hi Andrei, all
I'll get to this later but first thought is that your model looks like a
linear differential equation.
put v = state vector whose components are the compartments.
dv/dt = A%*%v where A is a matrix with a lot of 0s and some parameters
which you've estimated from the literature. If that's right, the solution
is
v(t) = exp(tA)%*%v(0)
to compute exp(tA), diagonalise it.
anyway I'll look when I can.
Greg
> Hi Greg and all,
>
> Yes, I agree with you - I think (am hoping?!) this is going to backfire
> quite spectacularly on the conservatives. A silver lining we might not
> want...
>
> I've now put my code up on the web:
>
> * https://0xacab.org/asm/covid19
>
> I will reiterate it is *very* crude - the number of deaths is circa 10
> million or more for the UK, which is clearly ridiculous. The main point
> I was trying to make was about "flattening the curve" - I want to show
> how this relates to ITU bed occupation at some point, but don't have
> time at present. I'm also not retired and guess I should do some 'real'
> work at some point ;-)
>
> Anyway, would love to hear your thoughts about it. I don't have any data
> to hand about long term immunity - my guess is it's pretty high, but it
> really depends on the disease. For instance, we all have *some* immunity
> to the flu, but different strains mutate and circulate etc, so that
> level is different every year.
>
> Tomorrow I'm on call, I'm not quite sure if/when I'll be able to catch
> up with the flood of emails that is bound to come to this list. But
> great to see the list being used in productive ways!
>
> Best wishes,
>
> -- Andrei
>
> On Sat, Mar 14, 2020 at 10:15:31PM -0000, Greg Dropkin wrote:
>> Date: Sat, 14 Mar 2020 22:15:31 -0000 (UTC)
>> hi
>>
>> even without any modelling, if they think 60% is the threshold they are
>> aiming for over 30m adults to be infected, which means over 300,000
>> deaths
>> at 1%, and 100,000 deaths at 0.3%. Which you would have thought is
>> political suicide, once the public realises.
>>
>> if time permits I'll try your model and send you some R code to compare
>>
>> Do you have data for other diseases on the percentage of survivors who
>> get
>> long term immunity?
>>
>> Greg
>>
>> > Hi,
>> >
>> > Paul Fine is amazing, he taught me loads about infectious disease
>> > epidemiology and was the one who got me interested in the subject
>> > (albeit, as a secondary interest/hobby - my main focus is perinatal
>> and
>> > non-communicable disease epidemiology). Interestingly enough, he
>> started
>> > life as a veterinarian before getting into human epi...
>> >
>> > Anyway, the UK's herd immunity idea is, put mildly, bollocks. I've
>> > written another post today in which I've started to explain some of
>> the
>> > flaws with the UK strategy although I haven't completely elaborated
>> them
>> > - don't want to freak people out too much all at once! Please feel
>> free
>> > to comment, either directly on the article or on list or just directly
>> > to me via email. Both articles I've written are on my site:
>> >
>> > * https://www.andreimorgan.net
>> >
>> > Best wishes,
>> >
>> > -- Andrei
>> >
>> > On Sat, Mar 14, 2020 at 09:25:02PM +0000, Thomas Cox wrote:
>> >> I think the first two paragraphs should have made that clear.
>> >>
>> >> Abstract
>> >>
>> >> The term “herd immunity” is widely used but carries a variety of
>> >> meanings [1–7]. Some authors use it to describe the proportion immune
>> >> among individuals in a population. Others use it with reference to a
>> >> particular threshold proportion of immune individuals that should
>> lead
>> >> to a decline in incidence of infection. Still others use it to refer
>> to
>> >> a pattern of immunity that should protect a population from invasion
>> of
>> >> a new infection. A common implication of the term is that the risk of
>> >> infection among susceptible individuals in a population is reduced by
>> >> the presence and proximity of immune individuals (this is sometimes
>> >> referred to as “indirect protection” or a “herd effect”). We provide
>> >> brief historical, epidemiologic, theoretical, and pragmatic public
>> >> health perspectives on this concept.
>> >>
>> >> Though coined almost a century ago [8], the term “herd immunity” was
>> not
>> >> widely used until recent decades, its use stimulated by the
>> increasing
>> >> use of vaccines, discussions of disease eradication, and analyses of
>> the
>> >> costs and benefits of vaccination programs. An important milestone
>> was
>> >> the recognition by Smith in 1970 [9] and Dietz in 1975 [10] of a
>> simple
>> >> threshold theorem—that if immunity (ie, successful vaccination) were
>> >> delivered at random and if members of a population mixed at random,
>> such
>> >> that on average each individual contacted R0 individuals in a manner
>> >> sufficient to transmit the infection [11, 12], then incidence of the
>> >> infection would decline if the proportion immune exceeded (R0 −
>> 1)/R0,
>> >> or 1 –1/R0. This is illustrated in Figures 1 and 2.
>> >>
>> >>
>> >> Thomas Cox PhD RN
>> >> [log in to unmask]
>> >>
>> >>
>> >> On Saturday, March 14, 2020, 05:13:28 PM EDT, John Whittington
>> >> <[log in to unmask]> wrote:
>> >>
>> >> At 20:59 14/03/2020, Thomas Cox wrote:
>> >> >and yet...
>> >> >https://academic.oup.com/cid/article/52/7/911/299077
>> >>
>> >> After a very quick skip through, that all seems to be about
>> >> immunological herd immunity in the sense I described it. Could you
>> >> perhaps direct me to the part which you were wanting to bring to my
>> >> attention? Thanks
>> >>
>> >> Kind Regards,
>> >>
>> >>
>> >> John
>> >>
>> >> ----------------------------------------------------------------
>> >> Dr John Whittington, Voice: +44 (0) 1296 730225
>> >> Mediscience Services Fax: +44 (0) 1296 738893
>> >> Twyford Manor, Twyford, E-mail: [log in to unmask]
>> >> Buckingham MK18 4EL, UK
>> >> ----------------------------------------------------------------
>> >>
>> >>
>> >>
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>> >
>> > --
>> > Andrei Morgan MRCPCH, MSc, PhD (Epidemiology / Neonatology)
>> > https://www.andreimorgan.net
>> >
>> > Honorary Clinical Lecturer,
>> > Department of Neonatology,
>> > Institute for Women's Health,
>> > University College London
>> >
>> >
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>> > issues of our newsletter you are invited to visit our web site
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>> >
>>
>>
>
> --
> Andrei Morgan MRCPCH, MSc, PhD (Epidemiology / Neonatology)
> https://www.andreimorgan.net
>
> Honorary Clinical Lecturer,
> Department of Neonatology,
> Institute for Women's Health,
> University College London
>
>
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message will go only to the sender of this message.
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