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
39,557
77,474
460
364
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
2020-10-06 Summary: 6
10. Average new cases over past 7 days
Israel
Argentina
Spain
CzechRepublic
France
Belgium
Netherlands
Jordan
UnitedKingdom
Iraq
Colombia
USA
Brazil
Peru
Paraguay
Chile
Slovakia
Libya
Hungary
Austria
Ukraine
Honduras
Romania
Denmark
Portugal
Tunisia
Nepal
Switzerland
Mexico
Russia
India
Morocco
Canada
Ecuador
Iran
Poland
DominicanRepublic
Sweden
Bolivia
Belarus
Guatemala
Italy
Kyrgyzstan
Bulgaria
Greece
Venezuela
SouthAfrica
Germany
Philippines
Finland
Myanmar
Turkey
Indonesia
Uzbekistan
ElSalvador
SaudiArabia
Azerbaijan
Serbia
Malaysia
Ethiopia
Bangladesh
Angola
Mozambique
Tajikistan
Uganda
USA
None
1 in 5,000
1 in 2,500
1 in 1,667
1 in 1,250
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
2020-10-06 Summary: 10
13. Average daily deaths over past 7 days
Argentina
Mexico
Israel
Colombia
Bolivia
Ecuador
Brazil
Spain
Iran
Chile
Paraguay
Peru
Honduras
USA
Iraq
CzechRepublic
Romania
SouthAfrica
Libya
Ukraine
Jordan
Tunisia
France
Hungary
Belgium
Morocco
Russia
Bulgaria
SaudiArabia
Canada
India
Turkey
UnitedKingdom
Portugal
Poland
Guatemala
ElSalvador
DominicanRepublic
Philippines
Netherlands
Belarus
Myanmar
Austria
Indonesia
Greece
Italy
Nepal
Slovakia
Angola
Venezuela
Switzerland
Denmark
Kazakhstan
Sweden
Algeria
Azerbaijan
Bangladesh
Egypt
Serbia
Kenya
Germany
Uzbekistan
Australia
Syria
Ethiopia
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
2020-10-06 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 2020-10-06
2020-10-06 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
2020-10-06 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 2020-10-06
2020-10-06 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
2020-10-06 Summary: 18
19. Change in cases vs. change in deaths over
last 14 days
AL AK
AZ
AR
CA
CO
CT
DE
DC
FL
GA
HI
ID
IL
IA
KS
KY
LA
ME
MD
MA
MN
MO
MT
NV
NH
NJ
NM
NY
NC
OH
OK
OR
PA
RI
SC
SD
TN
TX
UT
VT
VA
WAWV
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 2020-10-06
Size is proportional total cases per capita
2020-10-06 Summary: 19
20. Total US COVID-19 Cases
California
Texas
Florida
NewYork
Georgia
Illinois
Arizona
NorthCarolina
NewJersey
Tennessee
Pennsylvania
Louisiana
Ohio
Alabama
Virginia
SouthCarolina
Michigan
Massachusetts
Missouri
Wisconsin
Maryland
Indiana
Minnesota
Mississippi
Iowa
Oklahoma
Washington
Arkansas
Nevada
Utah
Colorado
Kentucky
Kansas
Connecticut
Nebraska
Idaho
Oregon
NewMexico
RhodeIsland
SouthDakota
NorthDakota
Delaware
WestVirginia
DistrictofColumbia
Montana
Hawaii
NewHampshire
Alaska
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: 0.6, p governor: 0.86. NB: association != causation.
2020-10-06 Summary: 20
21. Total US COVID-19 Cases
Louisiana
Mississippi
Florida
Alabama
NorthDakota
Georgia
Arizona
Tennessee
Iowa
SouthCarolina
Arkansas
SouthDakota
Texas
Nevada
Nebraska
Idaho
Utah
Illinois
RhodeIsland
NewYork
NewJersey
Oklahoma
Wisconsin
Missouri
DistrictofColumbia
Delaware
Kansas
California
Maryland
NorthCarolina
Massachusetts
Indiana
Minnesota
Virginia
Connecticut
Kentucky
NewMexico
Michigan
Montana
Ohio
Pennsylvania
Colorado
Washington
Alaska
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: 0.046, p governor: 0.0083. NB: association != causation.
2020-10-06 Summary: 21
22. Average US COVID-19 cases over the past
7 days
NorthDakota
SouthDakota
Wisconsin
Montana
Utah
Idaho
Nebraska
Iowa
Arkansas
Oklahoma
Wyoming
Kansas
Missouri
Tennessee
Alaska
Alabama
Kentucky
Minnesota
Mississippi
Indiana
Illinois
Texas
SouthCarolina
Nevada
Delaware
NorthCarolina
RhodeIsland
NewMexico
Georgia
Michigan
Florida
Louisiana
Ohio
WestVirginia
Colorado
Virginia
Maryland
Connecticut
Massachusetts
Pennsylvania
California
NewJersey
Oregon
Arizona
Washington
Hawaii
NewYork
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 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: 0.0013, p governor: 0.01. NB: association != causation.
2020-10-06 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: 0.33. NB: association != causation.
