This is my daily update for COVID-19 trends for July 21, 2020.
Prior analyses and the R program code can be found at https://github.com/StevenLShafer/COVID19
1. Caveats and Comments
1
Overview:
This is my analysis, not Stanford’s. It is simply a set of regressions in R to understand the trajectory of COVID. It is not confidential and can be freely shared. The R
program code and all previous 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. If
you create new graphs, please let me know, as I may want to add them to my analyses.
I am attempting to keep the analysis and commentary apolitical. I am now including partisan lean as a metric. This is just more data to understand the COVID
epidemic. I occasionally point out misrepresentations by government officials. Additionally, as the crisis has worsened, I will point out where government
recommendations have placed Americans at increasing risk.
I try to provide a daily update in the morning. However, as an anesthesiologist at Stanford, when I have clinical duties my analysis my be delayed.
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: log 𝑐𝑢𝑚𝑢𝑙𝑎𝑡𝑖𝑣𝑒 𝑐𝑎𝑠𝑒𝑠 = 𝑐𝑢𝑟𝑟𝑒𝑛𝑡 𝑐𝑎𝑠𝑒𝑠 + 𝑚𝑎𝑥𝑖𝑚𝑢𝑚 𝑐𝑎𝑠𝑒𝑠 − 𝑐𝑢𝑟𝑟𝑒𝑛𝑡 𝑐𝑎𝑠𝑒𝑠 1 −
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)
8. 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 2020-07-21
8
9. 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
9
10. 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 2020-07-21
10
11. 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
11
12. Total cases per million
HI
VT
MT
AK
ME
WV
OR
WY
NH
KY
MO
WA
OK
OH
ND
CO
WI
KS
NM
PA
MI
MN
IN
ID
SD
VA
NC
CA
UT
AR
TN
NE
TX
NV
IA
IL
MD
CT
GA
SC
DE
AL
MS
DC
MA
FL
RI
NJ
AZ
LA
NY
0
5000
10000
15000
20000
0 10 20 30 40 50
State
Totalcasespermillionpopulation
Total cases to date
Total US COVID-19 Cases
12
13. Case rates per million
VT
HI
ME
NH
NJ
CT
NY
MA
PA
WV
SD
RI
WY
MI
CO
OR
AK
DC
IL
MT
IN
DE
MN
NE
KY
VA
OH
MD
WA
MO
ND
NM
WI
IA
KS
OK
NC
UT
AR
CA
ID
MS
TN
GA
TX
SC
NV
AZ
AL
LA
FL
0
200
400
0 10 20 30 40 50
State
Averagenewcasesperdaypermillionpopulation
Average over past 7 days
US COVID-19 Case Rates
13
14. Total deaths per million
HI
AK
MT
WY
WV
OR
ID
UT
ME
VT
KS
OK
AR
ND
TN
SD
TX
WI
KY
NC
NE
MO
WA
CA
NV
SC
FL
VA
IA
AL
OH
NM
MN
NH
GA
CO
AZ
IN
MS
DE
PA
MD
IL
MI
LA
DC
RI
MA
CT
NY
NJ
0
500
1000
1500
0 10 20 30 40 50
State
Totaldeathspermillionpopulation
Total deaths to date
Total US COVID-19 Deaths
14
15. Deaths rates per million
VT
AK
WA
ME
WV
HI
WI
NH
KS
CO
MI
DE
OR
WY
MO
OK
VA
ND
MN
NY
IL
PA
MT
IN
UT
SD
KY
MD
ID
OH
AR
NE
IA
NC
TN
DC
MA
NM
CT
GA
NV
RI
CA
NJ
LA
TX
AL
MS
FL
SC
AZ
0.0
2.5
5.0
7.5
10.0
0 10 20 30 40 50
State
Averagedeathsperdaypermillionpopulation
Averaged over past 7 days
US COVID-19 Death Rates
15
16. Percent tested by state
HI
WY
CO
OR
PA
ID
KS
MO
IN
OH
TX
ME
NH
WA
VA
AZ
KY
SD
SC
GA
OK
AL
NE
MD
NV
MT
MS
WV
IA
VT
WI
NC
FL
AR
UT
MI
MA
MN
DE
CA
RI
TN
ND
IL
CT
NJ
DC
NM
LA
AK
NY
0
10
20
0 10 20 30 40 50
State
PercentTested
Percent Tested
16
17. 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
17
18. 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
18
19. 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
MTNE
NV
NH
NJ
NM
NY
NC
ND
OH
OKOR
PA
RI
SC
SD
TN
TX
UT
VT
VA
WA
WVWI
WY
2.5
5.0
7.5
10 15 20 25
% Tested
%Mortality
Mortality vs. Testing as of 2020-07-21
19
73. Change in New Cases per Day
Direction
Increasing > +2%
Increasing between +0.5% and +2%
No Change (-0.5% to +0.5%)
Decreasing between -0.5% and -2%
Decreasing > -2%
NA
Trends by county as of 2020-07-21
NA = Inadequate data
73
74. Percent Change by Partisan Lean
-10
-5
0
5
10
0 25 50 75 100
Percent Republican
Percentchangeinnewcasesperday
25
50
75
Republican
Counties by 2016 presidential election results
Dark green line is a Friedman's supersmoother
74
75. Percent Change by Population
-10
-5
0
5
10
1,000 10,000 100,000 1,000,000 10,000,000
Population
Percentchangeinnewcasesperday
25
50
75
Republican
Counties by Population
Dark green line is a Friedman's 'super smoother'
75
76. Partisan Lean vs Population and Direction
1,000
10,000
100,000
1,000,000
10,000,000
0 25 50 75 100
Percent Republican
Population
Direction
Increasing > +2%
Increasing between +0.5% and +2%
No Change (-0.5% to +0.5%)
Decreasing between -0.5% and -2%
Decreasing > -2%
Partisan Lean vs Population and Direction
Dark green line is a Friedman's 'super smoother'
76
77. Cases as a Percent of Population
0.001%
0.01%
0.1%
1%
10%
20%
1,000 10,000 100,000 1,000,000 10,000,000
County Population
Totalcases
Total Cases as a Percent of County Population
Slanted lines are counties with small integer numbers of cases, green line: Friedman's 'super smoother'
77
78. Deaths as a Percent of Population
0.0001%
0.001%
0.01%
0.1%
1%
1,000 10,000 100,000 1,000,000 10,000,000
County Population
Totaldeaths
Total Deaths as a Percent of County Population
Slanted lines are counties with small integer numbers of cases, green line: Friedman's 'super smoother'
78
79. Case Mortality vs. Population
0.1%
1%
10%
100%
1,000 10,000 100,000 1,000,000 10,000,000
County Population
Casemortality
Case Mortality vs. County Population
79
172. Case Mortality vs. Testing
LUX
ARE
BHR
MLT
DNK
ISL
LTU
RUS
QAT
ISR
USA
AUS
PRT
MDVBLR
GBR
IRL
KWT
ITA
LVA
BEL
KAZ
CAN
NZL
SGP
AUT
ESP
EST
CHE
DEU
SRB
SAU
CHL
NOR
CZE
SVN
FIN
POL
TUR
ROU
NLD
SVK
PAN
ZAF
GRC
SLV
HUN
BGR
KOR
MYSMAR
IRN
URY
HRV
COLCUB
UKR
RWA
PRY
ARG
GHACRI
NPL
BOL
INDPHL
PER
ECU
THA
PAK
BRA
FJI
BGD
TUN
SEN
MEX
JPN
TGOKENTWNZWE
VNM
IDN
ETHMMR
NGA
0
5
10
15
0 20 40
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-07-21
172