R help - Mar 2017 - How to change parameter values as a function to time with the package "deSolve"

Hello,

I am trying to solve an ODE in R using deSolve. With the following code, I
expected the parameter ?gamma0? takes the values 5 at time step 0, 1, 2, 3, 4,
5, 6, 7, 8, 9 and 10, and 0 otherwise. However, the print(gamma0) shows that
?gamma0? stays at 0.

Here is my ODE:

param <- c(a = 0.1, b = 1)
yini <- c(alpha0 = 0, beta0 = 0)

mod <- function(times, yini, param) {

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

  gamma0 <- ifelse(times %in% seq(0,10,1), 5, 0)

  # print(gamma0)

  dalpha0 <- - a*alpha0 + gamma0
  dbeta0 <- a*alpha0 - b*beta0
  return(list(c(dalpha0, dbeta0)))

  })}

times <- seq(from = 0, to = 10, by = 1/24)
out <- ode(func = mod, times = times, y = yini, parms = param)
plot(out, lwd = 2, xlab = "day")


What am I doing wrong? Thanks in advance for your help!
Marine


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> On Mar 23, 2017, at 2:59 PM, Marine Regis <marine.regis at
hotmail.fr> wrote:
> 
> Hello,
> 
> I am trying to solve an ODE in R using deSolve. With the following code, I
expected the parameter ?gamma0? takes the values 5 at time step 0, 1, 2, 3, 4,
5, 6, 7, 8, 9 and 10, and 0 otherwise. However, the print(gamma0) shows that
?gamma0? stays at 0.
> 
> Here is my ODE:
> 
> param <- c(a = 0.1, b = 1)
> yini <- c(alpha0 = 0, beta0 = 0)
> 
> mod <- function(times, yini, param) {
> 
>  with(as.list(c(yini, parameters)), {
> 
>  gamma0 <- ifelse(times %in% seq(0,10,1), 5, 0)
> 
>  # print(gamma0)
> 
>  dalpha0 <- - a*alpha0 + gamma0
>  dbeta0 <- a*alpha0 - b*beta0
>  return(list(c(dalpha0, dbeta0)))
> 
>  })}
> 
> times <- seq(from = 0, to = 10, by = 1/24)
> out <- ode(func = mod, times = times, y = yini, parms = param)
> plot(out, lwd = 2, xlab = "day")
> 
> 
> What am I doing wrong? Thanks in advance for your help!
When I execute that code I get:

Error in as.list(c(yini, parameters)) : object 'parameters' not found

(The mistake seems fairly obvious when you look are the parameter list for your
`mod` function.)

Additionally: It's not generally good practice to use `with` inside
functions, but that's not the problem here.

-- 
David.
> Marine
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA

Thanks very much David for your answer. Sorry ! here is the code without the
error:


library(deSolve)
param <- c(a = 0.1, b = 1)
yini <- c(alpha0 = 6, beta0 = 2)

mod <- function(times, yini, param) {

  with(as.list(c(yini, param)), {

    gamma0 <- ifelse(times %in% seq(0,10,1), 5, 0)

    ## print(gamma0)

    dalpha0 <- - a*alpha0 + gamma0
    dbeta0 <- a*alpha0 - b*beta0
    return(list(c(dalpha0, dbeta0)))

  })}

times <- seq(from = 0, to = 10, by = 1/24)
out <- ode(func = mod, times = times, y = yini, parms = param)
plot(out, lwd = 2, xlab = "day")

Thanks in advance for your help!
Marine



________________________________
De : David Winsemius <dwinsemius at comcast.net>
Envoy? : vendredi 24 mars 2017 06:01
? : Marine Regis
Cc : r-help at r-project.org
Objet : Re: [R] How to change parameter values as a function to time with the
package "deSolve"

> On Mar 23, 2017, at 2:59 PM, Marine Regis <marine.regis at
hotmail.fr> wrote:
>
> Hello,
>
> I am trying to solve an ODE in R using deSolve. With the following code, I
expected the parameter ?gamma0? takes the values 5 at time step 0, 1, 2, 3, 4,
5, 6, 7, 8, 9 and 10, and 0 otherwise. However, the print(gamma0) shows that
?gamma0? stays at 0.
>
> Here is my ODE:
>
> param <- c(a = 0.1, b = 1)
> yini <- c(alpha0 = 0, beta0 = 0)
>
> mod <- function(times, yini, param) {
>
>  with(as.list(c(yini, parameters)), {
>
>  gamma0 <- ifelse(times %in% seq(0,10,1), 5, 0)
>
>  # print(gamma0)
>
>  dalpha0 <- - a*alpha0 + gamma0
>  dbeta0 <- a*alpha0 - b*beta0
>  return(list(c(dalpha0, dbeta0)))
>
>  })}
>
> times <- seq(from = 0, to = 10, by = 1/24)
> out <- ode(func = mod, times = times, y = yini, parms = param)
> plot(out, lwd = 2, xlab = "day")
>
>
> What am I doing wrong? Thanks in advance for your help!
When I execute that code I get:

Error in as.list(c(yini, parameters)) : object 'parameters' not found

(The mistake seems fairly obvious when you look are the parameter list for your
`mod` function.)

Additionally: It's not generally good practice to use `with` inside
functions, but that's not the problem here.

--
David.
> Marine
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
R-help Info Page - Homepage - SfS ? Seminar for
Statistics<https://stat.ethz.ch/mailman/listinfo/r-help>
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availability of new code, questions and answers about problems and solutions
using R ...


> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA


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