COVID-19 Update (Summary): July 31, 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)

3. Worldwide
25,825,982
909,457
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
Worldwide projection as of 2020-07-31
0
100,000
200,000
300,000
0
5,000
10,000
15,000
Cases/Day
Deaths/Day
Cases: 17,286,447 (266,309) -- Deaths: 673,075 (6,051) -- Case Mortality: 3.9% -- Daily Change: +1.3% Cases, +0.6% Deaths
2020-07-31 Summary: 3

4. USA
6,928,805
184,481
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 2020-07-31
Mother'sDay
MemorialDay
July4th
July15,2020
0
20,000
40,000
60,000
80,000
0
1,000
2,000
3,000
4,000
Cases/Day
Deaths/Day
Cases: 4,494,601 (67,619) -- Deaths: 152,055 (1,233) -- Case Mortality: 3.4% -- Daily Change: +0.0% Cases, +3.0% Deaths
2020-07-31 Summary: 4

5. Japan, South Korea, Thailand, Vietnam
76,894
1,422
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
Japan, South Korea, Thailand, Vietnam projection as of 2020-07-31
0
500
1,000
1,500
2,000
0
25
50
75
100
Cases/Day
Deaths/Day
Cases: 53,262 (1,854) -- Deaths: 1,366 (7) -- Case Mortality: 2.6% -- Daily Change: +7.3% Cases, +4.8% Deaths
2020-07-31 Summary: 5

6. Western Europe
1,565,213
170,471
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
Western Europe projection as of 2020-07-31
0
20,000
40,000
60,000
80,000
0
1,000
2,000
3,000
4,000
Cases/Day
Deaths/Day
Cases: 1,452,642 (7,827) -- Deaths: 167,094 (73) -- Case Mortality: 11.5% -- Daily Change: +4.4% Cases, -1.5% Deaths
2020-07-31 Summary: 6

7. Ukraine
97,921
2,374
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
Ukraine projection as of 2020-07-31
0
500
1,000
0
20
40
60
Cases/Day
Deaths/Day
Cases: 70,300 (1,222) -- Deaths: 1,697 (24) -- Case Mortality: 2.4% -- Daily Change: +2.9% Cases, +1.7% Deaths
2020-07-31 Summary: 7

8. Worldwide cases
USA
BRA
IND
RUS
ZAF
MEX
PER
CHL
GBR
IRN
ESP
PAK
COL
SAU
ITA
BGD
TUR
FRA
DEU
ARG
IRQ
CAN
IDN
EGY
KAZ
CHN
PHL
UKR
NLD
ROU
POL
NGA
AFG
JPN
GHA
DZA
UZB
MAR
KEN
NPL
VEN
CMR
AUS
ETH
CIV
KOR
SDN
MDG
COD
MYS
THA
LKA
MOZ
YEM
UGA
NER
BFA
SYR
TZA
VNM
TWN
MMR
USA
0
1,000,000
2,000,000
3,000,000
4,000,000
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Totalcasestodate
Worldwide cases
ZAF: South Africa, SAU: Saudi Arabia, PER: Peru, COL: Columbia
2020-07-31 Summary: 8

9. Worldwide cases per million
CHL
USA
PER
BRA
ZAF
SAU
ESP
COL
RUS
KAZ
GBR
IRN
ARG
ITA
IRQ
MEX
FRA
CAN
NLD
TUR
DEU
ROU
PAK
UKR
BGD
GHA
IND
AFG
POL
EGY
CMR
DZA
PHL
UZB
AUS
CIV
NPL
MAR
VEN
MDG
KEN
SDN
IDN
MYS
KOR
NGA
JPN
ETH
LKA
COD
MOZ
NER
YEM
BFA
CHN
THA
SYR
UGA
TWN
TZA
MMR
VNM
USA
0
5,000
10,000
15,000
20,000
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Totalcasestodatepermillion
Worldwide cases per million
ZAF: South Africa, SAU: Saudi Arabia, PER: Peru, COL: Columbia
2020-07-31 Summary: 9

10. Average daily cases per capita over past 7
days
BRA
ZAF
USA
COL
PER
ARG
CHL
KAZ
IRQ
SAU
MEX
ESP
ROU
IND
RUS
IRN
GHA
UZB
UKR
VEN
AUS
MAR
DZA
BGD
PHL
KEN
MDG
CAN
FRA
NLD
GBR
POL
TUR
DEU
JPN
IDN
CIV
ETH
NPL
EGY
PAK
CMR
ITA
NGA
AFG
MOZ
SDN
SYR
KOR
COD
MYS
YEM
LKA
BFA
UGA
CHN
VNM
NER
THA
TWN
MMR
TZA
USA
0
100
200
300
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Averagenewcasespercapita
Average daily cases per capita over past 7 days
ZAF: South Africa, SAU: Saudi Arabia, PER: Peru, COL: Columbia
2020-07-31 Summary: 10

