COVID-19 Update (Summary): July 29, 2020

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

2,586,092
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)

Worldwide
25,642,501
905,627
1
10
100
1,000
10,000
100,000
1,000,000
10,000,000
100,000,000
Phase
Pre-Model
Modeled
Deaths
Worldwide projection as of 2020-07-29
0
100,000
200,000
300,000
0
5,000
10,000
15,000
Cases/Day
Deaths/Day
Cases: 16,673,118 (194,286) -- Deaths: 659,279 (5,319) -- Case Mortality: 4.0% -- Daily Change: -0.1% Cases, +0.7% Deaths
2020-07-29 Summary: 3

USA
6,981,518
181,895
1
10
100
1,000
10,000
100,000
1,000,000
10,000,000
100,000,000
Phase
Pre-Model
Modeled
Deaths
Tests
USA projection as of 2020-07-29
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: 4,351,997 (61,660) -- Deaths: 149,256 (1,244) -- Case Mortality: 3.4% -- Daily Change: -0.9% Cases, +2.1% Deaths
2020-07-29 Summary: 4

Japan, South Korea, Thailand, Vietnam
72,677
1,414
1
10
100
1,000
10,000
100,000
1,000,000
10,000,000
100,000,000
Phase
Pre-Model
Modeled
Deaths
Tests
Japan, South Korea, Thailand, Vietnam projection as of 2020-07-29
0
300
600
900
0
20
40
Cases/Day
Deaths/Day
Cases: 50,110 (1,037) -- Deaths: 1,359 (3) -- Case Mortality: 2.7% -- Daily Change: +4.2% Cases, +3.7% Deaths
2020-07-29 Summary: 5

Western Europe
1,549,333
170,644
1
10
100
1,000
10,000
100,000
1,000,000
10,000,000
100,000,000
Phase
Pre-Model
Modeled
Deaths
Tests
Western Europe projection as of 2020-07-29
0
20,000
40,000
60,000
80,000
0
1,000
2,000
3,000
4,000
Cases/Day
Deaths/Day
Cases: 1,439,516 (4,577) -- Deaths: 166,914 (172) -- Case Mortality: 11.6% -- Daily Change: +4.2% Cases, -2.1% Deaths
2020-07-29 Summary: 6

Worldwide cases
USA
BRA
IND
RUS
ZAF
MEX
PER
CHL
GBR
IRN
ESP
PAK
SAU
COL
ITA
BGD
TUR
FRA
DEU
ARG
CAN
IRQ
IDN
EGY
CHN
KAZ
PHL
UKR
NLD
ROU
POL
NGA
AFG
GHA
JPN
DZA
UZB
MAR
NPL
KEN
CMR
VEN
CIV
AUS
ETH
KOR
SDN
MDG
MYS
COD
THA
LKA
MOZ
YEM
UGA
NER
BFA
SYR
TZA
TWN
VNM
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
2020-07-29 Summary: 7

Worldwide cases per million
CHL
USA
PER
BRA
SAU
ZAF
ESP
RUS
COL
KAZ
GBR
IRN
ITA
ARG
IRQ
MEX
FRA
CAN
NLD
TUR
DEU
ROU
PAK
UKR
BGD
GHA
AFG
IND
POL
EGY
CMR
PHL
DZA
UZB
CIV
AUS
NPL
VEN
MAR
MDG
KEN
SDN
IDN
MYS
KOR
NGA
JPN
ETH
LKA
COD
MOZ
NER
YEM
BFA
CHN
THA
UGA
SYR
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
2020-07-29 Summary: 8

Average daily cases per capita over past 7
days
BRA
ZAF
USA
COL
PER
ARG
CHL
KAZ
IRQ
SAU
MEX
ROU
ESP
RUS
IRN
IND
GHA
UZB
UKR
VEN
PHL
AUS
DZA
MDG
BGD
KEN
CAN
FRA
MAR
TUR
POL
GBR
NLD
CIV
ETH
IDN
EGY
CMR
DEU
PAK
JPN
NPL
ITA
NGA
AFG
SDN
MOZ
KOR
SYR
COD
MYS
LKA
YEM
BFA
UGA
NER
CHN
THA
VNM
TWN
MMR
TZA
USA
0
100
200
1 6 11 16 21 26 31 36 41 46 51 56 61
Rank
Averagenewcasespercapita
Average daily cases per capita over past 7 days
2020-07-29 Summary: 9

Worldwide deaths
USA
BRA
GBR
MEX
ITA
IND
FRA
ESP
PER
IRN
RUS
CHL
DEU
COL
CAN
ZAF
NLD
PAK
TUR
IDN
EGY
CHN
IRQ
ARG
BGD
SAU
ROU
PHL
POL
UKR
AFG
DZA
JPN
NGA
KAZ
SDN
YEM
CMR
MAR
KOR
KEN
ETH
COD
AUS
GHA
VEN
MYS
UZB
CIV
MDG
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
2020-07-29 Summary: 10

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
CMR
IDN
YEM
PHL
BGD
MAR
AUS
JPN
KEN
GHA
KOR
NGA
VEN
MYS
CIV
NER
MDG
UZB
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
2020-07-29 Summary: 11

