[R-sig-dyn-mod] Altering params for Simecol model at time step

[Thomas Petzoldt]

Hi,

please excuse the delay, it is weekend ;-)

Events are used to manipulate state variables, but you need to
change parameters. We call this a "forcing function" or an "input".

Inputs are, in principle, explained in Section 5.3 of the simecol
package vignette. However, instead of approx or approxTime I would
recommend to use approxfun, that is now much faster:



sir <- new("odeModel",
   main = function(time, init, parms, inputs, ...){
     with(as.list(c(init, parms)), {
       beta <- inputs(time)
       dS <- -beta*S*I
       dI <- beta*S*I-I*gamma
       dR <- I*gamma
       list(c(dS, dI, dR), beta=beta)
     })
   },
   parms = c(gamma=0.167),
   times = c(from=0, to=300, by=1),
   init = c(S=10000000, I=25, R=0),
   inputs = approxfun(c(0, 60, 300),
     c(0.18, 0.08, 0.08), method="constant", rule=2),
   solver = "lsoda"
)


sir <- sim(sir)
plot(sir)


If you need more than one input, make inputs a list:

inputs = list(
   beta=approxfun(c(0, 60, 300), c(0.18, 0.08, 0.08),
     method="constant", rule=2),
   gamma = approxfun ......
),


then call it like this:

beta <- inputs$beta(time)


Another hint: "by" should not be too small for performance reasons, but
on the other hand small enough so that solver does not jump over the
inputs. In your case, it is safe to increase "by" to 1.0

Does this help you?

Thomas


-- 
Dr. Thomas Petzoldt
Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of Hydrobiology
01062 Dresden, Germany

E-Mail: thomas.petzoldt at tu-dresden.de
http://tu-dresden.de/Members/thomas.petzoldt