1) This document provides an analysis of COVID-19 cases and projections for various locations around the world.
2) It outlines the models, data sources, and methods used to generate the analysis and projections.
3) The analysis is updated daily and made freely available online, with the goal of understanding the trajectory of the pandemic without a political agenda.
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Β
COVID-19 Update (Summary): August 18, 2020
1. Caveats and Comments
1
Overview:
This is my analysis, not Stanfordβs. 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 isnβt clear, please see the explanation on slide 2.
Data sources:
β’ 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
β’ 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
β’ USA Testing and Hospitalization Data: https://raw.githubusercontent.com/COVID19Tracking/covid-tracking-data/master/data/states_daily_4pm_et.csv
β’ 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
β’ 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
β’ Global Testing Data: https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv
β’ Mobility Data: https://www.gstatic.com/covid19/mobility/Global_Mobility_Report.csv
β’ Partisan Lean: MIT Election Data and Science Lab: https://doi.org/10.7910/DVN/VOQCHQ/HEIJCQ
β’ 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 ππ’ππ’πππ‘ππ£π πππ ππ =
ππ’πππππ‘ πππ ππ + πππ₯πππ’π πππ ππ β ππ’πππππ‘ πππ ππ 1 β πβπ π‘ . This is a naΓ―ve 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
(yesterdayβs cases)
and cumulative deaths
(yesterdayβs 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
PER
COL
BRA
ISR
ARG
USA
BOL
ESP
IRQ
CHL
DOM
ZAF
ECU
LBY
GTM
PRY
HND
ROU
IND
MEX
BEL
SAU
SLV
KGZ
PHL
FRA
NLD
VEN
SRB
SWE
MAR
RUS
IRN
UKR
KAZ
DNK
CHE
UZB
AUT
CZE
PRT
BGR
NPL
GRC
ZMB
GBR
POL
BGD
TUR
DEU
DZA
AUS
KEN
ETH
AZE
CAN
SEN
BLR
GHA
GIN
IDN
ITA
JPN
SVK
ZWE
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
2020-08-18 Summary: 9
12. Average daily deaths over past 7 days
PER
COL
BOL
MEX
BRA
ZAF
ARG
CHL
USA
IRN
IRQ
DOM
ROU
KAZ
GTM
ISR
HND
ECU
PRY
SLV
SAU
BGR
SRB
BEL
IND
LBY
AUS
RUS
MAR
KGZ
UKR
PHL
ESP
ITA
BLR
SWE
ZWE
ZMB
VEN
PRT
DZA
AFG
AZE
POL
IDN
TUR
EGY
BGD
SEN
FRA
GRC
ETH
KEN
GBR
UZB
HTI
CAN
MWI
NPL
MDG
AGO
GHA
AUT
NLD
CZE
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
2020-08-18 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
NZL
SAU
LVA
KAZ
SRB
SGP
AUT
DEU
ESP
CHL
CHE
EST
NOR
FINROU
CZE
ITA
NLD
GRC
SVN
TURPAN
POL
ZAF
SVK
BGR
MAR
SLV
COL
URY
HUN
MYS
IRN
HRV
KOR
IRQ
UKR
CUB
RWA
IND
PRYCRI
ARG
NPL
BOL
PHL
GHA
ECU
BRA
JPN
PER
PAK
TUN
FJI
MEX
SEN
BGD
KEN
UGA
TGO
THA
ZWE
CIV
IDN
ETHTWN
VNM
MMR
NGA
USA
0
5
10
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-08-18
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-18 Summary: 13
14. CV for Cases and Deaths
NLD
ITA ESPGBR FRA
CHE
CHN BEL
DEU
DNKFIN CAN CUBMYS TCD
SWE HUN AUTMLI
KOR
BFA
PRT
SLESSDCMR
TURPAK TUNCZE
JPN
ECUAFG GRCSDN SVKPOLYEMEGY CIV USABLR CHL BENNGACOD
RUS NIC DZAGIN
HTI BRASAU BGDIRNAZE KGZUKRSRB IDNMEX PHLSEN ROUDOM IRQGTMGHAHND ISRBGRPER SLV INDBOLTGO SYRKENRWA MOZ COLZAFMWI ZMBARG VENUZBKAZ MARMDG AGONPL ETH LBYAUS
PRYZWE
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 2020-08-18
CV calculated over last 28 days
2020-08-18 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 2020-08-18
2020-08-18 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
2020-08-18 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 2020-08-18
2020-08-18 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
2020-08-18 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
-4
-2
0
2
4
-8 -4 0 4
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days as of 2020-08-18
2020-08-18 Summary: 20
21. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
AZ
NJ
NC
LA
TN
PA
MA
OH
AL
VA
SC
MI
MD
IN
MS
MO
WA
WI
MN
NV
CO
AR
IA
CT
OK
UT
KY
KS
NE
ID
NM
OR
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: 0.39, p governor: 0.73. NB: association != causation.
2020-08-18 Summary: 21
22. Total US COVID-19 Cases
LA
FL
AZ
MS
GA
AL
NY
NJ
SC
NV
TN
RI
TX
DC
MA
AR
DE
IA
MD
IL
CA
NE
ID
UT
CT
NC
VA
OK
IN
KS
SD
MN
WI
ND
MO
NM
MI
PA
OH
CO
WA
KY
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: 0.19. NB: association != causation.
