[R] Problems with the deSolve package

Thomas Petzoldt thpe at simecol.de
Thu Feb 25 09:08:16 CET 2016


to diagnose your problem, I tried the model with your original 
parameters, using a Runge-Kutta fixed step integrator and smaller time 
steps. You may try to make them even smaller.

rk4 has no warranted accuracy, so it is less reliable than "lsoda" etc. 
However, it can be useful for debugging, because it runs constantly 
through, even if NA or NaN's occur. We see that the states grow 
drastically to extremely high (or even negative) values.

This points indeed to unrealistic parameter values, or to a 
model-misspecification, which means that necessary feedback mechanisms 
are missing, so that i12 can grow, even if nothing is left (i1, i2) from 
which it can grow from.

Regards, Thomas

init <- c(i1=10, i2=10, i12=0)
parameters <- c(alpha1=0.7, alpha2=0.5, beta1=0.5, beta2=0.3,
   gamma1=0.5, gamma2=0.5, delta=0.5, N=100)
times <- seq(0, 10, by=.01)

simul <- as.data.frame(ode(y = init, times = times, func = system,
   parms = parameters, method="rk4"))

head(simul, 200)
     time            i1            i2          i12
1   0.00  1.000000e+01  1.000000e+01 0.000000e+00
2   0.01  1.685572e+01  1.433028e+01 6.451953e-01
3   0.02  2.567008e+01  1.875164e+01 4.259949e+00
4   0.03  3.251911e+01  2.091655e+01 4.215409e+01
5   0.04 -1.270280e+00 -1.988876e+00 1.581789e+02
6   0.05 -8.108876e+02 -4.992572e+02 2.631133e+04
7   0.06 -4.166359e+73 -2.975971e+73 6.427467e+98
8   0.07           NaN           NaN          NaN
9   0.08           NaN           NaN          NaN


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

E-Mail: thomas.petzoldt at tu-dresden.de

More information about the R-help mailing list