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Profil korisnika/ce NeuroOscillator
Ty
Ty
Ty
@NeuroOscillator

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Ty

@NeuroOscillator

Neurobiomathemastatistician. Collector of professional hats. Math PhD student/viral dynamics/circadian rhythms/public health. Kentuckian. 🌈(He)

Vrijeme pridruživanja: veljača 2011.

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    Ty‏ @NeuroOscillator 2. velj
    • Prijavi Tweet

    Ok, so I said I'd do an R0 thread and there's plenty of classical epidemiologists that have done threads on the concept by now, but I've not seen anyone talk about the dynamical system perspective.

    20:12 - 1. velj 2020.
    • 47 proslijeđenih tweetova
    • 133 oznake „sviđa mi se”
    • Stefan Anon Anon Kim M.Sc.E.🚀🌱🥋🏳️‍🌈🌈♻️ Alan F. Schultz Lin Zhu, PhD John McLaughlin Neil Chenoweth Salvo R. jsp
    7 replies 47 proslijeđenih tweetova 133 korisnika označavaju da im se sviđa
      1. Novi razgovor
      2. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So first, preliminary: an R0, or R-naught, is a term describing the reproductive capacity of an organism. In epidemiology it refers to the number of secondary cases that result from a single case in an entirely susceptible population.

        1 reply 2 proslijeđena tweeta 11 korisnika označava da im se sviđa
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      3. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        There's a practically identical concept in ecology about the reproductive capacity of an organism in an environment, so I should note early on that it's a common theme in math epi, you'll see parallels in math ecology.

        1 proslijeđeni tweet 13 korisnika označava da im se sviđa
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      4. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Now, epidemiologists on the ground tend to chase cases and take documented reports. Folks with my training tend to take that information, build simplified models, and run simulations. The more advanced of these incorporate things like delay from exposure and geographic info.

        1 proslijeđeni tweet 13 korisnika označava da im se sviđa
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      5. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So to give a little taste of how the mathy side looks, I'm going to introduce you to one of the most humble and familiar models a mathematical epidemiologist will encounter: the SIR model.

        1 reply 3 proslijeđena tweeta 12 korisnika označava da im se sviđa
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      6. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        It's named as such because it's a system of three differential equations, one for each "compartment" of people: Susceptible, Infectious (or Infected), and Recovered classes. Try not to let the diffeq part intimidate you too much. We've got a ways to go.

        1 reply 2 proslijeđena tweeta 9 korisnika označava da im se sviđa
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      7. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Here's the system. (Isn't it cute? 😍) I'll break it down line by line in the subsequent tweets. Apologies for going slow since I'm doing the pen and paper treatment.pic.twitter.com/IRj7jHZgSL

        1 reply 2 proslijeđena tweeta 19 korisnika označava da im se sviđa
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      8. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        First, as you can guess, S refers to the susceptible population. The dS/dt means change in the size of the susceptible class with respect to time - the first derivative. Lambda is a (fixed) birth rate, and mu is a (fixed) death rate. We're not getting too fancy here yet...pic.twitter.com/4Y9jbbt0Aq

        1 reply 1 proslijeđeni tweet 10 korisnika označava da im se sviđa
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      9. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        We'll return to those and look at them more closely when I talk about the disease-free equilibrium (DFE). The action here is in the middle term though - beta S I. As you can guess, I refers to the number of infected individuals. Beta is a "force of infection."

        1 reply 1 proslijeđeni tweet 10 korisnika označava da im se sviđa
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      10. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        If you've ever looked at chemical kinetics, you might recognize it as a "mass action" term, where reagents A and B bind with some reaction coefficient, and you can increase the reaction by increasing the concentration of reagent A or B. It's the same thing here.

        1 reply 1 proslijeđeni tweet 12 korisnika označava da im se sviđa
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      11. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So the idea is that, when a susceptible person and an infectious person meet, there's some probability that the susceptible person catches the disease and leaves the susceptible class - hence the minus sign. Where do they go, though?

        1 reply 1 proslijeđeni tweet 11 korisnika označava da im se sviđa
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      12. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Let's look at the next line! Here is the change in time of the infectious class. And we have a positive beta*S*I term here! They just moved to this compartment.pic.twitter.com/f0SFKjUQYk

        1 reply 1 proslijeđeni tweet 9 korisnika označava da im se sviđa
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      13. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        What else have we got on this line? Well, the mu is the same population-wide death rate as before. But that alpha? What's happening there when someone leaves the infectious class that way?

        1 reply 1 proslijeđeni tweet 7 korisnika označava da im se sviđa
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      14. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Look down at the last line and we have the change over time of the size of the recovered class. And look, we have a positive alpha*I! So that must mean recovery, and alpha is a recovery rate.pic.twitter.com/W2C92kRAX4

        1 reply 1 proslijeđeni tweet 8 korisnika označava da im se sviđa
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      15. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        And the only way people leave the recovered class is by dying at our natural death rate mu. So to recap, and maybe see another picture before going on...

