covidlag 0.0.3

lag time and death rate per infection

covidlag

Data science is useful to investigate the progression of the pandemic.

covidlag is an open-source program which is available in public and can be installed by the PyPI package command (pip). covidlag can calculate the lag time between infection peaks and death peaks. covidlag can also compute death rate per infection or case fatality ratio (CFR). CFR is the proportion of individuals diagnosed with a disease who die from that disease and is therefore a measure of severity among detected cases.

CFR is a dynamic value depending on the environment, but the current computation of CFR is not suitable for time series data.

Because CFR is deterimined by imprecise cases.

Unless all individuals are tested several times a day, the number of infected individuals or that of cases is not accurate.

We must understand that CFR is an imprecise estimate.

According to CDC: https://www.cdc.gov/foodnet/reports/data/case-fatality.html

the CFR is calculated by: CFR=(number of cases in which patient died/number of cases).

The CDC method for CFR is appropriate for annual statistics, but not for time series data analysis.

In the current CFR calculation, we need to determine the range of sampled days. The start and end dates have a significant impact on the CFR results.

There is no algorithm to select the optimal range of sampled days.

In the proposed algorithm, multiple peaks of time series daily infection and mutiple peaks of time series daily death are calculated by two curve fitting functions respectively.

The peak of infection is associated with the peak of its death.

The difference between the peak of infection and that of death indicates a time lag.

The death rate per infection or case fatality ratio (CFR) can be also calculated by dividing the number of peak deaths by the number of peak infections.

In the proposed algorithm, the peak of infection is strongly correlated with the peak of death.

The detailed method is under review.

Polynomial curve-fitting algorithm is used for detecting infection peaks and death peaks.

The lag time is a difference between a infection peak and a death peak.

case fatality ratio (CFR) can be also calculated by the peak infection and the peak death.

When the lag time is shortened, infected patients must be treated urgently.

With a longer time lag, we have to provide adequate hospitals for patients.

When the death rate per infection or the CFR is high, the policy needs to be strengthened.

How to install covidlag

Covidlag is available in public and can be installed by the following PyPI packaging command:

$ pip install covidlag

How to run covidlag

covidlag needs at least three parameters (country name, sampled days, regression polinomial degree).

Run the following command composed of the country name, sampled days, the degree of polynomial curve-fitting, and options (L: left, R: right, C: center):

$ covidlag Japan 400 13 L

This example is for "Japan" with the "13th" degree polynomial curve-fitting using "400" sampled days. The result shows the polynomial curve-fitting that r-squared of infections is 0.923 and r-squared of deaths is 0.706.

The death peaks are [152 267 374].
death peak: 2021-01-29 <-
death peak: 2021-05-24 <-
death peak: 2021-09-08 <-

The case peaks are [27 133 252 258].
case peak: 2020-09-26
case peak: 2021-01-10 <-
case peak: 2021-05-09 <-
case peak: 2021-08-23 <-

The lag time between infections and deaths is 152-133=19 days, 267-252=15 days, 
and 374-258=16 days respectively.

The number of every death peak is [88 92 54].

The number of every case peak is [526 4421 5902 20029]

Therefore, death rate of peaks or CFR is 88/4421=0.019, 92/5902=0.015, and 54/20029=0.0026 respectively.

The CFR is significantly decreasing.

$ covidlag 'United States' 600 13 L

This example shows that r-squared of infections:0.803 and r-squared of deaths:0.733

The death peaks are [71 189 337 470 579]

death peak: 2020-04-23
death peak: 2020-08-19
death peak: 2021-01-14
death peak: 2021-05-27
death peak: 2021-09-13

The case peaks are [52 156 315 448 566]

case peak: 2020-04-04
case peak: 2020-07-17
case peak: 2020-12-23
case peak: 2021-05-05
case peak: 2021-08-31

The lag time between infections and deaths is 19 days, 33 days, 22 days, 22 days, 13 days.

The number of every death peak is [1944 1005 3109 632 1943].

The number of every case peak is [28858 57877 207829 44827 178454]

The death rate per infection is 1944/28858=0.067,1005/57877=0.017, 3109/207829=0.015,632/44827=0.014,1943/178454=0.011

CFR in the US is slowly decreasing. But, it is still high compared with that of Japan.

$ covidlag Canada 400 13 L

death peak: 2020-09-07
death peak: 2021-01-06
death peak: 2021-05-08
death peak: 2021-09-25
case peak: 2020-09-07
case peak: 2020-12-26
case peak: 2021-04-21
case peak: 2021-09-19

The lag time is 11 days, 17 days,...

The death rate per infection is 0.018,0.006,...