Circulatory Shock, types and stages, compensatory mechanisms
COVID-19 Update (Summary): August 13, 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
ZAF
CHL
IRQ
DOM
ESP
ECU
KGZ
HND
GTM
SLV
BEL
ROU
MEX
KAZ
IND
SAU
LBY
SRB
NLD
PHL
PRY
RUS
VEN
IRN
MAR
FRA
SWE
UKR
BGR
UZB
DNK
CHE
CZE
GHA
PRT
BGD
ZMB
POL
AUS
GBR
KEN
TUR
GRC
DZA
NPL
AUT
AZE
DEU
CAN
BLR
SEN
JPN
MDG
IDN
GIN
ETH
SVK
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
2020-08-13 Summary: 9
12. Average daily deaths over past 7 days
COL
MEX
BOL
PER
ZAF
BRA
ARG
CHL
USA
IRN
IRQ
GTM
HND
DOM
ROU
KAZ
SLV
ECU
ISR
KGZ
SRB
SAU
BGR
GBR
RUS
IND
ZMB
LBY
AUS
PRY
UKR
BEL
MAR
ZWE
SWE
PHL
AZE
DZA
PRT
POL
HTI
AFG
VEN
BLR
IDN
EGY
SEN
ESP
BGD
KEN
MWI
UZB
AGO
TUR
MDG
ETH
CAN
GHA
CHE
FRA
TGO
NPL
ITA
YEM
DNK
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
2020-08-13 Summary: 12
13. Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISLISR
RUS
LTU
AUS
USA
QAT
PRT
MDV
BEL
GBR
BLR
IRL
KWT
CAN
KAZ
SGP
LVA
SAU
SRB
AUT
ESP
NZL
DEU
CHL
CHE
ESTNOR
FINROU
ITA
CZE
NLD
SVN
GRC
TURPAN
POL
ZAF
SVK
BGR
SLV
MAR
COL
URY
HUN
MYS
IRN
HRV
KOR
UKR
CUB
RWA
PRYCRI
INDARG
NPL
BOL
PHL
GHA
BRA
ECU
PER
JPNPAK
TUN
FJI
MEX
BGD
SEN
KEN
UGA
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 2020-08-13
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-13 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 2020-08-13
2020-08-13 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
2020-08-13 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 2020-08-13
2020-08-13 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
2020-08-13 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
RI
SC
SD
TN
TX
UT
VT
VA
WA
WV
WI
WY
-6
-3
0
3
6
-5 0 5
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days 2020-08-13
2020-08-13 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
MN
WI
NV
CO
AR
CT
IA
OK
UT
KY
KS
NE
ID
NM
OR
RI
DE
DC
SD
WV
ND
NH
MT
ME
HI
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: 0.35, p governor: 0.72. NB: association != causation.
2020-08-13 Summary: 20
21. Total US COVID-19 Cases
LA
AZ
FL
MS
NY
AL
GA
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
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: 0.92, p governor: 0.22. NB: association != causation.
2020-08-13 Summary: 21
22. Average US COVID-19 cases over the past
7 days
GA
FL
MS
AL
ID
LA
TN
TX
NV
AR
SC
CA
OK
MO
ND
AZ
IA
KS
IL
IN
NE
WI
KY
NC
UT
VA
HI
MD
MN
MT
SD
DC
OH
NM
WA
RI
AK
DE
CO
MI
OR
WV
PA
MA
WY
NJ
NY
CT
NH
VT
ME
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: 0.031, p governor: 0.012. NB: association != causation.
2020-08-13 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
MN
WA
MO
TN
RI
WI
NV
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: 0.057, p governor: 0.19. NB: association != causation.
2020-08-13 Summary: 23
24. Total US COVID-19 Deaths
NJ
NY
MA
CT
RI
LA
DC
MS
MI
IL
DE
MD
AZ
PA
IN
GA
SC
FL
AL
NM
TX
CO
NV
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: 0.029, p governor: 0.2. NB: association != causation.
2020-08-13 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
MS
AZ
LA
FL
SC
TX
GA
AL
NV
AR
CA
TN
NC
IA
ID
NM
ND
WV
OK
MT
OH
WA
MA
MD
IN
VA
SD
NE
MN
IL
MO
PA
OR
KS
UT
KY
WI
DC
HI
MI
RI
DE
CO
NJ
NY
CT
WY
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: 0.46, p governor: 0.019. NB: association != causation.
2020-08-13 Summary: 25
27. Percent of Positive COVID Tests
AZ
MS
FL
AL
SC
TX
ID
GA
NV
KS
IA
NE
MD
MA
AR
RI
IN
PA
CO
LA
VA
SD
MO
NJ
DE
UT
NC
TN
MN
WA
CA
OK
NY
IL
WI
OH
DC
CT
KY
WY
OR
ND
MI
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: 0.23, p governor: 0.017. NB: association != causation.
2020-08-13 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
2020-08-13 Summary: 28
29. Change in positive tests over past 14 days
HI
MT
WA
ND
OK
TX
NV
MO
ID
MN
AR
MS
KY
OR
AL
FL
TN
KS
WY
WV
NC
UT
SD
SC
WI
IA
IN
AK
GA
VA
CA
NE
LA
OH
CO
AZ
RI
NM
DE
PA
IL
VT
NH
MD
MI
MA
NJ
NY
DC
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: 0.094, p governor: 0.11. NB: association != causation.
2020-08-13 Summary: 29
30. Current hospitalizations as a percent of peak
since FebruaryHI
KY
MT
ND
WV
MO
AR
AK
AL
MS
TN
UT
NC
KS
ID
GA
WY
OK
OH
NV
VA
SC
NE
CA
OR
FL
IN
WA
LA
NM
TX
SD
WI
IA
MN
AZ
CO
IL
MD
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: 0.09, p governor: 0.051. NB: association != causation.
2020-08-13 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
2020-08-13 Summary: 31
32. Change in hospitalizations over past 14
days
HI
WI
SD
MT
WV
ND
RI
NE
KY
IN
MN
MA
IL
MO
VA
AR
WA
IA
KS
OR
AL
AK
UT
CT
NM
MS
NH
TN
NC
MI
PA
DC
WY
CO
MD
GA
ID
OH
OK
NY
SC
LA
NV
CA
NJ
FL
TX
ME
DE
AZ
VT
-5.0
-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: 0.86, p governor: 0.95. NB: association != causation.
2020-08-13 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 40
% Tested
%Mortality
Mortality vs. Testing as of 2020-08-13
2020-08-13 Summary: 33