        1 reply 1 proslijeđeni tweet 7 korisnika označava da im se sviđa
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      16. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Everyone loves flow charts, right? Here's another way to picture this model. We've got all the classes in boxes, and ways to enter and leave them in arrows.pic.twitter.com/Yw3KIaJRu4

        1 proslijeđeni tweet 15 korisnika označava da im se sviđa
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      17. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Before we analyze anything I want to point out some features we have (or rather, don't have) here. The death rate, mu? It's the same for everyone. So in this model we don't have any disease-induced mortality.

        1 reply 0 proslijeđenih tweetova 8 korisnika označava da im se sviđa
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      18. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        We also see instant transmission. More advanced models can introduce delays by throwing an Exposed class in there (making it an SEIR model) or by building what are called delay differential equations (DDEs). The latter are terrible beasts not for the faint of heart.

        1 reply 0 proslijeđenih tweetova 11 korisnika označava da im se sviđa
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      19. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Anyway, we have a humble system of equations. "Great!" you say. "But what are you supposed to do with them? I don't want to do a bunch of calculus." And I'll say, "That's wonderful because I only care about equilibria and I'm only going to need some algebra!"

        1 reply 1 proslijeđeni tweet 9 korisnika označava da im se sviđa
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      20. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        This is not entirely an oversimplification. Most of these types of (nonlinear) models don't give you nice things you can integrate by hand, so we let computers do that. But the equilibria? Stand back, we're going to do dynamics!

        1 reply 0 proslijeđenih tweetova 11 korisnika označava da im se sviđa
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      21. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So I've said equilibria a few times without really explaining the meaning yet. The other terms used are steady state and fixed point, and it describes a system at rest. Which, in other words, means nothing is changing. Which means all those derivatives are zero!

        0 proslijeđenih tweetova 9 korisnika označava da im se sviđa
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      22. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So what's it mean if all those are zero? Well, it means for each class, S, I, and R, the number of people entering and leaving is the same, so the size of each of those populations is constant.

        1 reply 0 proslijeđenih tweetova 6 korisnika označava da im se sviđa
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      23. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        First, let's look at what we call the Disease Free Equilibrium (DFE). If you built a reasonable model, this should always be something you can calculate. After all, how are people going to move to the infected and recovered classes if you don't have any disease to start with?

        1 reply 0 proslijeđenih tweetova 8 korisnika označava da im se sviđa
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      24. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So let's look at this line, where we've now said the number of susceptibles is staying constant (and that dS/dt is zero). That beta*S*I term? With no infected folk in the population, it's zero! So all we really have to deal with is 0=Lambda - mu*Spic.twitter.com/rzQb2jA47n

        1 reply 0 proslijeđenih tweetova 7 korisnika označava da im se sviđa
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      25. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Just a little algebra tells us that our steady-state value of the susceptible population, with no disease, is Lambda/mu. So we have, for our DFE, S=Lambda/mu, I=0, R=0. "Great, but what about the disease stuff?" you say?

        1 reply 0 proslijeđenih tweetova 8 korisnika označava da im se sviđa
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      26. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        We're still not really to the R0 business, but we have to see both equilibria for the dynamical interpretation to make sense, so next we need to talk about the endemic equilibrium. I've got the full system of equations below.pic.twitter.com/S0TyBLlOX8

        1 reply 0 proslijeđenih tweetova 6 korisnika označava da im se sviđa
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      27. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        The endemic equilibrium, or EE, if it exists, has to satisfy these equations for I>0. (Negatives don't make much sense here!) Now I'm gonna spare you the step by step for solving these and just write them out, and maybe make myself a drink in the process...

        1 reply 0 proslijeđenih tweetova 8 korisnika označava da im se sviđa
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      28. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        After a minor phone problem we're live again. And with a cocktail. (Recipe: Willett bourbon, Ancho Reyes chile liquor, angostura bitters, and Luxardo cherries. Proportion as a Manhattan.)pic.twitter.com/a6jk00COIk

        5 replies 2 proslijeđena tweeta 24 korisnika označavaju da im se sviđa
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      29. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        Anyway since I promised I wouldn't get too far in the weeds with the calculation I've got all the work below. I've numbered the equations, and the work references the equation number.pic.twitter.com/g57Nkn0WP3

        1 reply 0 proslijeđenih tweetova 9 korisnika označava da im se sviđa
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      30. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        So notice how I put a little more work into factoring out that term where I have a (Lambda*beta)/(mu*(mu*alpha)) for the expressions for the steady states for I and R? That's because, as we'll see, that's actually our R0!

        1 reply 0 proslijeđenih tweetova 9 korisnika označava da im se sviđa
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      31. Ty‏ @NeuroOscillator 2. velj
        • Prijavi Tweet

        I've rewritten the entire EE here (as E*) with all three parts. So you know how I said the model only makes sense for positive values? You can see by how I wrote this that we only have positive values for these if the thing I've called my R0 is greater than 1.pic.twitter.com/cMNbZ19sxq

        1 reply 0 proslijeđenih tweetova 9 korisnika označava da im se sviđa
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      32. Još 13 drugih odgovora

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