[R-sig-dyn-mod] Help with function

[Austin Mullings]

Daniel,

I apologize for the confusion. I feel bad asking for this much help. As
earlier stated, I am still extremely new to R. I have only used it on
extremely simple linear statistics (e.g., multiple regression, ANOVA, etc).
I am trying to learn deSolve and do not know what the program requires for
my syntax to run on my data. Specifically, what I need to name my variable
in the dataset or name the variable in equation syntax.

For example, below is my equation and a link to my dataset variable names.
When I run the syntax for that model, it does not run on my data and give
me a summary of the fit and other results. I was wondering if you could
help me learn to run it, and after this example, I would hopefully be able
to run these models on my own.

Link:
http://s1074.photobucket.com/user/austinmullings89/media/Picture%20of%20Levy%20Model%20data.jpg.html

Equation syntax:

library(deSolve)

myfn <- function(t, y, p) {

  dy <- numeric(6)
  dy[1] <- p[1] - p[2]*y[4] - p[3]*y[1]
  dy[2] <- y[5]*dy[1]*(1+y[6]) - p[5]*y[2] - (p[6]*y[3]*y[4]*y[1] - p[7])
  dy[3] <- p[8] - p[9]*y[2]
  dy[4] <- y[6]*dy[1] - p[10]*y[4] + p[11]*(p[6]*y[3]*y[4]*y[1] - p[7]) +
p[4]
  dy[5] <- 1.0 - y[5]*(y[1] + y[4] + 1)
  dy[6] <- 1.0 - y[6]*(y[1] + 1)

  return(list(dy))

}

pars <- runif(11)
yini <- runif(6)
times <- seq(0, 10, .01)


out <- ode(yini, times, myfn, pars)
plot(out)

On Thu, Mar 12, 2015 at 8:23 AM, Daniel Kaschek <
daniel.kaschek at physik.uni-freiburg.de> wrote:

> Hi Austin,
>
> On Mi, 2015-03-11 at 10:03 -0600, Austin Mullings wrote:
> > I had one more question, which may be a novice question, but how do I
> need
> > to create my dataset in a way that this function will run off of it?
> > Specifically, I am trying to run it on some mock data (until I learn more
> > about simulation), and do not know how R and this package expects my
> > function or dataset column/variable names to be for it to run. Here is a
> > picture of my mock data, if you wouldn't mind letting me know whether I
> > have the variable names ordered incorrectly or need to rename them
> > accordingly.
>
> I think you cannot send pictures via the mailing list. Unfortunately, I
> didn't get your question. What do you mean by "data to run your
> simulation on"?
>
> Concerning the sorting of variables: In the example below, I
> initialized
>
> yini <- runif(6)
>
> resulting in a vector yini of length 6. The i'th element of yini is y[i]
> in myfn (at time point 0). This means that the i'th element is the
> initial value of the i'th state, which in turn will be the i'th column
> next to the time column of the ode() output.
>
> Cheers,
> Daniel
>
> >
> >
> >
> >
> > On Tue, Feb 17, 2015 at 2:04 AM, Daniel Kaschek <
> > daniel.kaschek at physik.uni-freiburg.de> wrote:
> >
> > > Hi Austin,
> > >
> > > one possibility to do this is the code below. In this example code, I
> > > randomly initialize your parameters and the initial state. Instead of
> > > using the indexes to access parameter values or states you can use the
> > > names as well (see ?ode, first example). However, in my experience, the
> > > function with() slows down your code considerably.
> > >
> > > Best wishes,
> > > Daniel
> > >
> > >
> > > library(deSolve)
> > >
> > > myfn <- function(t, y, p) {
> > >
> > >   dy <- numeric(6)
> > >   dy[1] <- p[1] - p[2]*y[4] - p[3]*y[1]
> > >   dy[2] <- y[5]*dy[1]*(1+y[6]) - p[5]*y[2] - (p[6]*y[3]*y[4]*y[1] -
> p[7])
> > >   dy[3] <- p[8] - p[9]*y[2]
> > >   dy[4] <- y[6]*dy[1] - p[10]*y[4] + p[11]*(p[6]*y[3]*y[4]*y[1] -
> p[7]) +
> > > p[4]
> > >   dy[5] <- 1.0 - y[5]*(y[1] + y[4] + 1)
> > >   dy[6] <- 1.0 - y[6]*(y[1] + 1)
> > >
> > >   return(list(dy))
> > >
> > > }
> > >
> > > pars <- runif(11)
> > > yini <- runif(6)
> > > times <- seq(0, 10, .01)
> > >
> > >
> > > out <- ode(yini, times, myfn, pars)
> > > plot(out)
> > >
> > >
> > > On Mo, 2015-02-16 at 13:15 -0700, Austin Mullings wrote:
> > > > I am trying to get this equation to work with deSolve, and can't
> seem to
> > > > get it to work. Does someone know how one would write the function
> for
> > > this?
> > > >
> > > > dY1(t)/dt = a - bY3(t) Y4(t) - cY1(t),
> > > > dY2(t)/dt = Y5(t) [dY1(t)/dt] [1 + Y6(t)] - eY2(t) - {f Y3(t) Y4(t)
> > > Y1(t) -
> > > > g},
> > > > dY3(t)/dt = h - iY2(t),
> > > > dY4(t)/dt = Y6(t) [dY1(t)/dt] - jY4(t) + k {f Y3(t) Y4(t) Y1(t) - g}
> + d,
> > > > dY5(t)/dt = 1.0 - Y5(t) [Y1(t) + Y4(t) + 1],
> > > > dY6(t)/dt = 1.0 - Y6(t) [Y1(t) + 1].
> > > >
> > > >       [[alternative HTML version deleted]]
> > > >
> > > > _______________________________________________
> > > > R-sig-dynamic-models mailing list
> > > > R-sig-dynamic-models at r-project.org
> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models
> > >
> > > --
> > > Daniel Kaschek
> > > Institute of Physics
> > > Freiburg University
> > >
> > > Room 210
> > > Phone: +49 761 2038531
> > >
> > > _______________________________________________
> > > R-sig-dynamic-models mailing list
> > > R-sig-dynamic-models at r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models
> > >
> >
> >
> >
>
> --
> Daniel Kaschek
> Institute of Physics
> Freiburg University
>
> Room 210
> Phone: +49 761 2038531
>
> _______________________________________________
> R-sig-dynamic-models mailing list
> R-sig-dynamic-models at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models
>



-- 
Austin F. Mullings
Graduate Student, Research Assistant
Department of Psychology, Clinical Psychology
University of Colorado at Colorado Springs

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