On 03-03-2013, at 00:57, Louise Stevenson <louise.steven...@lifesci.ucsb.edu>
wrote:
> Hi,
>
> I'm trying to set up R to run a simulation of two populations in which every
> 3.5 days, the initial value of one of the populations is reset to 1.5. I'm
> simulation an experiment we did in which we fed Daphnia populations twice a
> week with algae, so I want the initial value of the algal population to reset
> to 1.5 twice a week to simulate that feeding. I've use for loops and if/else
> loops before but I can't figure out how to syntax "if t is in this vector of
> possible t values, do this command, else, do this command" if that makes
> sense. Here's what I have (and it doesn't work):
>
> params = c(1, 0.15, 0.164, 1)
> init = c(1.5, 0.05)
> t=seq(1,60, by=0.5) #all time values, experiment ran for 60 days
>
> #feeding sequence - every "3.5 days"
> feed_days = seq(1,60,by=3.5)
>
> Daphnia <- function(t,x,params){
> C_D = x[2];
> C_A = 0;
> for(t %in% feed_days){
> if t == TRUE {
> C_A = 1.5
> }
> else{
> C_A = 0
> }}
> gamma = params[1]; m_D = params[2]; K_q = params[3]; q_max = params[4];
> M_D = m_D * C_D
> I_A = (C_D * q_max * C_A) / (K_q + C_A)
> r_D = gamma * I_A
> return(
> list(c(
> - I_A,
> r_D - M_D
> )))
> }
>
> library(deSolve)
> results <- ode(init, t, Daphnia, params, method = "lsoda")
>
You have been given a correction for expression for (t %in% feed_days).
But even with that correction things will not do as you seem to want.
The argument "t" of function Daphnia is the integration time the ode solver is
passing and almost certainly is NOT an element of the vector t defined at the
start of your script. That "t" is the "the time sequence for which output is
wanted" (see ode help); it is what is put into the output of ode.
There is no reason to assume that the Daphnia argument t is an element of
feed_days. You can easily check this by inserting a print(t) in Daphnia. So C_A
will be 0 most of the time.
It would certainly help if you named the elements of the init vector and the
return list of Daphnia.
In Daphnia x[2] is C_D. But what is x[1] (C_A?)?
I think you will have to look at deSolve events but I'm not sure if that is
possible or required/desired with your model.
Berend
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