FloridaCovid

Hugh whelan

Updated on 2020-11-30

R Code

All code used to produce this site can be found on Github

Median Age of Covid Cases by Event Date

Median Age of Cases From Last 7 Days By County

% of Cases Aged >= 65 Years Old vs Case Death Rate

ED-only and Hospitalization Demographics

Age Demographics Of FL Covid Deaths

Hospitalization Status of FL Covid Deaths

Covid: Place Of Death vs. US averages

Covid Death and Cases Percentages By Gender

Most recent 4 weeks yield erratic values for percentage of death because of the small number of deaths.

Case Trend In Select Counties

Distribution of Death by Age: From All Causes vs. Covid Deaths Alone

The 2019 and 2020 All Causes age distribution is from Public Health data. The 2020 All Cause data is only through September – so the 2020 All Cause percent distribution does not fully reflect the impact of Covid deaths this year. Covid deaths are up to date to the current date.

Gompertz & Network Graph fits to FL Covid Death data

Gompertz equations have been proposed as good functional fits to model deaths as an infection spreads within a system (like the state of Florida). If you are interested in the topic, I have a separate site that uses these to look at US Covid death data. With the second surge in FL deaths, FL is no longer following a simple Gompertz process. I have modeled it using two additive Gompertz curves.

These plots use FL data on Covid deaths by actual death date available on their Arcgis site. I adjust the last 14 days of reported deaths upward using an adjustment factor developed by Marc Bevand documented here. I also omit the last two days of adjusted deaths due to their incompleteness.

The “2 Gompertz” fit to daily deaths is shown below.

Simple Extrapolation of Declining Growth Rate of Cumulative Covid Deaths

Michael Levitt (@MLevitt_NP2013) is the first one to observe that the growth rate of Covid cumulative deaths declines linearly in many regions infected with Covid. As noted above, Florida no longer follows a simple linear decline. Extrapolating the red line indicates there will be approximately 1,052 additional Covid deaths that will be added to Florida’s totals.

Model forecasts for FL Covid Deaths

The CDC periodically summarizes approximately 20 model forecasts for FL Covid deaths. These forecasts are higher than the Gompertz/Network “forecasts” above. It may be that the Gompertz/Network equations are better viewed as “after the fact” mathematical descriptors than forecasts.

model forecast_date target_week_end_date point quantile_0.025 quantile_0.25
UT 2020-11-23 2020-12-19 19218 18680 18986
Walmart 2020-11-23 2020-12-19 19218 18680 19030
UGA-CEID 2020-11-23 2020-12-19 19739 18786 19404
Covid19Sim 2020-11-23 2020-12-19 19753 19592 19724
MIT-ORC 2020-11-23 2020-12-19 19761 19500 19671
UM 2020-11-23 2020-12-19 19852 19772 19826
DDS 2020-11-23 2020-12-19 19856 18997 19436
UCLA 2020-11-23 2020-12-19 19860 19651 19779
PSI 2020-11-23 2020-12-19 19887 19685 19817
NotreDame-Mobility 2020-11-23 2020-12-19 19917 19820 19884
UCSB 2020-11-23 2020-12-19 19963 17930 19573
Google-HSPH 2020-11-23 2020-12-19 20139 17930 18736
JCB 2020-11-23 2020-12-19 20159 19308 19866
ISU 2020-11-23 2020-12-19 20199 19918 20089
MSRA 2020-11-23 2020-12-19 20320 20282 20299
Ensemble 2020-11-23 2020-12-19 20325 19610 19942
Karlen 2020-11-23 2020-12-19 20330 19759 20034
LANL 2020-11-23 2020-12-19 20332 19040 19922
UA 2020-11-23 2020-12-19 20429 20058 20337
JHU-CSSE 2020-11-23 2020-12-19 20439 20044 20263
CovidComplete 2020-11-23 2020-12-19 20484 19208 19812
Oliver Wyman 2020-11-23 2020-12-19 20488 19119 19963
USC 2020-11-23 2020-12-19 20551 19294 20254
LSHTM 2020-11-23 2020-12-19 20654 19222 20083
BPagano 2020-11-23 2020-12-19 20787 19667 20393
GT-DeepCOVID 2020-11-23 2020-12-19 20929 20627 20818
JHU-APL 2020-11-23 2020-12-19 20986 19628 20445
UMass-MB 2020-11-23 2020-12-19 21219 19808 20554
Columbia 2020-11-23 2020-12-19 21275 20337 20966
JHU-IDD 2020-11-23 2020-12-19 21495 19705 20565
MOBS 2020-11-23 2020-12-19 21504 18435 21353
UCSD-NEU 2020-11-23 2020-12-19 21531 21051 21366

