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JohnNichols

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04-08-2020
09:33 AM

49 Views

CV mach 3

20 Replies

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JohnNichols

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04-08-2020
09:34 AM

39 Views

We lost 2 days - but it is back on track -- losing 2 days may not be a peak

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JohnNichols

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04-08-2020
10:54 AM

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JohnNichols

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04-08-2020
10:57 AM

39 Views

The Chines ODE matches well so far, the HIME model says this is close to the peak -- at 2200 -- this model is really close to standard data for Wuhan except for the rate to quarantine -- which is half the Wuhan rate.

The harmonic is due to a Weiner process on one of the varaible, at 0.5% level -- this thing is really sensitive -

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JohnNichols

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04-08-2020
11:12 AM

39 Views

Can I rewind a file if i just opened it?

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andrew_4619

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04-09-2020
12:39 AM

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Nichols, John wrote:Can I rewind a file if i just opened it?

Yes

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JohnNichols

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04-09-2020
10:55 AM

39 Views

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JohnNichols

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04-09-2020
11:05 AM

39 Views

This is the Fortran ODE Solver coupled with CONREC -- the Fortran CONREC was written by Paul Bourke from Australia. He published the original code in BYTE.

I translated the Fortran into C# for modelling FFT results from an accelerometer.

This shows the plot of the ODE solutions for time along the X axis -- 512 days

and the alpha value for the ODE's from 0.1 to 0.01 on the Y axis.

The z values are scaled by taking the fourth root otherwise you end up with only a few contours because of the huge differential - taking the log is a problem for the zeros.

John

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JohnNichols

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04-14-2020
05:48 PM

39 Views

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JohnNichols

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04-14-2020
06:04 PM

39 Views

SUBROUTINE derivs(x,y,dydx) implicit none INTEGER nrhs REAL x,y(*),dydx(*), alpha, pop, Beta,NBeta, lambda, kappa, delta, gamma, randdata, rho COMMON nrhs common /RAND/ randdata(1000000), alpha,Beta,gamma, lambda, kappa, delta, rho nrhs=nrhs+1 ! if(nrhs .lt. 32) then ! else ! rho = 0.5 ! end if pop = 1.0 Beta = 1.0 ! Infection Rate NBeta = Beta/pop gamma = 0.5 ! latency time 2 days lambda = 0.015 ! cure rate Wuhan 0.1 to 0.2 - time based kappa = 0.01 ! mortality rate delta = 1.0/7.4 ! quarantine time 7.4 days lambda = lambda * ((0.005*randdata(nrhs)) + 0.995) write(*,1000)nrhs,lambda,alpha 1000 format(i4,2(' ', F6.4)) ! y(1) is susceptible ! y(2) is exposed ! y(3) is infected ! y(4) is quarantined ! y(5) is recovered ! y(6) is Death ! y(7) is Insusceptible dydx(1) = -rho*NBeta*y(1)*y(3) - alpha*y(1) ! Equation 1 !dydx(1) = -NBeta*y(1)*y(3) - alpha*y(1) ! Equation 1 dydx(2) = (rho*Nbeta*y(1)*y(3)) - gamma*y(2) ! Equation 2 !dydx(2) = (Nbeta*y(1)*y(3)) - gamma*y(2) ! Equation 2 dydx(3) = gamma*y(2) - delta*y(3) ! Equation 3 dydx(4) = delta*y(3) - lambda*y(4) - kappa*y(4) ! Equation 4 dydx(5) = lambda*y(4) ! Equation 5 dydx(6) = kappa* y(4) ! Equation 6 - correct dydx(7) = alpha*y(1) ! Equation 7 ! write(*,120) nrhs, dydx(1),dydx(2),dydx(3),dydx(4),dydx(5),dydx(6),dydx(7) 120 Format(1x,i4, 7(2x,f14.6)) return END

The original model matches well upto 40th day, but the stuff after does not make great sense, the idea is to introduce RHO into the equations, but this poor match and now we have a 900 death jump in one day -- RHO will never predict this properly -- one idea is that RHO has a dependence on something else - say temperature.

Can I ask each of you to give me some idea if your area got a lot colder in the last 24 hours - the death increase was not spotty it was across the board.

This virus is a beast.

Any ideas on fixing the model -- I have tried other models but they all end up with the same overall shape.

JMN

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JohnNichols

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04-14-2020
06:34 PM

39 Views

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JohnNichols

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04-14-2020
06:42 PM

39 Views

If I play with lambda with the random offset -- the above is 0.1% random variation in lambda -- results in the above graph.