11. Worldwide deaths
USA
BRA
GBR
MEX
IND
ITA
FRA
ESP
PER
IRN
RUS
COL
CHL
DEU
CAN
ZAF
NLD
PAK
TUR
IDN
EGY
IRQ
CHN
ARG
BGD
SAU
ROU
PHL
POL
UKR
AFG
DZA
JPN
NGA
KAZ
SDN
YEM
CMR
MAR
KEN
KOR
ETH
COD
AUS
GHA
VEN
UZB
MYS
MDG
CIV
NER
THA
BFA
NPL
SYR
TZA
MOZ
LKA
TWN
MMR
UGA
VNM
USA
0
50,000
100,000
150,000
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Totaldeathstodate
Worldwide deaths
ZAF: South Africa, SAU: Saudi Arabia, PER: Peru, COL: Columbia
2020-07-31 Summary: 11

12. Worldwide deaths per million
GBR
ESP
PER
ITA
CHL
FRA
USA
BRA
MEX
NLD
CAN
IRN
COL
ZAF
IRQ
DEU
ROU
SAU
RUS
ARG
TUR
EGY
KAZ
AFG
POL
UKR
DZA
PAK
IND
SDN
IDN
CMR
YEM
PHL
BGD
MAR
AUS
KEN
JPN
GHA
KOR
VEN
NGA
MDG
UZB
CIV
MYS
NER
CHN
BFA
COD
ETH
SYR
NPL
THA
LKA
MOZ
TZA
TWN
MMR
UGA
VNM
USA
0
200
400
600
800
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Totaldeathstodatepermillion
Worldwide deaths per million
ZAF: South Africa, SAU: Saudi Arabia, PER: Peru, COL: Columbia
2020-07-31 Summary: 12

13. Average daily deaths per capita over past 7
days
PER
COL
MEX
BRA
CHL
ZAF
USA
IRN
ARG
IRQ
KAZ
ROU
GBR
SAU
RUS
IND
EGY
UKR
AUS
AFG
DZA
IDN
BGD
CAN
MAR
MDG
POL
TUR
KEN
UZB
VEN
PAK
YEM
PHL
FRA
GHA
ETH
ITA
SDN
DEU
NLD
CMR
SYR
NGA
ESP
NPL
CIV
COD
JPN
KOR
UGA
MYS
CHN
BFA
MOZ
MMR
NER
LKA
TWN
TZA
THA
VNM
USA
0
10
20
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Averagenewdeathspercapita
Average daily deaths per capita over past 7 days
ZAF: South Africa, SAU: Saudi Arabia, PER: Peru, COL: Columbia
2020-07-31 Summary: 13

14. Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISL
RUS
LTU
ISR
QAT
USA
AUS
PRT
MDV
BLR
GBR
IRL
KWT
ITA
SGP
BEL
LVA
CAN
KAZ
AUT
SRB
DEU
NZL
ESP
SAU
CHE
EST
CHLNOR
CZE
FIN
SVN
ROU
POL
NLD
TUR
GRC
PAN
ZAF
SVK
BGR
SLV
HUN
MAR
KOR
MYS
IRN
HRVURY
COL
UKR
CUB
RWA
PRYCRI
IND
ARG
GHA
PHL
BOLBRA
NPL
PER
ECU
PAK
TUN
FJI
BGD
SEN
MEX
JPN
THAKEN
TGO
ZWE
CIV
TWN
IDN
ETH
VNM
MMR
NGA
USA
0
5
10
15
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-07-31
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-07-31 Summary: 14

15. Mortality Trends
0
2
4
6
8
10
12
14
CaseRateMortality
Mortality Type:
13 day rolling median
Cumulative
Daily Raw
Daily vs. Cumulative Case Rate Mortality
Last week excluded because deaths are often backdated
2020-07-31 Summary: 15

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 2020-07-31
2020-07-31 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
2020-07-31 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 2020-07-31
2020-07-31 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
2020-07-31 Summary: 19

