CAD CAM DENTURES IN PROSTHODONTICS : Dental advancements
COVID-19 Update (Summary): August 24, 2020
1. Caveats and Comments
1
Overview:
This is my analysis, not Stanford’s. My goal is to understand the trajectory of COVID. It is not confidential and can be freely shared. The R program code is
available at https://github.com/StevenLShafer/COVID19/. The daily analysis are available at https://1drv.ms/u/s!AuOyHP_aTIy7rowrt2AjGpWm_frnEQ?e=KBcNbh.
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)
9. Average new cases over past 7 days
PER
COL
BRA
ISR
ARG
USA
ESP
BOL
IRQ
CHL
DOM
HND
PRY
ZAF
ECU
IND
GTM
FRA
LBY
ROU
MEX
BEL
SAU
UKR
MAR
PHL
SLV
RUS
NLD
IRN
CHE
VEN
KGZ
AUT
NPL
CZE
SWE
GRC
SRB
UZB
ZMB
DNK
PRT
POL
AZE
GBR
ETH
BGR
TUR
KAZ
BGD
DEU
BLR
ITA
DZA
SVK
CAN
AUS
TUN
RWA
SEN
IDN
KEN
GIN
JPN
USA
None
1 in 20,000
1 in 10,000
1 in 6,667
1 in 5,000
1 in 4,000
1 in 3,333
1 in 2,857
1 6 11 16 21 26 31 36 41 46 51 56 61 66
Rank
Averagecases/day
Average new cases over past 7 days
Excludes countries with population < 5,000,000
2020-08-24 Summary: 9
12. Average daily deaths over past 7 days
COL
PER
BOL
BRA
MEX
ARG
ZAF
CHL
USA
ISR
IRQ
GTM
IRN
ECU
ROU
DOM
HND
PRY
SAU
KAZ
SLV
MAR
BGR
LBY
IND
AUS
ESP
RUS
BEL
UKR
PHL
BLR
SRB
SWE
IDN
POL
DZA
TUR
BGD
NLD
ETH
ZWE
VEN
PRT
KEN
UZB
ZMB
FRA
CZE
NPL
TUN
GRC
AZE
EGY
SYR
CAN
CHE
SEN
GHA
GBR
YEM
NIC
AGO
ITA
MWI
USA
None
1 in 500,000
1 in 250,000
1 in 166,667
1 in 125,000
1 6 11 16 21 26 31 36 41 46 51 56 61 66
Rank
Averagedeaths/day
Average daily deaths over past 7 days
Excludes countries with population < 5,000,000
2020-08-24 Summary: 12
13. Case Mortality vs. Testing
LUX
AREBHR
MLT
DNK
ISL
ISR
RUS
AUS
LTUUSA
QATMDV
BEL
GBR
PRT
BLR
IRL
NZL
KWT
CAN
SAU
SRBLVA
SGP
AUT
KAZ
DEU
CHL
ESP
CHE
NOREST
FINROU
GRC
ITA
CZE
NLD
TUR
SVN
POL
PANZAF
SVK
BGR
COL
MAR
URYSLV
HUN
HRV
MYS
IRN
KOR
IRQ
UKR
CUB
RWA
IND
PRY
CRI
ARG
PHL
BRA
NPL
BOL
PER
GHA
ECU
JPNPAK
TUN
MEX
BGD
SEN
FJI
KEN
UGA
IDN
TGO
ETH
ZWE
THA
CIV
TWN
VNM
MMR
NGA
USA
0
5
10
0 20 40 60
% Tested
%CaseMortality
Case Mortality vs. Testing as of 2020-08-24
ARE: United Arab Emirates, BHR:Bahrain, MLT: Malta, ISR: Israel, LTU: Lithuania, ISL: Iceland
2020-08-24 Summary: 13
15. 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 2020-08-24
2020-08-24 Summary: 15
16. 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
2020-08-24 Summary: 16
17. 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 2020-08-24
2020-08-24 Summary: 17
18. 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
2020-08-24 Summary: 18
19. Change in cases vs change in deaths
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
WV
WI
WY
-6
-3
0
3
6
-3 0 3 6
Change in cases (%/day)
Changeindeaths(%/day)
Change in cases vs change in deaths over last 14 days as of 2020-08-24
2020-08-24 Summary: 19
20. Total US COVID-19 Cases
CA
FL
TX
NY
GA
IL
AZ
NJ
NC
TN
LA
PA
MA
AL
OH
VA
SC
MI
MD
IN
MS
MO
WA
WI
MN
NV
AR
IA
CO
OK
CT
UT
KY
KS
NE
ID
OR
NM
RI
DE
DC
SD
ND
WV
NH
HI
MT
AK
ME
WY
VT
0
200,000
400,000
600,000
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 as of July 20, 2020: 0.41, p governor: 0.8. NB: association != causation.
