[R] Problems with the deSolve package
Alexandre Suire
alexandresuire at hotmail.fr
Fri Feb 19 09:42:55 CET 2016
Hello R-users,
I'm trying to build a SIR-like model under R,
using the "deSolve" package. I'm trying to do simulations of its dynamic
over time, with three differential equations. I'm also looking to
calculate the equilibrium state.
So far, my code looks like this
library(deSolve)
#This is my system, with three differential equations
system<-function(times, init, parameters){
with(as.list(c(init, parameters)),{
di1_dt=(alpha1*(N-i1-i2-i12)*(i1+i12))+(beta2*i12+gamma1*(N-i1-i2-i12))-(beta1*i1)-(delta*alpha2*i1*(i2+i12))
di2_dt=(alpha2*(N-i1-i2-i12)*(i2+i12))+(beta1*i12+gamma2*(N-i1-i2-i12))-(beta2*i2)-(delta*alpha1*i2*(i1+i12))
di12_dt=(delta*alpha2*i1*(i12+i2))+(delta*alpha1*i2*(i12*i1))+(delta*gamma1*i1)+(delta*gamma2*i2)-((beta1+beta2)*i12)
return(list(c(di1_dt,di2_dt,di12_dt)))
})
}
# Initials values and parameters
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(0,200, by=1)
simul <- as.data.frame(ode(y = init, times = times, func = system, parms = parameters, method="ode45"))
simul$time <- NULL
head(simul,200)
#Plotting the results
matplot(times,
simul, type = "l", xlab = "Time", ylab = "i1 i2 i12", main =
"Simulation", lwd = 2, lty = 2, bty = "l", col=c("darkblue",
"darkred","mediumseagreen"))
legend("bottomright", c("i1", "i2","i12"), lty=2,lwd=2, col = c("darkblue", "darkred", "mediumseagreen"))
At
first, I just tried studying with only the first two equations, and it
seems to work completely fine, but when I wanted to add the 3rd
equation, I sometimes get this message, even when I juggle the
parameters, when i launch the line:
#simul <- as.data.frame(ode(y = init, times = times, func = system, parms = parameters))
Warning messages:
1: In lsode(y, times, func, parms, mf = 10, ...) :
an excessive amount of work (> maxsteps ) was done, but integration was not successful - increase maxsteps
2: In lsode(y, times, func, parms, mf = 10, ...) :
Returning early. Results are accurate, as far as they go
Have I overlooked something ? I tried to use methods="ode45" and methods="adams", without any sucess.
Thank you for your time
Alex
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