[R] Problems with the deSolve package

[Abdel Halloway]

Okay, so if delta is high (say 0.5), the betas have to be extremely high
(around 5) to get good results. If delta is around 0.1, you can get good
results with smaller betas.

On Wed, Feb 24, 2016 at 9:21 AM, Abdel Halloway <abdel.halloway at gmail.com>
wrote:

> I think your delta is too high. If you reduce your delta (0.1 for
> example), you should be able to get good results.
>
> On Mon, Feb 22, 2016 at 3:37 AM, Alexandre Suire <
> alexandresuire at hotmail.fr> wrote:
>
>> 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
>> Alex
>>
>> ------------------------------
>> 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
>>
>> 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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>>
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>>
>

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