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COVID-19 Update (Summary): August 11, 2020
1. Caveats and Comments
1
Overview:
This is my analysis, not Stanfordโs. My plots and regressions are intended to understand the trajectory of COVID. It is not confidential and can be freely shared.
The R program code and PowerPoint files are available at https://github.com/StevenLShafer/COVID19/. Please contact me at steven.shafer@Stanford.edu if you
would like to be added or removed from the recipient list. Suggestions are most welcome! 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 isnโt clear, please see the explanation on slide 2.
Data sources:
โข 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
โข 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
โข USA Testing and Hospitalization Data: https://raw.githubusercontent.com/COVID19Tracking/covid-tracking-data/master/data/states_daily_4pm_et.csv
โข 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
โข 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
โข Global Testing Data: https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv
โข Mobility Data: https://www.gstatic.com/covid19/mobility/Global_Mobility_Report.csv
โข Partisan Lean: MIT Election Data and Science Lab: https://doi.org/10.7910/DVN/VOQCHQ/HEIJCQ
โข 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 ๐๐ข๐๐ข๐๐๐ก๐๐ฃ๐ ๐๐๐ ๐๐ =
๐๐ข๐๐๐๐๐ก ๐๐๐ ๐๐ + ๐๐๐ฅ๐๐๐ข๐ ๐๐๐ ๐๐ โ ๐๐ข๐๐๐๐๐ก ๐๐๐ ๐๐ 1 โ ๐โ๐ ๐ก . This is a naรฏve 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
(yesterdayโs cases)
and cumulative deaths
(yesterdayโs 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
PER
COL
ISR
BRA
USA
ARG
BOL
ZAF
CHL
DOM
ESP
IRQ
KGZ
HND
ECU
KAZ
SLV
BEL
GTM
ROU
MEX
IND
SRB
SAU
PHL
LBY
RUS
IRN
SWE
NLD
VEN
MAR
FRA
PRY
UKR
UZB
BGR
DNK
GHA
CZE
AUS
ZMB
CHE
AZE
POL
PRT
BGD
KEN
DZA
GBR
TUR
NPL
GRC
CAN
AUT
BLR
DEU
JPN
MDG
SEN
ZWE
IDN
GIN
ETH
ITA
USA
None
1 in 20,000
1 in 10,000
1 in 6,667
1 in 5,000
1 in 4,000
1 in 3,333
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
2020-08-11 Summary: 9
12. Average daily deaths over past 7 days
BOL
PER
COL
MEX
ZAF
BRA
CHL
ARG
USA
IRN
IRQ
KAZ
GTM
HND
DOM
ROU
ECU
SLV
KGZ
ISR
SRB
BGR
SAU
LBY
RUS
IND
ZMB
GBR
AUS
UKR
PRY
MAR
AZE
ESP
BEL
ZWE
SWE
PHL
DZA
BLR
IDN
PRT
VEN
EGY
POL
HTI
SEN
BGD
AGO
MDG
UZB
TUR
MWI
AFG
GHA
KEN
CAN
ETH
NIC
SDN
TGO
FRA
ITA
DNK
YEM
USA
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 56 61 66
Rank
Averagedeaths/day
Average daily deaths over past 7 days
Excludes countries with population < 5,000,000
2020-08-11 Summary: 12
13. Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISL
RUS
ISR
LTU
AUS
USA
QAT
PRT
BEL
MDV
GBR
BLR
IRL
KWT
CAN
KAZ
LVA
SGP
SRB
SAU
AUT
ESP
NZL
DEU
CHE
CHLESTNOR
FINROU
ITA
CZE
SVN
NLD
GRC
TUR
POL
ZAF
PAN
SVK
BGR
SLVURY
HUN
COL
MARMYS
IRN
HRV
KOR
UKR
CUB
RWA
PRY
IND
CRI
ARGPHL
NPL
BOL
GHA
BRA
ECU
PER
JPN
PAK
TUN
FJI
MEX
BGD
SEN
UGA
KEN
TGO
THAZWE
CIV
IDN
TWN
ETH
VNM
MMR
NGA
USA
0
5
10
15
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-08-11
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-11 Summary: 13
15. 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 2020-08-11
2020-08-11 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
2020-08-11 Summary: 16
17. 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 2020-08-11
2020-08-11 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
2020-08-11 Summary: 18
19. Change in cases vs change in deaths
AL
AK
AZ
AR
CA
COCT 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
-6
-3
0
3
6
-8 -4 0 4
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days 2020-08-11
2020-08-11 Summary: 19
20. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
AZ
NJ
NC
LA
PA
TN
MA
AL
OH
SC
VA
MI
MD
IN
MS
WA
MN
WI
MO
NV
CO
CT
AR
IA
UT
OK
KY
KS
NE
ID
NM
OR
RI
DE
DC
SD
WV
ND
NH
MT
ME
AK
HI
WY
VT
0
200,000
400,000
600,000
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: 0.35, p governor: 0.67. NB: association != causation.
