See it and Catch it! Recognizing the Thought Traps that Negatively Impact How...
COVID-19 Update (Summary): August 7, 2020
1. Caveats and Comments
1
Overview:
This is my analysis, not Stanford’s. 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 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
BRA
COL
PER
ISR
USA
ZAF
BOL
ARG
DOM
CHL
KGZ
IRQ
ESP
HND
KAZ
GTM
ECU
MEX
SRB
SLV
ROU
BEL
SAU
IND
PHL
IRN
RUS
LBY
BGR
AZE
SWE
VEN
PRY
NLD
MAR
UZB
UKR
GHA
AUS
CHE
FRA
ZMB
CZE
PRT
KEN
POL
DNK
DZA
ZWE
GBR
BGD
TUR
MDG
AUT
BLR
CAN
NPL
JPN
DEU
GRC
ETH
IDN
SEN
MWI
GIN
USA
None
1 in 20,000
1 in 10,000
1 in 6,667
1 in 5,000
1 in 4,000
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
2020-08-07 Summary: 9
12. Average daily deaths over past 7 days
BOL
COL
PER
MEX
ZAF
BRA
CHL
USA
IRN
HND
ARG
GTM
KGZ
IRQ
ECU
KAZ
ROU
DOM
SRB
ISR
SLV
BGR
SAU
GBR
RUS
IND
AZE
LBY
ZMB
SWE
UKR
AUS
ZWE
BLR
MAR
PRY
EGY
DZA
MWI
BEL
IDN
KEN
POL
PHL
TUR
PRT
BGD
VEN
MDG
SEN
UZB
CZE
CAN
SDN
ESP
FRA
HTI
ETH
AGO
NIC
GHA
ITA
YEM
AFG
PAK
USA
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 56 61 66
Rank
Averagedeaths/day
Average daily deaths over past 7 days
Excludes countries with population < 5,000,000
2020-08-07 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
SGP
LVA
SRB
AUT
SAU
DEU
NZL
ESP
CHE
EST
CHLNOR
FIN
ITA
CZE
ROU
SVN
NLD
TUR
GRC
POL
PAN
ZAF
SVK
BGR
SLV
HUN
URY
MAR
COL
KOR
MYS
IRN
HRV
UKR
CUB
RWA
PRYCRI
INDARGPHL
NPL
BOL
GHA
BRA
PER
ECU
PAK
JPN
TUN
FJI
MEX
BGD
SEN
UGA
KENTHATGOZWE
CIV
TWN
IDN
ETH
VNM
MMR
NGA
USA
0
5
10
15
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-08-07
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-07 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 2020-08-07
2020-08-07 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
2020-08-07 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 2020-08-07
2020-08-07 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
2020-08-07 Summary: 18
19. Change in cases vs change in deaths
AL
AK
AZ
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
RISC
SD
TN
TX
UT
VTVA
WA
WV
WI
WY
-6
-3
0
3
6
-5 0 5 10
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days 2020-08-07
2020-08-07 Summary: 19
20. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
NJ
AZ
NC
LA
PA
MA
TN
OH
SC
AL
VA
MI
MD
IN
MS
WA
MN
WI
MO
NV
CT
CO
IA
AR
UT
OK
KY
KS
NE
ID
NM
OR
RI
DE
DC
SD
WV
ND
NH
MT
ME
AK
WY
HI
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: 0.37, p governor: 0.66. NB: association != causation.
2020-08-07 Summary: 20
21. Total US COVID-19 Cases
LA
AZ
FL
MS
NY
NJ
AL
GA
SC
RI
DC
MA
NV
TN
TX
DE
AR
MD
IA
IL
NE
CT
CA
UT
ID
NC
VA
IN
SD
OK
MN
NM
KS
WI
MI
PA
ND
MO
CO
OH
WA
KY
WY
NH
OR
AK
MT
WV
ME
VT
HI
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: 0.8, p governor: 0.27. NB: association != causation.
2020-08-07 Summary: 21
22. Average US COVID-19 cases over the past
7 days
LA
MS
FL
AL
NV
GA
TN
TX
SC
AZ
ID
AR
OK
MO
CA
NC
IA
ND
NE
UT
WI
MD
IL
KS
KY
MN
IN
AK
VA
MT
OH
DE
NM
WA
RI
HI
DC
SD
CO
OR
MI
WY
WV
PA
MA
NJ
NY
CT
NH
ME
VT
None
1 in 10,000
1 in 5,000
1 in 3,333
1 in 2,500
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: 0.034, p governor: 0.012. NB: association != causation.
