[Scilab-users] Fwd: Re: Corona modelling
Chin Luh Tan
chinluh.tan at bytecode-asia.com
Thu Apr 30 18:44:57 CEST 2020
Just notice that this email was stuck due to the image attached was too large, and notice the new post by Claus with the SEIR model from Matlab, perhaps Scilabers could make the model more realistic together.
CL
============ Forwarded message ============
From: Chin Luh Tan <mailto:chinluh.tan at bytecode-asia.com>
To: "Users mailing list for Scilab"<mailto:users at lists.scilab.org>
Date: Thu, 30 Apr 2020 00:03:46 +0800
Subject: Re: [Scilab-users] Corona modelling
============ Forwarded message ============
Hi,
I just modified Stephane's nice GUI to make it able to load the real world data from internet so that we could overlapped the data to the SIR model to study the effect of locked-down, and the meaning of the coefficients.
>From some reading from the internet, the "Susceptible" population is kind of like difficult to determined, and some suggested to use "current cases" as "optimum model" assuming the condition is recovering. As or the "optional model", the "total population" is being used.
While "beta" is the transmission coefficient, "gamma" the recovery factor, can anyone explained more details, perhaps in layman term, how to relate these parameters to one country condition, such as the relationship between gamma with the number of days (what days is it referring to), beta "actual meaning" in layman term, and perhaps link with some "technical term" the newspaper always seen on papers?
I attached the GUI, which will load 3 sets of data from Johns Hopkins Github, (https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series)
which could be download using following 3 lines directly from the Scilab:
--> fn = getURL('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv')
--> fn = getURL('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv')
--> fn = getURL('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv')
and run the GUI as attached.
rgds,
CL
---- On Mon, 30 Mar 2020 14:13:40 +0800 Stéphane Mottelet <mailto:stephane.mottelet at utc.fr> wrote ----
Hello Heinz,
Here is an interactive version (made for my children last
week...) :
// Confinement COVID-19 !
// Stephane MOTTELET, UTC
// Tue Mar 24 08:55:03 CET 2020
//
function dydt=sir(t, y, bet, gam, N)
dydt=[-bet/N*y(1)*y(2)
bet/N*y(1)*y(2)-gam*y(2)
gam*y(2)];
endfunction
function draw(bet, gam)
t=0:1:360;
N=6e7;
if exists("gcbo") && is_handle_valid(gcbo)
sb = gcbo;
if sb.tag=="beta"
bet=sb.value;
gam=findobj("gamma").value
else
gam=sb.value;
bet=findobj("beta").value
end
y=ode('stiff',[N-1;1;0],0,t,list(sir,bet,gam,N));
curves = findobj("curves");
curves.children(1).data(:,2)=y(3,:);
curves.children(2).data(:,2)=y(2,:);
curves.children(3).data(:,2)=y(1,:);
else
y=ode('stiff',[N-1;1;0],0,t,list(sir,bet,gam,N));
scf(0)
clf
plot(t,y)
gce().tag="curves";
gce().children.thickness=2;
legend("Susceptible","Infected","Recovered",-1)
sb1 = uicontrol("style","slider",...
"units","normalized",...
"Position", [0.85,0.2,0.05,0.48],...
"BackgroundColor", [1,1,1],...
"Callback_Type",12,...
"sliderstep",[1/1000,1/10],...
"min",0.15,"max",0.3,"value",bet,...
"Callback","draw","tag","beta");
uicontrol("style","text",...
"string","$\beta$",...
"units","normalized",...
"Position", [0.85,0.125,0.05,0.08],...
"BackgroundColor", [1,1,1],...
"HorizontalAlignment","center");
sb1 = uicontrol("style","slider",...
"units","normalized",...
"Position", [0.90,0.2,0.05,0.48],...
"BackgroundColor", [1,1,1],...
"Callback_Type",12,...
"sliderstep",[1/1000,1/10],...
"min",0,"max",1/15,"value",gam,...
"Callback","draw","tag","gamma");
uicontrol("style","text",...
"string","$\gamma$",...
"units","normalized",...
"Position", [0.9,0.125,0.05,0.08],...
"BackgroundColor", [1,1,1],...
"HorizontalAlignment","center");
end
end
clf
draw(0.3,1/15)
Le 30/03/2020 à 02:14, Heinz Nabielek a
écrit :
Colleagues:
is there an straightforward Scilab approach for solving the three coupled nonlinear differential equations of first order given by the Standard Model of Epidemics?
S= number Susceptible: S'=-aSI
I= number Infected: I'=aSI - bI
R= number Recovered: R'=bI
whereby 'a' is the transmission coefficient, 'b' the recovery factor (after Reed-Frost 1928).
Initial values for S, I, R are available.
Thank you
Heinz
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--
Stéphane Mottelet
Ingénieur de recherche
EA 4297 Transformations Intégrées de la Matière Renouvelable
Département Génie des Procédés Industriels
Sorbonne Universités - Université de Technologie de Compiègne
CS 60319, 60203 Compiègne cedex
Tel : +33(0)344234688
http://www.utc.fr/~mottelet
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