Average daily deaths per capita over past 7
days
PER
MEX
COL
ZAF
BRA
CHL
IRN
USA
IRQ
ARG
KAZ
GBR
SAU
ROU
RUS
IND
EGY
AFG
UKR
IDN
DZA
AUS
BGD
TUR
CAN
KEN
YEM
MDG
MAR
POL
VEN
PAK
SDN
UZB
PHL
ITA
CMR
ETH
FRA
GHA
SYR
NLD
DEU
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
2020-07-29 Summary: 12

Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISL
RUS
LTU
ISR
QAT
USAPRT
AUS
MDV
BLR
GBR
IRL
KWT
ITA
BEL
LVA
CAN
SGP
KAZ
NZL
AUT
SRB
DEU
CHE
EST
ESP
SAU
CHLNOR
CZE
FIN
SVN
ROU
POL
TUR
NLD
SVKZAF
PAN
GRC
BGR
SLV
HUN
MAR
KOR
MYS
URY
HRV
IRN
COL
UKR
CUB
RWA
PRY
CRI
BRA
IND
GHA
ARG
NPL
BOL
PHL
PER
ECU
PAK
TUN
FJI
BGD
MEX
SEN
JPN
THAKENTGO
CIV
TWNZWE
IDN
ETH
VNM
MMR
NGA
USA
0
5
10
15
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-07-29
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-07-29 Summary: 13

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
2020-07-29 Summary: 14

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 2020-07-29
2020-07-29 Summary: 15

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
2020-07-29 Summary: 16

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 2020-07-29
2020-07-29 Summary: 17

Deaths as a Percent of Peak Deaths
HI TX FL
OK LA MS AL GA
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
2020-07-29 Summary: 18

Total US COVID-19 Cases
CA
FL
NY
TX
NJ
IL
GA
AZ
NC
MA
PA
LA
TN
MI
VA
OH
MD
SC
AL
IN
WA
MS
MN
WI
CT
CO
MO
NV
IA
AR
UT
OK
KY
KS
NE
NM
ID
RI
OR
DE
DC
SD
NH
ND
WV
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: 0.29, p governor: 0.54. NB: association != causation.
2020-07-29 Summary: 19

Total US COVID-19 Cases per Million
LA
AZ
NY
FL
NJ
MS
RI
DC
MA
AL
SC
GA
DE
NV
TN
MD
TX
IL
CT
IA
AR
NE
UT
CA
NC
ID
VA
SD
IN
NM
MN
KS
PA
MI
WI
OK
ND
CO
OH
MO
WA
KY
NH
WY
OR
AK
WV
MT
ME
VT
HI
0
5,000
10,000
15,000
20,000
25,000
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
2020-07-29 Summary: 20

Average US COVID-19 cases over the past
7 days
FL
LA
MS
AZ
TN
AL
NV
SC
GA
TX
ID
OK
AR
CA
MO
NC
UT
ND
WI
NM
NE
KS
IA
MD
AK
KY
VA
IN
MN
OH
DE
IL
DC
WA
CO
MT
RI
WY
SD
OR
PA
WV
MI
NJ
MA
CT
NY
HI
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
2020-07-29 Summary: 21

Total US COVID-19 Deaths
NY
NJ
CA
MA
IL
PA
MI
FL
TX
CT
LA
GA
MD
AZ
OH
IN
VA
NC
CO
MN
SC
WA
MS
AL
MO
RI
TN
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
2020-07-29 Summary: 22

Total US COVID-19 Deaths per Million
NJ
NY
MA
CT
RI
DC
LA
MI
IL
DE
MD
PA
MS
AZ
IN
GA
CO
AL
SC
NH
NM
OH
MN
FL
IA
NV
VA
CA
TX
WA
MO
NC
NE
KY
WI
TN
AR
SD
ND
OK
KS
ME
VT
ID
UT
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
2020-07-29 Summary: 23

Average US COVID-19 deaths over the past
7 days
FL
LA
MS
AZ
TN
AL
NV
SC
GA
TX
ID
OK
AR
CA
MO
NC
UT
ND
WI
NM
NE
KS
IA
MD
AK
KY
VA
IN
MN
OH
DE
IL
DC
WA
CO
MT
RI
WY
SD
OR
PA
WV
MI
NJ
MA
CT
NY
HI
NH
ME
VT
0
100
200
300
400
500
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
2020-07-29 Summary: 24

Percent Tested
AK
NY
LA
DC
NM
NJ
CT
TN
IL
ND
RI
CA
DE
MN
MI
MA
AR
FL
UT
NC
WI
MT
WV
OK
VT
NV
MS
IA
MD
GA
AL
NE
SC
KY
VA
WA
AZ
SD
TX
OH
ME
NH
IN
MO
KS
ID
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
2020-07-29 Summary: 25

Positive fraction trends
HI TX FL
OK LA MS AL GA
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
2020-07-29 Summary: 26

Hospitalizations trends
HI TX FL
OK LA MS AL GA
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
2020-07-29 Summary: 27

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
MSMO
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 2020-07-29
2020-07-29 Summary: 28

COVID-19 Update (Summary): July 29, 2020

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