2020-08-24 Summary: 20
21. Total US COVID-19 Cases
LA
FL
AZ
MS
GA
AL
NY
SC
NJ
NV
TN
TX
RI
DC
AR
MA
IA
IL
DE
MD
CA
ID
NE
UT
NC
CT
OK
VA
ND
KS
IN
SD
MO
MN
WI
NM
MI
PA
OH
KY
CO
WA
AK
WY
MT
OR
NH
WV
HI
ME
VT
None
1 in 200
1 in 100
1 in 67
1 in 50
1 in 40
1 in 33
1 in 29
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 as of July 20, 2020: 0.95, p governor: 0.15. NB: association != causation.
2020-08-24 Summary: 21
22. Average US COVID-19 cases over the past
7 days
MS
ND
TN
GA
TX
NV
AL
FL
MO
IA
AR
OK
LA
ID
SD
CA
KS
HI
IL
SC
NC
IN
WI
KY
MN
UT
NE
VA
AK
AZ
MD
MT
RI
OH
WY
WA
DC
NM
DE
MI
OR
WV
PA
CO
MA
NY
NJ
CT
ME
NH
VT
None
1 in 20,000
1 in 10,000
1 in 6,667
1 in 5,000
1 in 4,000
1 6 11 16 21 26 31 36 41 46 51
Rank
NewCases/Day
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 cases over the past 7 days
p masks as of July 20, 2020: 0.013, p governor: 0.0073. NB: association != causation.
2020-08-24 Summary: 22
23. Total US COVID-19 Deaths
NY
NJ
CA
TX
FL
MA
IL
PA
MI
GA
AZ
LA
CT
OH
MD
IN
NC
SC
VA
MS
AL
CO
WA
MN
TN
MO
NV
WI
IA
RI
KY
NM
OK
AR
DC
DE
NH
KS
OR
UT
NE
ID
WV
SD
ND
ME
MT
VT
HI
WY
AK
0
10,000
20,000
30,000
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalDeaths
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Deaths
p masks as of July 20, 2020: 0.067, p governor: 0.23. NB: association != causation.
2020-08-24 Summary: 23
24. Total US COVID-19 Deaths
NJ
NY
MA
CT
LA
RI
DC
MS
MI
AZ
IL
DE
MD
PA
SC
GA
FL
IN
AL
TX
NV
NM
OH
CO
IA
MN
NH
CA
VA
WA
NC
MO
TN
AR
NE
KY
WI
OK
SD
ND
ID
KS
UT
WV
OR
ME
VT
MT
WY
AK
HI
None
1 in 2,000
1 in 1,000
1 in 667
1 in 500
1 6 11 16 21 26 31 36 41 46 51
Rank
TotalDeaths
Masks
No
Yes
Governor
aa
Democratic
Republican
Total US COVID-19 Deaths
p masks as of July 20, 2020: 0.032, p governor: 0.22. NB: association != causation.
2020-08-24 Summary: 24
25. Average US COVID-19 deaths over the past
7 days
LA
MS
TX
SC
FL
GA
NV
AZ
TN
AR
AL
CA
ID
ND
IA
NC
OK
NM
KY
MA
IN
OH
MN
WA
MO
WY
IL
WV
SD
VA
DC
MD
NE
RI
PA
MT
WI
OR
MI
DE
KS
UT
AK
HI
NH
NJ
CO
ME
NY
CT
VT
None
1 in 500,000
1 in 250,000
1 in 166,667
1 in 125,000
1 6 11 16 21 26 31 36 41 46 51
Rank
Deaths/Day
Masks
No
Yes
Governor
aa
Democratic
Republican
Average US COVID-19 deaths over the past 7 days
p masks as of July 20, 2020: 0.21, p governor: 0.0087. NB: association != causation.