2020-08-11 Summary: 20
21. Total US COVID-19 Cases
LA
AZ
FL
MS
NY
AL
NJ
GA
SC
RI
NV
DC
TN
MA
TX
AR
DE
MD
IA
IL
NE
CA
CT
ID
UT
NC
VA
IN
OK
SD
MN
NM
KS
WI
ND
MO
MI
PA
CO
OH
WA
KY
WY
AK
OR
NH
MT
WV
ME
HI
VT
None
1 in 200
1 in 100
1 in 67
1 in 50
1 in 40
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: 0.86, p governor: 0.24. NB: association != causation.
2020-08-11 Summary: 21
22. Average US COVID-19 cases over the past
7 days
LA
GA
MS
AL
FL
ID
NV
TX
TN
AR
SC
CA
OK
ND
MO
AZ
NC
KS
IA
IL
IN
WI
VA
NE
UT
MD
MN
HI
KY
RI
SD
MT
DC
OH
WA
DE
NM
AK
CO
OR
MI
WV
PA
WY
MA
NJ
NY
CT
NH
ME
VT
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: 0.057, p governor: 0.025. NB: association != causation.
2020-08-11 Summary: 22
23. Total US COVID-19 Deaths
NY
NJ
CA
TX
MA
FL
IL
PA
MI
CT
LA
GA
AZ
OH
MD
IN
VA
NC
SC
MS
CO
AL
MN
WA
MO
TN
RI
WI
NV
IA
KY
NM
OK
DE
DC
AR
NH
KS
OR
NE
UT
ID
SD
WV
ME
ND
MT
VT
HI
WY
AK
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: 0.052, p governor: 0.17. NB: association != causation.
2020-08-11 Summary: 23
24. Total US COVID-19 Deaths
NJ
NY
MA
CT
RI
LA
DC
MI
MS
IL
DE
MD
PA
AZ
IN
GA
SC
FL
AL
NM
CO
TX
OH
NV
NH
MN
IA
VA
CA
WA
MO
NC
AR
TN
NE
KY
WI
SD
OK
ND
ID
KS
UT
ME
VT
OR
WV
MT
WY
AK
HI
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: 0.028, p governor: 0.18. NB: association != causation.
2020-08-11 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
MS
LA
TX
FL
AZ
SC
NV
GA
AL
AR
CA
ID
TN
NC
IA
NM
MA
OK
WV
WA
MT
VA
MD
SD
OH
UT
MO
ND
IL
IN
WI
KS
MN
NE
RI
KY
OR
PA
DC
MI
DE
HI
NJ
NY
WY
CT
CO
AK
VT
ME
NH
None
1 in 500,000
1 in 250,000
1 in 166,667
1 in 125,000
1 in 100,000
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: 0.54, p governor: 0.018. NB: association != causation.
2020-08-11 Summary: 25
27. Percent of Positive COVID Tests
AZ
MS
FL
AL
SC
TX
ID
GA
NV
KS
IA
NE
MA
MD
RI
IN
AR
PA
CO
LA
VA
NJ
SD
DE
MO
UT
TN
NC
MN
NY
OK
IL
CA
WA
WI
OH
DC
CT
KY
WY
OR
MI
ND
NH
NM
MT
HI
WV
ME
AK
VT
0.0
5.0
10.0
15.0
20.0
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: 0.24, p governor: 0.02. NB: association != causation.
2020-08-11 Summary: 27
28. 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
2020-08-11 Summary: 28
29. Change in positive tests over past 14 days
HI
MN
MT
ND
OK
MO
NV
WA
MS
ID
AR
TX
KY
OR
AL
WY
FL
TN
WV
KS
AK
UT
SC
SD
WI
IA
GA
IN
NE
CA
VA
NC
LA
AZ
OH
CO
RI
NM
DE
NH
PA
IL
MD
VT
MI
MA
NJ
NY
ME
DC
CT
0.0
2.0
4.0
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: 0.032, p governor: 0.058. NB: association != causation.
2020-08-11 Summary: 29
30. Current hospitalizations as a percent of peak
since FebruaryAL
AR
HI
KY
MO
MT
ND
WV
WY
AK
ID
OK
MS
KS
NC
TN
GA
UT
NV
OH
SC
VA
CA
NE
FL
OR
WA
LA
TX
NM
IN
SD
IA
WI
MN
AZ
CO
MD
IL
RI
PA
DC
MI
NH
ME
VT
DE
MA
NJ
CT
NY
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: 0.11, p governor: 0.032. NB: association != causation.
2020-08-11 Summary: 30
31. 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
2020-08-11 Summary: 31
32. Change in hospitalizations over past 14
days
HI
WI
MT
WV
SD
RI
NE
ND
KS
KY
IN
MN
AR
WA
MO
IL
MA
VA
AL
WY
IA
NM
MI
ID
CT
AK
MD
OK
MS
PA
NH
TN
NC
OR
GA
UT
CO
DC
LA
NV
OH
SC
NY
CA
FL
ME
TX
NJ
AZ
DE
VT
-4.0
0.0
4.0
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: 0.73, p governor: 0.89. NB: association != causation.
2020-08-11 Summary: 32
33. Case Mortality vs. Testing
AL
AK
AZ
AR
CA
CO
CT
DE
DC
FL
GA
HI ID
ILIN
IA
KS
KY
LA
ME
MD
MA
MI
MNMS
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
2.5
5.0
7.5
10 20 30
% Tested
%Mortality
Mortality vs. Testing as of 2020-08-11
2020-08-11 Summary: 33