2020-10-06 Summary: 23
24. Total US COVID-19 Deaths
NewJersey
NewYork
Massachusetts
Connecticut
Louisiana
RhodeIsland
Mississippi
DistrictofColumbia
Arizona
Michigan
Illinois
Florida
Georgia
SouthCarolina
Delaware
Maryland
Pennsylvania
Texas
Indiana
Nevada
Alabama
Arkansas
Iowa
NewMexico
Ohio
California
Virginia
Tennessee
Minnesota
NorthDakota
Colorado
Missouri
NorthCarolina
NewHampshire
Washington
SouthDakota
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: 0.048, p governor: 0.45. NB: association != causation.
2020-10-06 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
NorthDakota
Arkansas
SouthDakota
Tennessee
Florida
Mississippi
Louisiana
Iowa
SouthCarolina
Texas
Georgia
Missouri
Kansas
NorthCarolina
Massachusetts
Hawaii
Wisconsin
Nebraska
Illinois
Ohio
Montana
WestVirginia
Idaho
Indiana
California
Virginia
Minnesota
RhodeIsland
Kentucky
Oklahoma
Nevada
Delaware
Arizona
NewMexico
Alabama
DistrictofColumbia
Michigan
Pennsylvania
Utah
Washington
Oregon
Wyoming
Colorado
Connecticut
Maryland
NewYork
NewJersey
NewHampshire
Alaska
Maine
Vermont
None
1 in 500,000
1 in 250,000
1 in 166,667
1 in 125,000
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: 0.044, p governor: 0.048. NB: association != causation.
2020-10-06 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
2020-10-06 Summary: 26
27. Change in daily tests over past 14 days
Mississippi
Connecticut
Montana
Alaska
WestVirginia
Minnesota
Wyoming
Washington
Vermont
Nebraska
Tennessee
NorthCarolina
Kansas
NewYork
Colorado
California
Delaware
Idaho
NewMexico
Ohio
NorthDakota
Hawaii
Indiana
Maryland
Michigan
Illinois
Arkansas
Georgia
Pennsylvania
Massachusetts
Nevada
NewJersey
Maine
SouthDakota
Virginia
Florida
Wisconsin
Texas
Utah
Alabama
Oregon
Arizona
Louisiana
RhodeIsland
SouthCarolina
Iowa
Missouri
DistrictofColumbia
Kentucky
NewHampshire
Oklahoma
0
10
20
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: 0.71, p governor: 0.51. NB: association != causation.
2020-10-06 Summary: 27
29. Percent of Positive COVID Tests
NorthDakota
SouthDakota
Idaho
Wisconsin
Iowa
Missouri
Utah
Nevada
Nebraska
Kansas
Indiana
Alabama
Wyoming
Florida
Oklahoma
Pennsylvania
Delaware
RhodeIsland
Minnesota
Montana
Arizona
Texas
Georgia
Colorado
Oregon
Maryland
Tennessee
NorthCarolina
Hawaii
Mississippi
Virginia
SouthCarolina
Arkansas
NewHampshire
Massachusetts
NewMexico
Kentucky
Illinois
Washington
Louisiana
Alaska
Michigan
WestVirginia
Ohio
California
NewJersey
DistrictofColumbia
NewYork
Connecticut
Vermont
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: 0.00095, p governor: 0.01. NB: association != causation.
2020-10-06 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
2020-10-06 Summary: 30
31. Change in tests vs. change in positive tests
over last 14 days
AL
AK
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
PA
RI
SD TN
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 2020-10-06
Size is proportional daily deaths per capita over the past 7 days
2020-10-06 Summary: 31
32. Current hospitalizations as a percent of peak
since FebruaryMissouri
Montana
Nebraska
NorthDakota
SouthDakota
Wisconsin
Wyoming
Oklahoma
Arkansas
Iowa
WestVirginia
Kansas
Alaska
Kentucky
NorthCarolina
Utah
Indiana
Tennessee
Idaho
Minnesota
Ohio
Oregon
Georgia
Virginia
Alabama
Mississippi
Hawaii
NewMexico
Washington
Nevada
California
SouthCarolina
Illinois
Texas
Colorado
RhodeIsland
Louisiana
Delaware
Florida
DistrictofColumbia
Pennsylvania
Maryland
NewHampshire
Michigan
Maine
Arizona
Massachusetts
Connecticut
NewJersey
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: 0.0034, p governor: 0.058. NB: association != causation.
2020-10-06 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
2020-10-06 Summary: 33
34. Change in hospitalizations over past 14
days
Connecticut
Wyoming
Montana
Delaware
Wisconsin
Pennsylvania
NewHampshire
NewMexico
Iowa
NewYork
Michigan
Utah
Colorado
Kansas
Massachusetts
SouthDakota
NewJersey
Nebraska
Indiana
Minnesota
NorthDakota
Ohio
Tennessee
Missouri
Kentucky
Arkansas
Idaho
Arizona
Oklahoma
RhodeIsland
Alaska
NorthCarolina
Illinois
Texas
Alabama
WestVirginia
Maryland
DistrictofColumbia
Nevada
Washington
Virginia
Georgia
Oregon
Florida
Louisiana
California
Mississippi
SouthCarolina
Maine
Hawaii
Vermont
-3.0
0.0
3.0
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: 0.54, p governor: 0.57. NB: association != causation.
2020-10-06 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 2020-10-06
NA = Inadequate data
2020-10-06 Summary: 35