Creeping Stroke - Venous thrombosis presenting with pc-stroke.pptx
COVID-19 Update (Summary): August 19, 2020
1. Caveats and Comments
1
Overview:
This is my analysis, not Stanford’s. My goal is to understand the trajectory of COVID. It is not confidential and can be freely shared. The R program code is
available at https://github.com/StevenLShafer/COVID19/. The daily analysis are available at https://1drv.ms/u/s!AuOyHP_aTIy7rowrt2AjGpWm_frnEQ?e=KBcNbh.
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
PER
BRA
ISR
ARG
USA
BOL
ESP
IRQ
CHL
DOM
ZAF
ECU
GTM
LBY
HND
PRY
ROU
IND
MEX
SAU
BEL
KGZ
SLV
PHL
VEN
NLD
MAR
SRB
IRN
RUS
UKR
FRA
SWE
CHE
KAZ
AUT
DNK
CZE
UZB
NPL
BGR
GRC
PRT
GBR
ZMB
POL
BGD
TUR
DEU
DZA
ETH
AUS
AZE
KEN
CAN
GIN
BLR
GHA
SEN
NIC
IDN
ITA
JPN
SVK
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
2020-08-19 Summary: 9
12. Average daily deaths over past 7 days
PER
COL
BOL
MEX
BRA
ZAF
ARG
USA
CHL
KAZ
IRN
IRQ
DOM
ROU
GTM
ISR
ECU
PRY
HND
SAU
SLV
BGR
BEL
SRB
IND
LBY
RUS
MAR
AUS
UKR
KGZ
PHL
ITA
ZWE
BLR
SWE
VEN
PRT
ESP
DZA
POL
IDN
AZE
TUR
ZMB
BGD
EGY
ETH
GRC
FRA
NIC
CAN
AFG
KEN
UZB
SEN
GBR
HTI
GHA
NPL
MWI
NLD
CZE
MDG
SYR
USA
None
1 in 200,000
1 in 100,000
1 in 66,667
1 in 50,000
1 in 40,000
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
2020-08-19 Summary: 12
13. Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISLISR
RUS
LTU
AUS
USA
QATMDV
GBR
PRT
BEL
IRL
BLRKWT
NZL
CAN
SAU
SGP
LVA
KAZ
SRB
AUT
ESP
DEU
CHLEST
CHE
NOR
FINROU
NLD
CZE
ITA
GRC
TUR
SVN
POL
PANZAF
SVK
BGR
COL
MAR
SLVURY
HUN
MYS
IRN
HRV
KOR
IRQ
UKR
CUB
RWA
IND
PRYCRI
ARG
NPL
PHL
BOL
GHA
ECU
BRA
JPN
PER
PAK
TUN
MEX
FJI
BGD
SEN
KEN
UGA
TGO
THA
ZWE
CIV
ETH
IDN
TWN
VNM
MMR
NGA
USA
0
5
10
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-08-19
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-19 Summary: 13
14. CV for Cases and Deaths
NLD
GBR FRAITA ESP
CHE
CHN BELDEU
DNKFIN CANMYS CUBTCDMLI SWE
HUN AUT
KOR
BFA
PRT
CMRSSDSLE
PAK TUR
CZE
TUNECU JPNAFG SDN SVK GRCPOLYEMEGY CIV BENBLR USANGACHLCOD NICRUS DZAGIN
KGZHTI BRAAZESAU IRN BGDSRB UKRIDNMEXSEN PHLIRQROUDOMGTMHNDGHA ISRBGRPER SLV INDBOLTGO KEN SYRMOZCOLZAF MWIRWA ZMBARG VENUZBMDGKAZ MARAGONPL ETH LBYAUS
ZWEPRY
PNG
UGA
VNM
0.001
0.010
0.100
1.000
0.010.01 0.10 1.00
Cases CV
DeathsCV
Coefficient of variation for cases and deaths as of 2020-08-19
CV calculated over last 28 days
2020-08-19 Summary: 14
16. 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 2020-08-19
2020-08-19 Summary: 16
17. 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
2020-08-19 Summary: 17
18. 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 2020-08-19
2020-08-19 Summary: 18
19. 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
2020-08-19 Summary: 19
20. 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
VTVA
WA
WV
WI WY
-6
-3
0
3
-8 -4 0 4
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days as of 2020-08-19
2020-08-19 Summary: 20
21. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
AZ
NJ
NC
LA
TN
PA
MA
AL
OH
VA
SC
MI
MD
IN
MS
MO
WA
WI
MN
NV
CO
AR
IA
CT
OK
UT
KY
KS
NE
ID
OR
NM
RI
DE
DC
SD
ND
WV
NH
MT
HI
AK
ME
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: 0.38, p governor: 0.74. NB: association != causation.
2020-08-19 Summary: 21
22. Total US COVID-19 Cases
LA
FL
AZ
MS
GA
AL
NY
NJ
SC
NV
TN
TX
RI
DC
MA
AR
DE
IA
MD
IL
CA
ID
NE
UT
CT
NC
VA
OK
IN
KS
SD
MN
ND
MO
WI
NM
MI
PA
OH
CO
KY
WA
AK
WY
OR
MT
NH
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: 0.99, p governor: 0.17. NB: association != causation.
2020-08-19 Summary: 22
23. Average US COVID-19 cases over the past
7 days
GA
TX
FL
MS
NV
ID
TN
CA
MO
LA
AL
ND
OK
IA
KS
SC
HI
AR
KY
IL
IN
AZ
DE
NE
VA
WI
SD
NC
UT
MD
AK
MN
MT
DC
RI
OH
MI
WA
WV
NM
WY
OR
PA
CO
MA
NJ
NY
CT
NH
ME
VT
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
Rank
NewCases/Day
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 cases over the past 7 days
p masks: 0.039, p governor: 0.018. NB: association != causation.