20. Total US COVID-19 Cases
CA
FL
TX
NY
GA
NJ
IL
AZ
NC
MA
PA
LA
TN
MI
OH
VA
SC
MD
AL
IN
MS
WA
MN
WI
CT
MO
NV
CO
IA
AR
UT
OK
KY
KS
NE
NM
ID
RI
OR
DE
DC
SD
NH
WV
ND
ME
MT
AK
WY
HI
VT
0
100,000
200,000
300,000
400,000
500,000
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: 0.33, p governor: 0.61. NB: association != causation.
2020-07-31 Summary: 20

21. Total US COVID-19 Cases per Million
LA
AZ
FL
NY
NJ
MS
RI
AL
GA
DC
SC
MA
NV
DE
TN
TX
MD
IL
IA
CT
AR
NE
CA
UT
NC
ID
VA
SD
NM
IN
MN
KS
PA
OK
MI
WI
ND
CO
MO
OH
WA
KY
NH
WY
OR
AK
MT
WV
ME
VT
HI
0
10,000
20,000
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalCasesperMillion
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Cases per Million
p masks: 0.59, p governor: 0.46. NB: association != causation.
2020-07-31 Summary: 21

22. Average US COVID-19 cases over the past
7 days
FL
MS
LA
AL
GA
AZ
TN
NV
SC
TX
ID
AR
OK
MO
CA
NC
IA
UT
WI
ND
NM
NE
KS
MD
KY
AK
MN
VA
IN
MT
OH
DE
IL
WA
RI
CO
DC
WY
SD
OR
WV
MI
PA
CT
HI
NJ
MA
NY
NH
ME
VT
0
100
200
300
400
500
1 6 11 16 21 26 31 36 41 46 51
Rank
DailyCasesperMillion
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 cases over the past 7 days
p masks: 0.022, p governor: 0.01. NB: association != causation.
2020-07-31 Summary: 22

23. Total US COVID-19 Deaths
NY
NJ
CA
MA
IL
PA
FL
MI
TX
CT
LA
GA
AZ
MD
OH
IN
VA
NC
CO
SC
MN
MS
AL
WA
MO
TN
RI
WI
IA
NV
KY
NM
DC
DE
OK
AR
NH
KS
NE
OR
UT
ID
SD
ME
WV
ND
VT
MT
HI
WY
AK
0
10,000
20,000
30,000
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalDeathsperMillion
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Deaths
p masks: 0.047, p governor: 0.13. NB: association != causation.
2020-07-31 Summary: 23

24. Total US COVID-19 Deaths per Million
NJ
NY
MA
CT
RI
LA
DC
MI
IL
DE
MD
PA
MS
AZ
IN
GA
SC
AL
CO
FL
NH
NM
OH
MN
IA
NV
VA
CA
TX
WA
MO
NC
NE
KY
WI
TN
AR
SD
OK
ND
KS
ID
UT
VT
ME
OR
WV
MT
WY
AK
HI
0
500
1,000
1,500
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalDeathsperMillion
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Deaths per Million
p masks: 0.036, p governor: 0.13. NB: association != causation.
2020-07-31 Summary: 24

25. Average US COVID-19 deaths over the past
7 days
AZ
SC
TX
MS
FL
DE
LA
AL
GA
NV
CA
ID
TN
NM
AR
NC
OH
MA
IA
OK
MO
MD
WA
UT
KS
IN
MT
KY
SD
OR
VA
IL
NJ
NH
RI
WI
ND
PA
CO
NE
MN
CT
NY
WV
DC
MI
AK
ME
WY
VT
HI
0.0
3.0
6.0
9.0
12.0
1 6 11 16 21 26 31 36 41 46 51
Rank
DailydeathsperMillion
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 deaths over the past 7 days
p masks: 0.49, p governor: 0.066. NB: association != causation.
2020-07-31 Summary: 25

26. Percent Tested
AK
NY
LA
NM
DC
NJ
CT
TN
IL
ND
CA
RI
DE
MI
MN
MA
FL
AR
NC
UT
WI
MT
OK
WV
MS
NV
VT
IA
MD
GA
AL
NE
SC
KY
VA
WA
SD
TX
AZ
OH
ME
NH
MO
IN
ID
KS
OR
PA
WY
CO
HI
0
10
20
30
1 6 11 16 21 26 31 36 41 46 51
Rank
PercentTested
Masks
No
Yes
Governor
aa
Democratic
Republican
Percent Tested
p masks: 0.15, p governor: 0.27. NB: association != causation.
2020-07-31 Summary: 26

27. 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
2020-07-31 Summary: 27

28. 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
2020-07-31 Summary: 28

29. 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
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
WVWI
WY
2.5
5.0
7.5
10 15 20 25 30
% Tested
%Mortality
Mortality vs. Testing as of 2020-07-31
2020-07-31 Summary: 29