2020-08-18 Summary: 22
23. Average US COVID-19 cases over the past
7 days
GA
FL
TX
NV
ID
CA
TN
MS
MO
AL
LA
ND
KS
OK
SC
IA
AR
HI
NE
IL
KY
IN
DE
AZ
WI
NC
UT
MD
VA
MN
SD
AK
RI
MT
DC
OH
WA
MI
NM
WV
OR
PA
WY
CO
MA
NJ
CT
NY
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: 0.043, p governor: 0.023. NB: association != causation.
2020-08-18 Summary: 23
24. Total US COVID-19 Deaths
NY
NJ
CA
TX
FL
MA
IL
PA
MI
GA
LA
AZ
CT
OH
MD
IN
VA
NC
SC
MS
AL
CO
WA
MN
MO
TN
NV
WI
RI
IA
KY
NM
OK
AR
DC
DE
NH
KS
OR
UT
NE
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: 0.21. NB: association != causation.
2020-08-18 Summary: 24
25. Total US COVID-19 Deaths
NJ
NY
MA
CT
LA
RI
DC
MS
MI
IL
AZ
DE
MD
PA
IN
GA
SC
FL
AL
TX
NV
NM
CO
OH
IA
MN
NH
CA
VA
WA
MO
NC
TN
AR
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: 0.034, p governor: 0.21. NB: association != causation.
2020-08-18 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
AR
ND
IA
NM
OK
MA
NC
IN
OH
MO
WA
WV
PA
MN
KY
IL
MD
KS
NE
UT
DC
RI
SD
OR
WI
VA
MI
CO
MT
HI
NJ
CT
NY
WY
NH
AK
DE
ME
VT
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
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: 0.012. NB: association != causation.
2020-08-18 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
2020-08-18 Summary: 27
28. Change in daily tests over past 14 days
VT
HI
MA
VA
WV
NC
MO
ME
NJ
AR
IL
MI
CT
OK
MD
KS
IN
NY
IA
DC
CA
PA
AL
NE
KY
OR
OH
SC
ND
TX
TN
SD
CO
MN
RI
ID
NH
AK
LA
WY
DE
NV
MS
AZ
UT
FL
NM
MT
GA
WI
WA
-6.0
-3.0
0.0
3.0
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: 0.039, p governor: 0.77. NB: association != causation.
2020-08-18 Summary: 28
30. Percent of Positive COVID Tests
AZ
MS
FL
AL
ID
SC
TX
GA
NV
KS
IA
NE
IN
RI
MD
AR
PA
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: 0.013. NB: association != causation.
2020-08-18 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
2020-08-18 Summary: 31
32. Change in positive tests over past 14 days
HI
MT
WA
NC
ND
ID
MO
OK
KY
NV
MS
TX
AK
KS
FL
WY
WI
WV
TN
OR
CA
SD
UT
IA
MN
AR
IN
NE
GA
AL
DE
VA
OH
CO
LA
NM
RI
SC
AZ
IL
PA
VT
NH
MD
MI
NJ
CT
NY
MA
DC
ME
0.0
2.0
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: 0.077, p governor: 0.3. NB: association != causation.
2020-08-18 Summary: 32
33. Change in tests vs change in positive tests
AL
AK
AZ
ARCA
CO
CT
DE
DC
FL
GA
HI
ID
IL
INIA
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
WVWI WY
-1
0
1
2
3
4
-5.0 -2.5 0.0 2.5 5.0
Change in tests (%/day)
Changeinpositivetests(%/day)
Change in tests vs change in positive tests last 14 days as of 2020-08-18
2020-08-18 Summary: 33
34. Current hospitalizations as a percent of peak
since FebruaryHI
MT
ND
WV
AK
ID
KY
MO
MS
AR
KS
OH
TN
NC
GA
OK
AL
VA
NV
OR
NE
WY
UT
SC
CA
SD
IA
WA
IN
LA
FL
NM
WI
TX
MN
AZ
VT
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: 0.037, p governor: 0.058. NB: association != causation.
2020-08-18 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
2020-08-18 Summary: 35
36. Change in hospitalizations over past 14
days
HI
SD
VT
MT
WI
ND
WV
IA
RI
IL
MI
OR
NE
MA
MN
AK
IN
MO
ID
KY
WA
VA
MS
NY
AR
OH
DC
NM
KS
PA
CT
NC
GA
TN
OK
NV
AL
MD
CA
LA
SC
UT
WY
CO
FL
ME
TX
DE
NH
NJ
AZ
-2.5
0.0
2.5
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: 0.65, p governor: 0.77. NB: association != causation.
2020-08-18 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 2020-08-18
2020-08-18 Summary: 37
38. CV for Cases and Deaths
MA
LAIL
TNCA
OKIA NMFLIN NV SCNCMDWIKY OH MSALWA UTGAPATX ARMN ID AZOR MOKSMI
DC NEND MT SDRI CTCONY AK
MENJVA WY
WV 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 2020-08-18
CV calculated over last 28 days
2020-08-18 Summary: 38