2020-08-24 Summary: 25
26. Daily 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
Dailytestingfrommintomax
Daily testing trends from min to max
Line = Friedman's supersmoother
2020-08-24 Summary: 26
27. Change in daily tests over past 14 days
IL
HI
MA
TN
WV
ME
NC
MI
AL
OK
MD
AR
NY
IN
NJ
IA
VT
WY
ND
VA
DC
RI
SD
MN
CA
KY
OH
NH
AK
NM
PA
MO
NE
WI
LA
TX
ID
OR
NV
DE
AZ
SC
GA
KS
CT
UT
MS
FL
CO
MT
WA
-4.0
-2.0
0.0
2.0
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeindailytests(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in daily tests over past 14 days
p masks as of July 20, 2020: 0.14, p governor: 0.62. NB: association != causation.
2020-08-24 Summary: 27
29. Percent of Positive COVID Tests
AZ
MS
FL
SC
ID
AL
TX
GA
NV
KS
IA
NE
IN
RI
AR
CO
MD
PA
SD
MO
LA
MA
UT
VA
DE
NC
NJ
TN
WA
MN
OK
WI
CA
IL
KY
OH
NY
WY
ND
DC
CT
OR
MI
NH
HI
NM
MT
WV
ME
AK
VT
0.0
5.0
10.0
15.0
1 6 11 16 21 26 31 36 41 46 51
Rank
PercentofPositiveTests
Masks
No
Yes
Governor
aa
Democratic
Republican
Percent of Positive COVID Tests
p masks as of July 20, 2020: 0.098, p governor: 0.012. NB: association != causation.
2020-08-24 Summary: 29
30. 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
2020-08-24 Summary: 30
31. Change in positive tests over past 14 days
HI
MT
ND
WA
MS
AK
KY
MO
WY
NV
NC
ID
KS
SD
OK
WI
IA
TX
UT
FL
CA
OR
MN
NE
IN
GA
TN
WV
DE
CO
NM
OH
VA
SC
LA
IL
PA
AZ
AR
RI
AL
NH
MI
MD
VT
ME
NJ
CT
NY
MA
DC
-1.0
0.0
1.0
2.0
3.0
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeinpositivetests(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in positive tests over past 14 days
p masks as of July 20, 2020: 0.017, p governor: 0.45. NB: association != causation.
2020-08-24 Summary: 31
32. Change in tests vs change in positive tests
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
TXUT
VT
VA
WA
WV
WI
WY
-1
0
1
2
3
-4 -2 0
Change in tests (%/day)
Changeinpositivetests(%/day)
Change in tests vs change in positive tests last 14 days as of 2020-08-24
2020-08-24 Summary: 32
33. Current hospitalizations as a percent of peak
since FebruaryAK
HI
KS
MT
WV
WY
AR
MO
ND
KY
OK
ID
MS
NC
VA
TN
NE
OH
GA
IA
NV
AL
CA
WA
SD
SC
IN
OR
UT
WI
MN
LA
TX
FL
NM
IL
VT
MD
AZ
RI
CO
DC
PA
MI
DE
ME
NH
MA
NJ
CT
NY
0
30
60
90
1 6 11 16 21 26 31 36 41 46 51
Rank
Hospitalizations(%ofpeak)
Masks
No
Yes
Governor
aa
Democratic
Republican
Current hospitalizations as a percent of peak since February
p masks as of July 20, 2020: 0.023, p governor: 0.058. NB: association != causation.
2020-08-24 Summary: 33
34. 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
2020-08-24 Summary: 34
35. Change in hospitalizations over past 14
days
HI
MT
AK
WY
VT
IA
KS
WV
DE
SD
WI
AR
ND
MO
OK
IL
MN
NE
RI
DC
VA
MI
WA
ID
IN
KY
NY
NC
MS
CT
CA
MD
OH
MA
GA
PA
TN
NV
OR
CO
AL
SC
LA
TX
ME
FL
UT
NM
NJ
NH
AZ
-5.0
-2.5
0.0
2.5
1 6 11 16 21 26 31 36 41 46 51
Rank
Changeinhospitalizations(%/day)
Masks
No
Yes
Governor
aa
Democratic
Republican
Change in hospitalizations over past 14 days
p masks as of July 20, 2020: 0.3, p governor: 0.93. NB: association != causation.
2020-08-24 Summary: 35
36. Case Mortality vs. Testing
AL
AK
AZ
AR
CA
CO
CT
DE
DC
FL
GA
HI
ID
ILIN
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
WV
WI
WY
2.5
5.0
7.5
10 20 30 40
% Tested
%Mortality
Mortality vs. Testing as of 2020-08-24
2020-08-24 Summary: 36