There is nothing wrong with for-loops. The only thing you can vectorize is T
T=0:tmax;
for t=1:1:tmax
S(t+1)=S(t)+(a-d*S(t)-(lambda*S(t)*I(t)/(1+alpha1*I(t)+ alpha2*I(t)^2))+beta*R(t));
I(t+1)=I(t)+((lambda*S(t)*I(t)/(1+alpha1*I(t)+alpha2*I(t)^2))-(d+m+r)*I(t));
R(t+1)=R(t)+(m*I(t)-(d+beta)*R(t)+r*I(t));
end