Why do you think we get a cluster around 40 days in real data and model? Aside from the 0.1 this has been constant since about day 28.

it is weird,

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Hevia__Orlando

Beginner

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04-16-2020
05:55 AM

39 Views

Nichols, John wrote:

SUBROUTINE derivs(x,y,dydx) implicit none INTEGER nrhs REAL x,y(*),dydx(*), alpha, pop, Beta,NBeta, lambda, kappa, delta, gamma, randdata, rho COMMON nrhs common /RAND/ randdata(1000000), alpha,Beta,gamma, lambda, kappa, delta, rho nrhs=nrhs+1 ! if(nrhs .lt. 32) then ! else ! rho = 0.5 ! end if pop = 1.0 Beta = 1.0 ! Infection Rate NBeta = Beta/pop gamma = 0.5 ! latency time 2 days lambda = 0.015 ! cure rate Wuhan 0.1 to 0.2 - time based kappa = 0.01 ! mortality rate delta = 1.0/7.4 ! quarantine time 7.4 days lambda = lambda * ((0.005*randdata(nrhs)) + 0.995) write(*,1000)nrhs,lambda,alpha 1000 format(i4,2(' ', F6.4)) ! y(1) is susceptible ! y(2) is exposed ! y(3) is infected ! y(4) is quarantined ! y(5) is recovered ! y(6) is Death ! y(7) is Insusceptible dydx(1) = -rho*NBeta*y(1)*y(3) - alpha*y(1) ! Equation 1 !dydx(1) = -NBeta*y(1)*y(3) - alpha*y(1) ! Equation 1 dydx(2) = (rho*Nbeta*y(1)*y(3)) - gamma*y(2) ! Equation 2 !dydx(2) = (Nbeta*y(1)*y(3)) - gamma*y(2) ! Equation 2 dydx(3) = gamma*y(2) - delta*y(3) ! Equation 3 dydx(4) = delta*y(3) - lambda*y(4) - kappa*y(4) ! Equation 4 dydx(5) = lambda*y(4) ! Equation 5 dydx(6) = kappa* y(4) ! Equation 6 - correct dydx(7) = alpha*y(1) ! Equation 7 ! write(*,120) nrhs, dydx(1),dydx(2),dydx(3),dydx(4),dydx(5),dydx(6),dydx(7) 120 Format(1x,i4, 7(2x,f14.6)) return ENDThe original model matches well upto 40th day, but the stuff after does not make great sense, the idea is to introduce RHO into the equations, but this poor match and now we have a 900 death jump in one day -- RHO will never predict this properly -- one idea is that RHO has a dependence on something else - say temperature.

Can I ask each of you to give me some idea if your area got a lot colder in the last 24 hours - the death increase was not spotty it was across the board.

This virus is a beast.

Any ideas on fixing the model -- I have tried other models but they all end up with the same overall shape.

JMN

Is it possible you share the rest of the code?

In any case, thank you by the equations and values of parameters.

OPH.

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JohnNichols

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04-18-2020
11:03 AM

39 Views

Here is the complete code, you will need to add DISLIN -- not hard to find and download.

The code comes from Peng - see paper -- the Chinese gov has shut down all communication so contacting them is not recommended for their safety

The Feng module has been amended from her published algorithm as her code did not work -- I amended equation 1 -- do not use it -- until it is properly fixed

The alpha from the Chinese is 0.1 -- this is impossible a standard alpha is 0.5 refer to Brauer

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JohnNichols

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04-18-2020
11:34 AM

39 Views

One plausible explanation for these population increases is that the bubonic

plague invasions served to control the population size, and when this control

was removed the population size increased rapidly.

----------------------------------------------------------------------------------------------------------------

Cheery thought for the day as to why Fortran was invented -- bubonic plague went away

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JohnNichols

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04-18-2020
11:38 AM

39 Views

In developing countries it is quite common to have high birth rates and

high disease death rates. In fact, when disease death rates are reduced by

improvements in health care and sanitation it is common for birth rates to

decline as well, as families no longer need to have as many children to ensure

that enough children survive to take care of the older generations. Again, it

is plausible to assume that population size would grow exponentially in the

absence of disease but is controlled by disease mortality.

----------------------------------------------------------------------------------------------------------------

Who said to read this book to improve my Fortran models -- ok a Russian

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Hevia__Orlando

Beginner

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04-19-2020
09:43 AM

39 Views

Nichols, John wrote:Here is the complete code, you will need to add DISLIN -- not hard to find and download.

The code comes from Peng - see paper -- the Chinese gov has shut down all communication so contacting them is not recommended for their safety

The Feng module has been amended from her published algorithm as her code did not work -- I amended equation 1 -- do not use it -- until it is properly fixed

The alpha from the Chinese is 0.1 -- this is impossible a standard alpha is 0.5 refer to Brauer

Thank you very much!

I am user of DISLIN since the 90's, a great package.

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JohnNichols

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04-20-2020
12:09 PM

39 Views

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JohnNichols

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04-20-2020
12:11 PM

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The last picture shows the relationship between the deaths and the peak FFT for Australia, China, UK Germany and France and USA

This is the residuals for the linear regression

Darn that is a tight fit

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JohnNichols

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04-20-2020
12:12 PM

39 Views

On the bottom graph the four blue ones are Australia and USA for 28th March and 19th April

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