2020-08-19 Summary: 23
24. Total US COVID-19 Deaths
NY
NJ
CA
TX
FL
MA
IL
PA
MI
GA
LA
AZ
CT
OH
MD
IN
NC
VA
SC
MS
AL
CO
WA
MN
MO
TN
NV
WI
RI
IA
KY
NM
OK
AR
DC
DE
NH
KS
OR
NE
UT
ID
WV
SD
ND
ME
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: 0.059, p governor: 0.21. NB: association != causation.
2020-08-19 Summary: 24
25. Total US COVID-19 Deaths
NJ
NY
MA
CT
LA
RI
DC
MS
MI
IL
AZ
DE
MD
PA
IN
SC
FL
GA
AL
TX
NV
NM
OH
CO
IA
MN
NH
CA
VA
WA
MO
NC
TN
AR
NE
KY
WI
SD
OK
ND
ID
KS
UT
ME
OR
VT
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: 0.034, p governor: 0.21. NB: association != causation.
2020-08-19 Summary: 25
26. Average US COVID-19 deaths over the past
7 days
MS
FL
LA
SC
GA
AZ
TX
NV
AL
TN
CA
ID
IA
AR
ND
NC
OK
IN
OH
NM
MA
WA
MO
PA
KY
WV
MN
IL
DC
NE
MD
OR
SD
KS
RI
MT
MI
VA
UT
WI
CO
NJ
HI
AK
NY
NH
WY
CT
DE
ME
VT
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: 0.25, p governor: 0.017. NB: association != causation.
2020-08-19 Summary: 26
27. Daily testing 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
Dailytestingfrommintomax
Daily testing trends from min to max
Line = Friedman's supersmoother
2020-08-19 Summary: 27
28. Change in daily tests over past 14 days
HI
VA
MA
WV
NC
DC
GA
MO
AR
AL
OK
CT
MD
MI
ME
IN
NY
KS
IA
VT
NJ
CA
IL
KY
NE
WY
OR
OH
SC
SD
MN
NH
RI
TN
TX
DE
ND
ID
CO
PA
LA
NV
AK
MS
AZ
UT
NM
FL
MT
WI
WA
-4.0
-2.0
0.0
2.0
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeindailytests(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in daily tests over past 14 days
p masks: 0.1, p governor: 0.74. NB: association != causation.
2020-08-19 Summary: 28
30. Percent of Positive COVID Tests
AZ
MS
FL
AL
ID
SC
TX
GA
NV
KS
IA
NE
IN
RI
MD
PA
AR
MA
CO
LA
SD
MO
VA
UT
DE
NC
NJ
TN
WA
MN
OK
CA
WI
IL
NY
OH
KY
WY
DC
CT
ND
OR
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: 0.14, p governor: 0.014. NB: association != causation.
2020-08-19 Summary: 30
31. 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
2020-08-19 Summary: 31
32. Change in positive tests over past 14 days
HI
MT
NC
WA
ND
ID
MO
KY
NV
AK
OK
MS
KS
TX
WY
FL
WI
SD
WV
OR
CA
IA
TN
UT
MN
IN
NE
GA
AR
DE
AL
VA
OH
CO
NM
RI
LA
AZ
SC
IL
PA
VT
NH
MI
MD
NJ
NY
CT
MA
ME
DC
-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: 0.065, p governor: 0.34. NB: association != causation.
2020-08-19 Summary: 32
33. Change in tests vs change in positive tests
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
SDTN
TX
UT
VT
VA
WA
WV
WI WY
-1
0
1
2
3
-4 -2 0
Change in tests (%/day)
Changeinpositivetests(%/day)
Change in tests vs change in positive tests last 14 days as of 2020-08-19
2020-08-19 Summary: 33
34. Current hospitalizations as a percent of peak
since FebruaryAK
HI
MT
ND
WV
MO
KY
AR
MS
ID
OH
KS
TN
OK
NC
GA
AL
VA
NE
NV
OR
SD
UT
CA
IA
WY
SC
WA
IN
LA
FL
WI
NM
TX
MN
VT
AZ
IL
MD
RI
CO
PA
MI
DC
ME
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: 0.031, p governor: 0.048. NB: association != causation.
2020-08-19 Summary: 34
35. 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
2020-08-19 Summary: 35
36. Change in hospitalizations over past 14
days
HI
VT
SD
MT
WI
IA
ND
WV
AK
NE
MI
OR
IL
MA
MO
VA
MN
WA
IN
RI
KY
MS
NY
ID
AR
OH
DC
PA
NM
OK
NC
TN
GA
KS
CA
AL
CT
NV
MD
LA
ME
SC
UT
TX
FL
WY
DE
CO
NJ
AZ
NH
-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: 0.62, p governor: 0.93. NB: association != causation.
2020-08-19 Summary: 36
37. 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 2020-08-19
2020-08-19 Summary: 37
38. CV for Cases and Deaths
LAIL MACA
NC
FLOK NMSCNV TNIN MSOHMDIA WA ARUTOR GAKY TX PAIDKS WIMN MO ALNE AZMI
MTSDDC RIND
AKNY CO CT
NJVA ME
WYWV
NH
HI
VT
DE
0.010.01
0.10
1.00
0.010.01 0.10 1.00
Cases CV
DeathsCV
Coefficient of variation for cases and deaths as of 2020-08-19
CV calculated over last 28 days
2020-08-19 Summary: 38