This document provides an overview and analysis of COVID-19 data from the United States and other parts of the world. It includes caveats about the analysis being the author's own and not affiliated with Stanford University. Charts and graphs show trends in cases, deaths, testing rates, and other metrics over time for various locations. The author aims to keep the analysis apolitical and share data sources and models used.
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Caveats and Comments Analysis
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
cases on Jyly 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 2020-07-11
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 2020-07-11
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
MT
AK
VT
WV
ME
OR
WY
KY
NH
MO
OK
WA
OH
ND
ID
WI
CO
KS
NM
MN
IN
MI
PA
NC
CA
VA
SD
NV
TX
TN
UT
AR
SC
AL
GA
NE
IA
FL
MS
MD
IL
DE
CT
DC
LA
AZ
MA
RI
NJ
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
NH
ME
HI
CT
NJ
MA
NY
RI
MI
WY
AK
PA
MT
CO
DC
OR
WV
SD
MD
KY
IN
VA
MN
IL
ND
WA
NE
MO
OH
WI
DE
NM
KS
OK
IA
NC
UT
AR
CA
TN
ID
MS
NV
AL
GA
TX
SC
LA
FL
AZ
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
AR
OK
TX
TN
ND
SD
KY
WI
NC
NE
CA
MO
SC
WA
NV
FL
AL
VA
IA
NM
OH
MN
GA
AZ
NH
CO
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
HI
WV
WY
NE
WI
CO
AK
KS
ME
ID
OK
OR
MT
CT
MO
ND
MN
DE
MI
IA
NC
KY
UT
WA
GA
NH
OH
AR
SD
IN
PA
NY
MD
TN
RI
VA
NM
CA
NV
TX
DC
FL
MA
AL
LA
SC
IL
MS
NJ
AZ
0
2
4
6
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
CO
ID
OR
WY
PA
MO
KS
IN
OH
TX
WA
ME
VA
AZ
SC
NH
KY
GA
SD
AL
MD
OK
NE
MT
NV
NC
MS
WV
FL
IA
WI
VT
AR
UT
MI
MN
CA
MA
DE
TN
IL
CT
ND
RI
DC
NJ
NM
AK
LA
NY
0
5
10
15
20
25
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
MT
NE
NV
NH
NJ
NM
NY
NC
ND
OH
OK
OR
PA
RI
SC
SD
TNTX
UT
VT
VA
WA
WVWI
WY
2.5
5.0
7.5
10 15 20
% Tested
%Mortality
Mortality vs. Testing as of 2020-07-11
19
72. 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 2020-07-11
NA = Inadequate data
72
73. 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
73
74. 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'
74
75. 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'
75
76. 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'
76
77. 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'
77
78. 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
78
161. Case Mortality vs. Testing
LUX
BHR
MLT
DNK
ISL
LTU
RUS
QAT
PRT
ISRAUS
BLR
USA
MDV
GBR
KWT
IRL
ITA
BEL
NZL
LVA
KAZ
EST
CAN
SGP
ESP
CHE
DEU
AUT
SRBCHL
NOR
SWE
SAU
CZE
SVN
FIN
TUR
POL
ROU
SVK
NLD
PAN
GRC
ZAF
HUN
SLV
KOR
MYS
BGR
IRN
MAR
HRV
URY
COL
UKR
CUB
RWA
PRYGHA
ARGTHA
PER
CRI
IND
BOL
PHL
ECU
BRA
PAK
TUN
FJI
BGD
SEN
MEX
NPL
UGA
JPN
TGOKEN
TWN
VNM
ZWE
ETH
IDN
MMR
NGA
0
5
10
15
0 10 20 30 40
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-07-11
161