[R-sig-dyn-mod] R-sig-dynamic-models Digest, Vol 106, Issue 1

[Titus Kassem]

Good day Jose,
Here is the code:

rm(list=ls())
library(ReacTran)
N <-200
alpha12<-0.0034
alpha21<-0.05
omega<-0.7
sigma<-1.2
rho<-1.5
mu<-0.02
gamma<-0.01
Grid <- setup.grid.1D(x.up = 0, x.down = 1, N = N)
Xini<-rep(x= 1, times= N)
Yini <- rep(x = 3, times = N)
Zini<-rep(x=4, times=N)
yini <- c(Xini, Yini, Zini)
Predator_prey <- function(t, y, parms) {
  X <- y[1:N]
  Y <- y[(N+1):(2*N)]
  Z <- y[(2*N+1):(3*N)]
  dX <- X*(1-X-alpha12*Y)-omega*X^2*Z/(1+X^2)+
    tran.1D (C = X, C.up = 0, C.down = 1,
             D = 0.1, dx = Grid)$dC+tran.1D (C = Z, C.up = NULL, C.down =
NULL,
                                              D = 1, dx = Grid)$dC
  dY <-  rho*Y*(1-Y-alpha21*X)+
    tran.1D (C = Y, C.up = NULL, C.down = NULL,
             D = 0.1, dx = Grid)$dC
  dZ <- sigma*X^2*Z/(1+X^2)-mu*Z-gamma*Z
    tran.1D (C = Z, C.up = NULL, C.down = NULL, flux.up = NULL, flux.down =
NULL,
             D = 0.1, dx = Grid)$dC+tran.1D (C = X, C.up = NULL, C.down =
NULL,
                                              D= -1, dx = Grid)$dC
  list(c(dX, dY, dZ))
}
times <- seq(from = 0, to = 100, by = 0.01)
print(system.time(
  out <- ode.1D(y = yini, func = Predator_prey,
                times = times, parms = NULL, nspec = 3,
                names = c("X", "Y","Z"), dimens = N)
))
matplot(out[,"time"], out[,2], type = "l", xlab = "time", ylab = "",
         main = "", lwd = 2)

Regards

Titus Kassem

On Thu, Jul 7, 2016 at 11:00 AM, <r-sig-dynamic-models-request at r-project.org
> wrote:

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>    1. Spatial Model (Titus Kassem)
>    2. Re: Spatial Model (Flores, Jose)
>
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 6 Jul 2016 12:52:52 +0100
> From: Titus Kassem <gtkassem at gmail.com>
> To: r-sig-dynamic-models at r-project.org
> Subject: [R-sig-dyn-mod] Spatial Model
> Message-ID:
>         <
> CAG92UYB9ecG4Qh1eoedrZnErLjuefTraOcX4N9duT_FZpEkbTA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Karline,
>
> I have a predator-prey model model with competition that I have trying to
> simulated. I added a diffusion term but i seem to be having problem as the
> figure is not impressive enough. I think something must be wrong with the
> code. Please can you help out?
> Attached is the code and the model.
>
> Thanks
>
>
> Titus Kassem
>
> University of Jos
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 6 Jul 2016 14:10:08 +0000
> From: "Flores, Jose" <Jose.Flores at usd.edu>
> To: Special Interest Group for Dynamic Simulation Models in R
>         <r-sig-dynamic-models at r-project.org>
> Subject: Re: [R-sig-dyn-mod] Spatial Model
> Message-ID: <0704B4BB-15B5-4C6F-9A49-3E12CC4241E3 at usd.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Where is the code to take a look at it?
>
> Jose
>
>
> > On Jul 6, 2016, at 6:52 AM, Titus Kassem <gtkassem at gmail.com> wrote:
> >
> > Hi Karline,
> >
> > I have a predator-prey model model with competition that I have trying to
> > simulated. I added a diffusion term but i seem to be having problem as
> the
> > figure is not impressive enough. I think something must be wrong with the
> > code. Please can you help out?
> > Attached is the code and the model.
> >
> > Thanks
> >
> >
> > Titus Kassem
> >
> > University of Jos
> > _______________________________________________
> > R-sig-dynamic-models mailing list
> > R-sig-dynamic-models at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models
>
>
>
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> End of R-sig-dynamic-models Digest, Vol 106, Issue 1
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