Showing posts with label projection. Show all posts
Showing posts with label projection. Show all posts

Wednesday, July 1, 2020

Plateau for start

Graph 1 Total number of cases, number of active cases, and rate of change in the United States, logarithmic scale.
   On May 30, there was maximum number of active cases (1 176 025),  on June 16, it was surpassed (1 186 227). The number of active cases on July 1, 2020 is 1 454 397.
Graph 2 Daily number of tests and percentage of detected cases in the United States

   On June 14 (111 day of the epidemic), the minimum percentage of detected cases (2.8%) was reached and the trend reversed.
Graph 3 Graph of the total number of infected  people and  number of active cases in Russia

   Although the infection in Russia started 19 days later than in the United States, the percentage of active  cases in Russia is significantly lower.
Graph 4 Daily number of tests and percentage of detected  cases in Russia

   "Saw" in number of tests characterizes the work of laboratories: war by war, and the lunch is by schedule. It is possible that many of them do not work on weekends. On June 30, the epidemic reached another minimum of 1.9 % on day 106 from the beginning of the epidemic.
Graph 5 Charts of normalized Rt reproduction number in the USA and Russia

   If Rt n is greater than 1, the infection widens, and if it less than 1, it fades. In the US, the plateau was not a maximum, but a respite before real growth. In this graph, the difference between the beginning of the epidemic in the United States and Russia is not 19 but 21 days, to  align weekly cycles. As you can see the risk to catch the desease in the US is, at least 30% higher on Saturdays, than on Tuesdays.
   Whether Russia will follow the well-trodden American path, or Russians mostly overcome the desease, will be revealed in a week.




Tuesday, June 2, 2020

How to calculate the Rt reproduction number in your state, and why I don't expect peak in Russia before June 18

   During the first 3-4 weeks, the infection develops according to the classic scenario when the number of infected is easily calculated using the geometric progression formula. For Chinese flu, R0 (basic reproduction number) is 2...3, and the serial interval (the time between infections) is 5 days. Then the quarantine comes into effect, the number of patients who have been ill increases, and  Rt statistical number is used to assess the epidemy.
According to the Rospotrebnadzor (Russian Federal Service for Surveillance on Consumer Rights Protection) methodology, the Rt infection rate is an indicator that determines the average number of people infected by one patient before isolation. The Agency focuses on the regions on the transition to the I phase of the lifting of restrictions at a rate of less than 1.0; II phase - if Rt  is below 0.8.
   Is it possible to calculate this mysterious reproduction number in your state? Last Sunday I finally got to the Rospotrebnadzor manual and now I am happy to share its secret formula with the audience of my blog.

 
X1 ...X8  number of new cases a day. Rt =(X5+X6+X7+X8)/(X1+X2+X3+X4)

Now let's look at the dynamics of Rt in the US and in Russia. Day zero was taken when the number of cases exceeded 50. The comparison is particularly useful because the development of infection in America is 17 days ahead of Russian history. And if the Russian statistics is not very false, then we can predict what will happen in the next 2-3 weeks.

Rt in Russia and the US . X  axis -  days since the beginning of epidemic in the country.

The 7-day cycle of the Rt  in the US and its absence in Russia is immediately noticeable, but otherwise the indicators of development of infection  behave like twins. So, we can project that Russia is unlikely to reach the peak of epidemy before June 18.