Florida Covid Testing Volume

Florida Hospitalization/Case Ratio, Case Fatality Ratio and Death/Hospitalization By Month

Values for the latest month are effected by increases in testing volume which can increase the number of cases (the denominator), and by lags (as much as 21 days) between case identification and death (which can suppress the numerator).

Hospitalization/Case Ratio By Month Number
Age_group 2 3 4 5 6 7 8 9 10
0-4 years NA 4.2% 7.1% 7.7% 2.4% 2.1% 2.0% 3.0% 2.1%
05-14 years 0.0% 3.7% 3.4% 2.4% 1.1% 0.6% 0.9% 0.9% 0.8%
15-24 years 4.3% 4.1% 3.8% 3.3% 1.2% 0.9% 0.9% 0.8% 0.7%
25-34 years 6.7% 7.5% 6.3% 5.1% 2.2% 1.4% 1.5% 1.9% 1.3%
35-44 years 12.5% 14.1% 9.9% 8.0% 4.0% 2.4% 2.3% 3.2% 2.3%
45-54 years 14.3% 18.6% 13.0% 12.2% 6.5% 3.7% 3.5% 4.7% 3.4%
55-64 years 21.0% 23.7% 20.5% 19.0% 10.4% 6.7% 6.5% 7.5% 5.6%
65-74 years 22.6% 38.0% 34.4% 32.3% 18.9% 13.4% 13.0% 13.6% 11.1%
75-84 years 52.6% 53.5% 48.8% 41.6% 28.5% 23.5% 22.2% 21.1% 20.8%
85+ years 33.3% 68.7% 52.7% 48.4% 35.9% 29.9% 28.4% 25.0% 28.6%
CFR By Month Number
Age_group 2 3 4 5 6 7 8 9 10
0-4 years NA 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
05-14 years 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
15-24 years 0.0% 0.0% 0.0% 0.1% 0.0% 0.0% 0.0% 0.0% 0.0%
25-34 years 3.3% 0.2% 0.3% 0.1% 0.1% 0.1% 0.1% 0.1% 0.0%
35-44 years 2.5% 0.8% 0.7% 0.4% 0.3% 0.2% 0.2% 0.3% 0.1%
45-54 years 0.0% 1.5% 1.3% 1.2% 0.7% 0.6% 0.5% 0.4% 0.3%
55-64 years 4.8% 3.3% 3.7% 2.7% 2.2% 2.0% 1.8% 1.5% 0.8%
65-74 years 3.2% 9.4% 12.5% 10.3% 6.5% 6.4% 5.7% 5.1% 2.6%
75-84 years 15.8% 20.0% 23.3% 18.7% 15.3% 16.0% 13.3% 11.6% 7.9%
85+ years 66.7% 41.2% 39.0% 33.2% 31.0% 29.0% 24.9% 22.8% 18.8%
Covid Death/Hospitalization Ratio By Month Number
Age_group 2 3 4 5 6 7 8 9 10
0-4 years NA 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
05-14 years NaN 0.0% 0.0% 0.0% 4.1% 1.1% 1.6% 3.0% 0.0%
15-24 years 0.0% 0.0% 0.0% 2.3% 3.5% 3.5% 2.2% 0.7% 0.0%
25-34 years 50.0% 3.2% 4.8% 2.3% 2.5% 4.5% 7.5% 3.8% 1.3%
35-44 years 20.0% 5.3% 7.4% 5.1% 7.6% 9.4% 7.0% 8.4% 3.2%
45-54 years 0.0% 8.1% 10.3% 9.5% 10.5% 15.2% 13.6% 9.2% 8.1%
55-64 years 23.1% 13.9% 18.1% 14.1% 21.5% 29.3% 27.6% 20.3% 13.9%
65-74 years 14.3% 24.7% 36.3% 31.8% 34.4% 48.3% 44.0% 37.5% 23.8%
75-84 years 30.0% 37.4% 47.7% 44.8% 53.9% 68.1% 60.1% 54.7% 38.2%
85+ years 200.0% 60.0% 74.1% 68.6% 86.4% 96.8% 87.8% 91.3% 65.9%
Total Deaths and Cases By Month (based on Event Date)
Month Deaths Cases
1 0 100
2 11 251
3 784 16,197
4 1,592 22,767
5 1,121 24,002
6 2,338 132,428
7 6,923 313,948
8 3,086 134,957
9 1,438 75,360
10 1,099 103,792
11 344 168,859