2020-08-07 Summary: 22
23. Total US COVID-19 Deaths
NY
NJ
CA
MA
TX
IL
FL
PA
MI
CT
LA
GA
AZ
OH
MD
IN
VA
NC
SC
CO
MS
AL
MN
WA
MO
TN
RI
WI
IA
NV
KY
NM
OK
DE
DC
AR
NH
KS
NE
OR
UT
ID
SD
ME
WV
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: 0.16. NB: association != causation.
2020-08-07 Summary: 23
24. Total US COVID-19 Deaths
NJ
NY
MA
CT
RI
LA
DC
MI
IL
MS
DE
MD
PA
AZ
IN
GA
SC
FL
AL
CO
NM
OH
NH
MN
TX
NV
IA
VA
CA
WA
MO
NC
NE
TN
AR
KY
WI
SD
OK
ND
KS
ID
UT
VT
ME
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: 0.039, p governor: 0.17. NB: association != causation.
2020-08-07 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
MS
AZ
FL
SC
LA
TX
NV
GA
AL
CA
ID
AR
TN
NC
VA
IA
OK
NM
OH
MA
SD
WA
MD
IN
UT
WI
IL
MT
MO
KS
ND
PA
MN
MI
NE
KY
WV
OR
RI
DE
NH
CO
NY
DC
AK
NJ
CT
VT
ME
HI
WY
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: 0.22, p governor: 0.026. NB: association != causation.
2020-08-07 Summary: 25
27. Percent of Positive COVID Tests
AZ
MS
FL
AL
SC
GA
TX
ID
NV
KS
NE
MA
IA
MD
RI
PA
IN
AR
CO
LA
NJ
VA
DE
SD
UT
MO
TN
NC
NY
MN
IL
CA
OK
OH
DC
WI
WA
CT
WY
KY
MI
OR
ND
NH
NM
MT
WV
ME
HI
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: 0.26, p governor: 0.023. NB: association != causation.
2020-08-07 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
2020-08-07 Summary: 28
29. Change in positive tests over past 14 days
HI
MN
MT
MO
AK
OK
NV
ID
MS
ND
AL
KY
AR
FL
OR
KS
WV
TN
WY
TX
UT
WA
SC
GA
WI
IA
SD
NE
NM
AZ
CA
IN
LA
NC
VA
CO
NH
OH
RI
PA
DE
IL
MD
VT
MA
MI
ME
NY
NJ
DC
CT
-1.0
0.0
1.0
2.0
3.0
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: 0.012, p governor: 0.029. NB: association != causation.
2020-08-07 Summary: 29
30. Current hospitalizations as a percent of peak
since FebruaryAR
HI
ID
KS
KY
MT
NV
ND
TN
WV
WY
AL
MS
OK
GA
UT
AK
NC
MO
OH
SC
VA
CA
FL
NE
TX
OR
LA
WA
NM
IN
IA
MN
AZ
WI
SD
MD
CO
IL
RI
VT
DC
PA
ME
MI
NH
DE
MA
NJ
NY
CT
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: 0.087, p governor: 0.058. NB: association != causation.
2020-08-07 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
2020-08-07 Summary: 31
32. Change in hospitalizations over past 14
days
KS
HI
MT
WV
NE
ID
RI
WY
MN
IN
ND
KY
WA
VA
DC
IA
MD
AR
WI
AK
NV
MI
TN
IL
AL
MS
NM
OK
UT
GA
NC
MO
LA
OR
ME
NH
OH
MA
CO
SC
PA
CT
CA
FL
NY
TX
SD
DE
VT
NJ
AZ
-4.0
-2.0
0.0
2.0
4.0
6.0
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: 0.7, p governor: 0.87. NB: association != causation.
2020-08-07 Summary: 32
33. Case Mortality vs. Testing
AL
AK
AZ
AR
CA
CO
CT
DE
DC
FL
GA
HI ID
IL
IN
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
WVWI
WY
2.5
5.0
7.5
10 20 30
% Tested
%Mortality
Mortality vs. Testing as of 2020-08-07
2020-08-07 Summary: 33