arizona
Louisiana
Ohio
Connecticut
Maryland
Indiana
NorthCarolina
SouthCarolina
Virginia
Mississippi
Tennessee
Alabama
Missouri
Washington
Minnesota
Colorado
Nevada
Arkansas
Iowa
Wisconsin
Kentucky
RhodeIsland
Oklahoma
NewMexico
Kansas
Delaware
DistrictofColumbia
Oregon
Nebraska
Idaho
Utah
NewHampshire
WestVirginia
NorthDakota
SouthDakota
Montana
Hawaii
Maine
Alaska
Vermont
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: 0.082, p governor: 0.47. NB: association != causation.
2020-10-08 Summary: 23
24. Total US COVID-19 Deaths
NewJersey
NewYork
Massachusetts
Connecticut
Louisiana
RhodeIsland
Mississippi
DistrictofColumbia
Arizona
Illinois
Michigan
Florida
Georgia
SouthCarolina
Delaware
Maryland
Pennsylvania
Texas
Indiana
Nevada
Alabama
Arkansas
Iowa
NewMexico
Ohio
California
NorthDakota
Tennessee
Virginia
Minnesota
Missouri
Colorado
NorthCarolina
NewHampshire
SouthDakota
Washington
Idaho
Kentucky
Oklahoma
Nebraska
Kansas
Wisconsin
WestVirginia
Montana
Utah
Oregon
Hawaii
Maine
Vermont
Wyoming
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: 0.061, p governor: 0.52. NB: association != causation.
2020-10-08 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
NorthDakota
Arkansas
SouthDakota
Florida
Tennessee
Mississippi
Missouri
SouthCarolina
Texas
Georgia
Iowa
Louisiana
Kansas
Hawaii
Idaho
Wisconsin
Massachusetts
Illinois
NorthCarolina
Alabama
Indiana
Ohio
Nebraska
Montana
Minnesota
Oklahoma
Delaware
California
Nevada
WestVirginia
Arizona
Virginia
RhodeIsland
Utah
Kentucky
Pennsylvania
NewMexico
Michigan
DistrictofColumbia
Washington
Colorado
Oregon
Wyoming
NewHampshire
Connecticut
Maryland
NewYork
Alaska
NewJersey
Maine
Vermont
None
1 in 500,000
1 in 250,000
1 in 166,667
1 in 125,000
1 in 100,000
1 in 83,333
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: 0.013, p governor: 0.0083. NB: association != causation.
2020-10-08 Summary: 25
26. 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
2020-10-08 Summary: 26
27. Change in daily tests over past 14 days
Mississippi
SouthDakota
Alaska
Connecticut
Kansas
Nebraska
Montana
California
NewYork
Delaware
Louisiana
Tennessee
Oklahoma
Wyoming
Ohio
NorthDakota
RhodeIsland
Pennsylvania
NewMexico
Wisconsin
WestVirginia
Indiana
Michigan
Florida
Idaho
Massachusetts
DistrictofColumbia
Colorado
Arizona
Illinois
NewJersey
Maryland
Minnesota
Utah
SouthCarolina
NorthCarolina
Georgia
Hawaii
Washington
Iowa
Kentucky
Missouri
Maine
Virginia
Oregon
Alabama
Texas
Nevada
Vermont
Arkansas
NewHampshire
-5.0
0.0
5.0
10.0
15.0
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: 0.15, p governor: 0.77. NB: association != causation.
2020-10-08 Summary: 27
29. Percent of Positive COVID Tests
NorthDakota
Idaho
SouthDakota
Wisconsin
Iowa
Nevada
Missouri
Wyoming
Utah
Indiana
Nebraska
Kansas
Alabama
Florida
Montana
Oklahoma
Texas
Minnesota
Pennsylvania
Arkansas
Delaware
Kentucky
Colorado
Georgia
Arizona
Mississippi
Hawaii
Tennessee
RhodeIsland
Oregon
Maryland
NorthCarolina
SouthCarolina
Virginia
NewMexico
Massachusetts
Louisiana
Washington
Illinois
NewHampshire
WestVirginia
Michigan
Ohio
Alaska
California
NewJersey
Vermont
DistrictofColumbia
NewYork
Connecticut
Maine
0
10
20
30
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: 0.002, p governor: 0.021. NB: association != causation.
2020-10-08 Summary: 29
30. Percent Positive 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
1
10
100
1
10
100
1
10
100
1
10
100
1
10
100
1
10
100
1
10
100
1
10
100
PercentPositive(logscale)
Percent Positive Trends
2020-10-08 Summary: 30
31. tests vs. change in positive tests over last 14
days
AL
AK
AZ
AR
CA
CO CT
DE
DC
FL
GA
HI
ID
IL
IN
IA KS
KY
LA
ME
MD
MA MIMN
MS
MO
MT
NE
NV
NH
NJ
NM
NY
NC
ND
OH
OK
OR
PA
RISC
SD
TNTX
UT
VT
VA
WA
WV
WI
WY
-10
-5
0
5
10
-6 -3 0 3 6
Change in tests (%/day)
Changeinpositivetests(%/day)
Change in tests vs. change in positive tests over last 14 days as of 2020-10-08
Size is proportional daily deaths per capita over the past 7 days
2020-10-08 Summary: 31
32. Current hospitalizations as a percent of peak
since FebruaryArkansas
Iowa
Missouri
Montana
NorthDakota
Oklahoma
SouthDakota
Wisconsin
Wyoming
Nebraska
WestVirginia
Kentucky
Kansas
Alaska
NorthCarolina
Utah
Tennessee
Ohio
Indiana
Idaho
Virginia
Oregon
Minnesota
Georgia
NewMexico
Alabama
Mississippi
Nevada
SouthCarolina
Hawaii
Washington
California
Illinois
Texas
Colorado
RhodeIsland
Delaware
Louisiana
Pennsylvania
DistrictofColumbia
Maryland
Florida
Arizona
Michigan
Maine
NewHampshire
Massachusetts
NewJersey
Connecticut
NewYork
Vermont
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: 0.006, p governor: 0.042. NB: association != causation.
2020-10-08 Summary: 32
33. Hospitalizations 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
Hospitalizationsfrommintomax
Hospitalizations trends from min to max
2020-10-08 Summary: 33
34. Change in hospitalizations over past 14
days
Wyoming
Connecticut
Delaware
Montana
Wisconsin
NewMexico
Pennsylvania
NewYork
NewJersey
Tennessee
Colorado
Iowa
Michigan
Massachusetts
SouthDakota
Arizona
NewHampshire
Ohio
Utah
Indiana
Oklahoma
NorthDakota
Nebraska
Minnesota
Kentucky
Arkansas
Kansas
NorthCarolina
Idaho
Alabama
Texas
Missouri
Alaska
Maryland
Nevada
RhodeIsland
Illinois
DistrictofColumbia
Virginia
Florida
WestVirginia
Washington
California
Louisiana
Oregon
Georgia
Mississippi
Maine
SouthCarolina
Hawaii
Vermont
-10.0
-5.0
0.0
5.0
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: 0.73, p governor: 0.7. NB: association != causation.
2020-10-08 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 2020-10-08
NA = Inadequate data
2020-10-08 Summary: 35