Estimating Deaths Using Case Fatality Ratio

Comparison of FL DOH caseline files by date show that a significant number of deaths are added to the last 15 days of reported Event Dates. We can estimate the “missing” deaths that have either not occurred yet or not been reported using the Case Fatality Ratio by age group from 15 days ago. The chart below shows the development of CFR over time.

The chart below estimates daily Covid deaths for the last 15 days using the 15-day ago CFR. This projects approximately 166 deaths will be added to the last 15 Event Dates (from 18,736 to 18,902).

FL Covid Deaths As A Percentage Of All FL Deaths In 2020

CDC data on FL lags the FL DOH data (which is where the CDC gets their data), but the weekly percentage of All FL Deaths due to Covid should be accurate unless Covid deaths are reported with a greater/lesser lag than other deaths. The last weekly CDC value indicates Covid deaths now comprise 3.3% of all FL deaths, down from a maximum weekly value of 26.1%.

FL Deaths From All Causes vs. Prior Years

The chart below compares 2020 to prior years. Deaths for prior years have been adjusted upwards to account for population growth. Through week 45, total deaths were 15,948 above the mean of the 4 prior years.

Florida Provisional CDC Cause of Death Data

Data for this table can be found here. It should be interpreted carefully as it is provisional. It also only includes selected causes of death, so numbers do not sum to the natural cause total. It also only compares to one year (2018 was a much worse flu year) and is not adjusted for population growth (approx. 1.1% p.a.). This table is through 2020-11-07 (I don’t use the most recent reported week because it suffers from lagged reporting). Most of the difference between “Covid multiple cause of death” and “Covid underlying cause” is counted in “influenza and pneumonia.” The large increase in “symptoms signs and abnormal” includes a large group of potential causes. Much of this category could be reassigned (note both diseases of the heart and malignant neoplasms are running unusually low).

CDC Partial Cause Of Death Data
2019 partial 2020 partial Difference Pct Change
all_cause 184,056 209,995 25,939 14.1%
natural_cause 166,908 192,014 25,106 15.0%
septicemia_a40_a41 2,212 2,294 82 3.7%
malignant_neoplasms_c00_c97 40,361 40,070 -291 -0.7%
diabetes_mellitus_e10_e14 5,439 6,498 1,059 19.5%
alzheimer_disease_g30 5,755 6,301 546 9.5%
influenza_and_pneumonia_j09_j18 2,370 2,873 503 21.2%
chronic_lower_respiratory 10,649 10,449 -200 -1.9%
other_diseases_of_respiratory 2,506 2,312 -194 -7.7%
nephritis_nephrotic_syndrome 2,889 2,846 -43 -1.5%
symptoms_signs_and_abnormal 2,663 4,959 2,296 86.2%
diseases_of_heart_i00_i09 42,021 43,318 1,297 3.1%
cerebrovascular_diseases 12,316 13,535 1,219 9.9%
covid_19_u071_multiple_cause_of_death 0 17,303 17,303 Inf
covid_19_u071_underlying_cause_of_death 0 15,403 15,403 Inf

