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COVID-19 Update (Summary): August 14, 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
COL
BRA
PER
ISR
ARG
USA
BOL
CHL
ZAF
IRQ
ESP
DOM
ECU
KGZ
GTM
HND
BEL
SLV
ROU
MEX
IND
LBY
SAU
KAZ
SRB
NLD
PRY
PHL
VEN
RUS
IRN
MAR
SWE
FRA
UKR
DNK
UZB
CHE
CZE
PRT
BGR
POL
BGD
ZMB
AUS
GRC
AUT
KEN
NPL
TUR
DZA
GBR
GHA
DEU
AZE
CAN
SEN
BLR
JPN
ETH
IDN
MDG
GIN
ZWE
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
2020-08-14 Summary: 9
12. Average daily deaths over past 7 days
COL
BOL
MEX
PER
BRA
ZAF
ARG
CHL
USA
IRN
DOM
IRQ
GTM
HND
ROU
KAZ
SLV
ISR
ECU
SAU
KGZ
SRB
BGR
RUS
IND
ZMB
GBR
LBY
AUS
BEL
PRY
UKR
MAR
ZWE
PHL
PRT
AZE
ESP
AFG
VEN
DZA
HTI
POL
BLR
IDN
EGY
SEN
BGD
KEN
SWE
MDG
TUR
UZB
CAN
FRA
ETH
AGO
NPL
MWI
SDN
GRC
GHA
CHE
DNK
ITA
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
2020-08-14 Summary: 12
13. Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISLISR
RUS
LTU
AUS
USA
QAT
PRT
MDV
GBR
BEL
BLR
IRL
KWT
CAN
KAZ
LVA
SGP
SAU
SRB
DEU
AUT
NZL
ESP
CHLEST
CHE
NOR
FINROU
ITA
CZE
NLD
SVN
GRC
TUR
POL
PAN
ZAF
SVK
BGR
MAR
SLVURY
COL
HUN
MYS
IRN
HRV
KORUKR
CUB
RWA
IND
PRYCRI
ARG
NPL
BOL
PHL
GHA
ECU
BRA
PER
JPNPAK
TUN
FJI
MEX
BGD
SEN
UGA
KEN
TGO
THA
ZWE
CIV
ETH
IDN
TWN
VNM
MMR
NGA
USA
0
5
10
15
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-08-14
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-14 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 2020-08-14
2020-08-14 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
2020-08-14 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 2020-08-14
2020-08-14 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
2020-08-14 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
KS KYLA
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
VTVA
WA
WV
WI
WY
-6
-3
0
3
6
-4 0 4
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days 2020-08-14
2020-08-14 Summary: 19
20. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
AZ
NJ
NC
LA
TN
PA
MA
AL
OH
SC
VA
MI
MD
IN
MS
WA
MO
WI
MN
NV
CO
AR
CT
IA
OK
UT
KY
KS
NE
ID
NM
OR
RI
DE
DC
SD
ND
WV
NH
MT
HI
ME
AK
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: 0.36, p governor: 0.72. NB: association != causation.
2020-08-14 Summary: 20
21. Total US COVID-19 Cases
LA
AZ
FL
MS
NY
GA
AL
NJ
SC
RI
NV
TN
DC
TX
MA
AR
DE
MD
IA
IL
NE
CA
ID
CT
UT
NC
VA
OK
IN
SD
MN
KS
NM
WI
ND
MO
MI
PA
CO
OH
WA
KY
AK
WY
OR
NH
MT
WV
HI
ME
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: 0.93, p governor: 0.22. NB: association != causation.
2020-08-14 Summary: 21
22. Average US COVID-19 cases over the past
7 days
GA
FL
AL
MS
ID
TN
LA
NV
TX
AR
CA
SC
ND
MO
OK
AZ
IN
NE
IA
KS
KY
IL
HI
WI
NC
VA
UT
MD
MN
MT
SD
DC
OH
RI
AK
WA
DE
NM
MI
CO
WV
OR
PA
MA
NJ
WY
NY
CT
NH
VT
ME
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 in 2,857
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: 0.01. NB: association != causation.
