[R] Problems with the deSolve package

Alexandre Suire alexandresuire at hotmail.fr
Mon Feb 22 10:37:10 CET 2016

Hello Abdel, 
I'm trying to model the spread of two viruses between different states, which are i1 and i2, and i12 if you got both viruses, but you can go back to the previous state with given probabilities (alpha, beta). The gamma probabilities are just additional infection (without contact) and delta an interaction factor between virus 1 and 2. 

I tried lowering the time steps, and, as you said, i1 and i2 are going 
negative, but it stops after a few steps. In effect, that's not what I'm
 looking for. I just want to model the dynamic of this system, and do some king of sensitivity analysis. I tried different set of parameters, but it still gives me the same error message. Maybe this has to do with my equations ? But I really doubt it. 

Thank you for your time

From: abdel.halloway at gmail.com
Date: Sat, 20 Feb 2016 11:01:00 -0600
Subject: Re: [R] Problems with the deSolve package
To: alexandresuire at hotmail.fr
CC: r-help at r-project.org

I think your parameters are off. If you look at the simul data frame, it gives you a bunch of NaNs after the first initialization. If you put lower the timesteps s.t.

times<-seq(0,200, by=0.01)

it begins to run but soon your values diverge, i1 & i2 going negative while i12 goes way high. Not sure what you are modeling but I assume those values aren't to be like that. Try again with different parameters and see.

On Fri, Feb 19, 2016 at 2:42 AM, Alexandre Suire <alexandresuire at hotmail.fr> wrote:
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


#This is my system, with three differential equations

system<-function(times, init, parameters){

with(as.list(c(init, parameters)),{







# 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


#Plotting the results


 simul, type = "l", xlab = "Time", ylab = "i1 i2 i12", main =

"Simulation", lwd = 2, lty = 2, bty = "l", col=c("darkblue",


legend("bottomright", c("i1", "i2","i12"), lty=2,lwd=2, col = c("darkblue", "darkred", "mediumseagreen"))


 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


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