This document provides an analysis of COVID-19 cases in the United States and around the world. It includes 3 caveats: the analysis represents the author's views and not Stanford's, the data sources and R code are publicly available, and the author tries to maintain an apolitical perspective. Graphs presented show trends in cases, deaths, testing, and other metrics for the US overall as well as for individual states and other countries.
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 outmisrepresentations.
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://usafactsstatic.blob.core.windows.net/public/data/covid-19/covid_confirmed_usafacts.csv
• USA Death Data: https://usafactsstatic.blob.core.windows.net/public/data/covid-19/covid_deaths_usafacts.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
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 -- Deaths: 98,220 -- Deaths per 10,000: 3.1 -- 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
Cumulative deaths
/ population *
10,000
Blue line: today
Blue dots: cumulative cases not
used to estimate Gompertz
function
Yesterday’s
total cases
and 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
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 2020-06-30
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 2020-06-30
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
13. Percent Population Tested
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
5
10
15
20
0
5
10
15
20
0
5
10
15
20
0
5
10
15
20
0
5
10
15
20
0
5
10
15
20
0
5
10
15
20
0
5
10
15
20
PercentPopulationTested
Testing as a Percent of State Population
13
14. 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
Numberofdailytestsfrommintomax
Testing trends from min to max
14
15. Percent Positive Tests
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
5
10
15
0
5
10
15
0
5
10
15
0
5
10
15
0
5
10
15
0
5
10
15
0
5
10
15
0
5
10
15
PercentPositive(%)
Percent Positive Tests Over Last 28 Days
15
16. 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
16
17. 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
17
18. 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
MNMS
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
5 10 15 20
% Tested
%Mortality
Mortality vs. Testing as of 2020-06-30
18
71. 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 2020-06-30
NA = Inadequate data
71
72. 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
72
73. 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'
73
74. 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'
74
75. 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'
75
76. 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'
76
77. 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
77
152. Case Mortality vs. Testing
BHR
LUX
ISL
DNK
LTU
RUS
QAT
PRT
BLR
ISR
USA
AUS
KWT
ITA
MDV
NZL
IRL
BEL
EST
LVA
KAZ
GBR
CAN
ESP
AUT
CHE
DEU
SGP
NOR
SRBCHL
CZE
SVN
SAU
SWE
FIN
TUR
SVK
ROU
POL
NLD
GRC
HUN
PANZAF
SLV
KOR
MYS
BGRIRN
HRV
URY
MAR
CUB
UKR
COL
RWA
GHAPRY
ARG
PER
THA
ECU
BOLIND
PHL
TUN
PAK
CRI
SEN
NPL
BGD
MEX
JPN
UGA
TWN
KEN
VNM
BRA
ETH
ZWE
IDN
MMR
NGA
0
5
10
15
0 10 20 30
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-06-30
152