2020-08-14 Summary: 22
23. Total US COVID-19 Deaths
NY
NJ
CA
TX
FL
MA
IL
PA
MI
GA
CT
LA
AZ
OH
MD
IN
VA
NC
SC
MS
AL
CO
WA
MN
MO
TN
NV
RI
WI
IA
KY
NM
OK
DC
DE
AR
NH
KS
OR
NE
UT
ID
WV
SD
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: 0.19. NB: association != causation.
2020-08-14 Summary: 23
24. Total US COVID-19 Deaths
NJ
NY
MA
CT
RI
LA
DC
MS
MI
IL
DE
AZ
MD
PA
IN
GA
SC
FL
AL
TX
NV
NM
CO
OH
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: 0.031, p governor: 0.21. NB: association != causation.
2020-08-14 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
MS
LA
AZ
FL
SC
GA
TX
NV
AL
CA
TN
AR
NC
ID
IA
MA
WV
ND
MT
WA
IN
NM
OK
MD
OH
SD
PA
MN
OR
IL
KS
VA
NE
DC
KY
MO
HI
WI
UT
MI
RI
DE
CO
WY
NJ
CT
NH
AK
NY
VT
ME
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: 0.55, p governor: 0.022. NB: association != causation.
2020-08-14 Summary: 25
27. Percent of Positive COVID Tests
AZ
MS
FL
AL
SC
ID
TX
GA
NV
KS
NE
IA
MD
AR
RI
IN
MA
PA
CO
LA
VA
SD
MO
UT
DE
NJ
NC
TN
MN
WA
OK
CA
IL
NY
WI
OH
DC
KY
CT
WY
OR
ND
MI
NH
NM
HI
MT
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: 0.2, p governor: 0.015. NB: association != causation.
2020-08-14 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
2020-08-14 Summary: 28
29. Change in positive tests over past 14 days
HI
MT
WA
ND
TX
OK
ID
MO
NV
AR
NC
MS
KY
OR
FL
AL
TN
KS
WV
UT
WY
SD
SC
WI
MN
IA
IN
CA
GA
AK
NE
VA
OH
CO
LA
AZ
RI
NM
DE
PA
VT
IL
MD
NH
MI
MA
NJ
DC
NY
ME
CT
-1.0
0.0
1.0
2.0
3.0
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: 0.14, p governor: 0.085. NB: association != causation.
2020-08-14 Summary: 29
30. Current hospitalizations as a percent of peak
since FebruaryAK
HI
KY
MT
ND
WV
MO
KS
AR
ID
MS
AL
NC
TN
OK
GA
OH
UT
WY
NV
VA
SC
NE
OR
CA
FL
IN
WA
LA
SD
NM
TX
WI
IA
MN
AZ
CO
IL
MD
RI
PA
VT
DC
MI
ME
NH
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: 0.052, p governor: 0.055. NB: association != causation.
2020-08-14 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
2020-08-14 Summary: 31
32. Change in hospitalizations over past 14
days
HI
SD
WI
MT
WV
ND
RI
NE
IN
KY
MN
MA
AK
IL
KS
IA
MO
VA
OR
WA
AR
NM
MI
CT
MS
ID
AL
PA
NC
TN
DC
OH
OK
GA
CO
NH
UT
MD
NY
SC
WY
LA
NV
CA
ME
FL
TX
VT
NJ
DE
AZ
-2.5
0.0
2.5
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: 0.73, p governor: 0.74. NB: association != causation.
2020-08-14 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
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
2.5
5.0
7.5
10 20 30 40
% Tested
%Mortality
Mortality vs. Testing as of 2020-08-14
2020-08-14 Summary: 33