[Scilab-users] Covid19 model

[Claus Futtrup]

Hi Scilabers

A friend (Lars Risbo) published some MATLAB code in LinkedIn for 
simulating the infection with a company lockdown after some time. I 
figured I'd try to convert it to Scilab.

The code uses ODE45 and I'm not sure that I understand how to convert 
this MATLAB code to Scilab. I hope you can explain what I need to do to 
make the code work. Some of the original MATLAB code is found in the 
comments.

// covid19risbo.sce
//
// SEIRsim1
// Susceptible-Exposed-Infectious-Recovered (SEIR)

function  dydt=odefun(t, y)
     if  t<days
       R=R0;
     else
       R=0.6;  // Change reproductive rate after lockdown
     end
     A=[0     0    -delta*R*y(1)/Npop   0  0  0;...
       0    -gam  delta*R*y(1)/Npop   0  0  0;...
       0     gam  -delta         0  0  0;...
       0     0    delta*(1-Fhosp)    0  0  0;...
       0     0    delta*Fhosp      0  -1/Thosp  0;...
       0     0    delta*R*y(1)/Npop   0  0  0];
     dydt=A*y;
end

Begin=datenum(2020,02,20,0,0,0);  // begin date
Dlock=datenum(2020,03,12,0,0,0);  // date of lockdown
days=Dlock-Begin;
R0=2.6;    // inital R value
gam=  1/3;  // gamma, the inverse of average latent time
delta=  1/5;  // inv time constant which infectious people either recover or enter 
hospital
Fhosp=0.16;  // fraction of recovering people going to hospital
Thosp=14;   // average time of hospitalisation
Npop=6e6;   // total initial population of sensitive
y0=[Npop;50;50;0;0;0];// [S E I R Hosp ] intial cond.
t1  =  0:60;
y1  =  ode(y0,  0,  60,  odefun);  // [t1,y1] = ode45(@odefun,[0 60],y0); // run 1st scernario
idx=[3:6];
scf();
a  =  gca();
plot(Begin+t1,y1(:,idx),'-');  // semilogy(Begin+t1,y1(:,idx),'-','LineWidth',3)
a.log_flags  =  "nln";
xlabel('Date')
ylabel('Number of cases')
xgrid();
// ax=gca;
// ax.YLim=[10 max(max(y2(:,idx)))];
xtitle({'Danish Corona lock down on 20.03.12, vs 14 days later','R goes 
from 2.6 to 0.6 at lockdown'});
legend('Infected','Recovered','Hospitalised','Total Cases');

P.S. Attached a simple graph of what the output should look like (file 
covid19risbo.jpg < 50 kb), at least partially - because I deleted an 
alternative case with a later lockdown date = dashed lines.

Best regards,

Claus



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