Circulatory Shock, types and stages, compensatory mechanisms
COVID-19 Update (Summary): August 6, 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
PER
COL
ISR
USA
ZAF
BOL
ARG
DOM
CHL
KGZ
IRQ
KAZ
ESP
HND
GTM
MEX
SRB
SLV
ECU
ROU
SAU
BEL
IND
PHL
IRN
RUS
AZE
BGR
LBY
SWE
UZB
VEN
MAR
AUS
UKR
PRY
GHA
NLD
CHE
ZMB
CZE
PRT
KEN
DZA
POL
FRA
DNK
BGD
ZWE
AUT
TUR
BLR
MDG
CAN
GBR
JPN
NPL
DEU
GRC
IDN
ETH
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 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
2020-08-06 Summary: 9
12. Average daily deaths over past 7 days
BOL
COL
PER
BRA
MEX
ZAF
CHL
USA
HND
IRN
ARG
GTM
KGZ
ECU
IRQ
KAZ
ROU
DOM
SRB
SLV
ISR
BGR
SAU
RUS
SWE
GBR
AZE
IND
LBY
AUS
UKR
BLR
ZWE
MAR
EGY
ZMB
DZA
BEL
KEN
MWI
IDN
PRY
POL
TUR
PHL
PRT
BGD
UZB
MDG
VEN
CAN
ESP
SDN
SEN
HTI
ETH
CZE
GHA
NIC
AGO
FRA
YEM
ITA
PAK
AFG
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
2020-08-06 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 2020-08-06
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-06 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 2020-08-06
2020-08-06 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
2020-08-06 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 2020-08-06
2020-08-06 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
2020-08-06 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
MIMN
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
-5 0 5 10
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days 2020-08-06
2020-08-06 Summary: 19
20. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
NJ
AZ
NC
LA
PA
MA
TN
OH
SC
VA
AL
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: 0.65. NB: association != causation.
2020-08-06 Summary: 20
21. Total US COVID-19 Cases
LA
AZ
FL
NY
MS
NJ
AL
GA
SC
RI
DC
MA
NV
TN
TX
DE
AR
MD
IA
IL
NE
CT
CA
UT
ID
NC
VA
IN
SD
NM
OK
MN
KS
WI
PA
MI
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: 0.76, p governor: 0.29. NB: association != causation.
2020-08-06 Summary: 21
22. Average US COVID-19 cases over the past
7 days
LA
MS
FL
NV
GA
AL
TX
AZ
SC
TN
AR
ID
OK
MO
CA
NC
IA
NE
ND
WI
MD
KS
UT
KY
IL
AK
MN
VA
IN
MT
NM
DE
OH
WA
SD
RI
HI
DC
CO
OR
MI
WV
WY
MA
PA
NJ
CT
NY
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: 0.037, p governor: 0.012. NB: association != causation.
2020-08-06 Summary: 22
23. Total US COVID-19 Deaths
NY
NJ
CA
MA
IL
TX
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
DE
DC
OK
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: 0.047, p governor: 0.15. NB: association != causation.
2020-08-06 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
NV
IA
VA
TX
CA
WA
MO
NC
NE
AR
KY
TN
WI
SD
OK
ND
KS
ID
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: 0.036, p governor: 0.15. NB: association != causation.
2020-08-06 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
MS
AZ
FL
SC
LA
TX
NV
AL
GA
ID
CA
AR
NC
TN
VA
NM
IA
OK
OH
SD
MA
MT
MD
UT
IN
WI
KS
MO
ND
IL
WA
NE
WV
MN
OR
PA
CO
KY
DE
NH
RI
MI
DC
NY
AK
CT
NJ
ME
WY
VT
HI
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: 0.18, p governor: 0.016. NB: association != causation.
2020-08-06 Summary: 25
27. Percent of Positive COVID Tests
AZ
MS
FL
AL
SC
GA
TX
ID
NV
KS
MA
NE
MD
IA
RI
PA
IN
CO
AR
LA
NJ
VA
DE
SD
UT
MO
TN
NC
NY
MN
IL
CA
DC
OH
OK
WI
CT
WA
KY
WY
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: 0.31, p governor: 0.029. NB: association != causation.
2020-08-06 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
2020-08-06 Summary: 28
29. Change in positive tests over past 14 days
HI
MN
MO
MT
AK
OK
MS
ID
NV
ND
KY
AL
FL
OR
KS
AR
WV
TN
WY
UT
SC
TX
GA
WI
WA
IA
NM
CA
AZ
SD
LA
NE
IN
NC
CO
VA
NH
RI
OH
PA
DE
IL
MD
VT
MA
ME
MI
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: 0.011, p governor: 0.037. NB: association != causation.
2020-08-06 Summary: 29
30. Current hospitalizations as a percent of peak
since FebruaryAR
HI
ID
KS
KY
MT
NV
ND
WV
WY
TN
AL
MS
GA
UT
OK
NC
AK
OH
MO
SC
CA
VA
FL
NE
TX
NM
LA
OR
WA
IN
IA
AZ
MN
WI
SD
CO
MD
IL
VT
RI
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: 0.09, p governor: 0.06. NB: association != causation.
2020-08-06 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
2020-08-06 Summary: 31
32. Change in hospitalizations over past 14
days
HI
KS
MT
WV
NE
ID
WY
RI
MN
IN
IA
ND
DC
MD
WA
KY
WI
AR
VA
NV
AK
MI
NM
MS
AL
TN
GA
IL
OK
UT
NC
NH
LA
OH
ME
OR
MO
CO
SC
CA
CT
MA
FL
PA
VT
NY
TX
DE
SD
NJ
AZ
0.0
5.0
10.0
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: 0.55, p governor: 0.95. NB: association != causation.
2020-08-06 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 2020-08-06
2020-08-06 Summary: 33