March - October All Deaths vs. Covid Deaths

Florida publishes preliminary total deaths from all causes by month at this link. We can compare the total of all deaths from March through October in 2020 to those from prior years (October data is not yet complete). The table below subtracts the average of the population growth adjusted March - October deaths from a 2018-2019 baseline (I assume population has grown by 1.2% by year) from 2020’s March - October deaths. This is a gross “Excess Death” number. The Covid Deaths are from the New York Times database through October. The last column of the table subtracts the Covid deaths from the Excess Deaths to estimate Excess Deaths not attributable to Covid.

Totals for the state are shown on the first row.

county 2019-18adjBase 2020AllDeaths 2020vs2018-19Delta Covid Deaths nonCovidDelta
TOTAL 135574 159301 23727 13963 9764
alachua 2456 2643 187 60 127
baker 113 122 9 13 -4
bay 1302 1486 184 108 76
bradford 133 109 -24 9 -33
brevard 5027 5512 485 298 187
broward 10154 12481 2327 1396 931
calhoun 109 120 11 11 0
charlotte 1854 2172 318 136 182
citrus 1642 1959 317 106 211
clay 1399 1660 261 100 161
collier 2305 2681 376 221 155
columbia 605 743 138 58 80
desoto 199 212 13 25 -12
dixie 72 66 -6 9 -15
duval 6602 7726 1124 394 730
escambia 3108 3543 435 235 200
flagler 931 1070 139 27 112
franklin 59 73 14 4 10
gadsden 172 212 40 47 -7
gilchrist 93 96 3 12 -9
glades 43 45 2 4 -2
gulf 79 108 29 14 15
hamilton 44 66 22 8 14
hardee 92 100 8 11 -3
hendry 126 148 22 42 -20
hernando 1867 2130 263 127 136
highlands 1093 1308 215 89 126
hillsborough 7946 9269 1323 646 677
holmes 145 167 22 8 14
indian river 1469 1585 116 119 -3
jackson 387 411 24 80 -56
jefferson 69 73 4 9 -5
lafayette 37 48 11 12 -1
lake 2673 3122 449 193 256
lee 4885 5662 777 468 309
leon 1797 2290 493 77 416
levy 156 286 130 9 121
liberty 25 24 -1 8 -9
madison 126 127 1 20 -19
manatee 2725 3372 647 291 356
marion 3329 3935 606 290 316
martin 1241 1557 316 143 173
miami-dade 13924 18122 4198 3280 918
monroe 344 389 45 22 23
nassau 454 473 19 45 -26
okaloosa 1274 1467 193 115 78
okeechobee 264 314 50 27 23
orange 6559 7570 1011 457 554
osceola 1524 1955 431 153 278
palm beach 10200 12218 2018 1369 649
pasco 4109 4492 383 209 174
pinellas 8607 9412 805 753 52
polk 4497 5386 889 531 358
putnam 563 599 36 40 -4
santa rosa 767 867 100 77 23
sarasota 3926 4491 565 258 307
seminole 2435 2560 125 214 -89
sumter 1404 1700 296 70 226
suwannee 221 261 40 71 -31
taylor 116 118 2 13 -11
union 78 101 23 16 7
volusia 4874 5477 603 249 354
wakulla 108 147 39 10 29
walton 458 473 15 25 -10
washington 179 190 11 22 -11