R help - Aug 2011 - deSolve, extracting variable values from inside ode function

I'm just getting to grips with using ode function and have used the 
examples and vignettes to produce a small model of a one-pool, 
michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate 
into pool A is constant (fluxoa) however the rate of flux out of pool A 
is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A 
))     ).  This function works fine and gives correct answers for the 
size of the pool of quantity of substrate in pool A at all times, 
however if possible I'd like to also extract the values of interim 
variables at each time t.  Could anyone give me a clue of how to include 
the value of CA at each time t, along with QA in the results?

Thanks

Jim

R code
=================parameters <- c(vola = 17.3629, vmax = 4.7, mmk = 0.5435,
fluxoa                  2.389)
state <- c(QA=9.437)

MM <- function(t, state, parameters) {
   with(as.list(c(state, parameters)),{
     ## concentration of substrate in pool A, quantity
     ## divided by the volume of the solvent pool
     CA <- QA/vola
     ## output of substrate from pool A
     fluxao <- vmax / (1 + (mmk/CA))
     ## rate of change of quantity of substrate
     ## in pool A
     dA <- fluxoa - fluxao
     ## return the rate of change
     list(dA)
   })
}

times <- seq(0, 100, by = 5)
library(deSolve)
out1 <- ode(y = state, times = times, func = MM, parms = parameters)
head(out1)


-- 
Dr. Jim Maas
University of East Anglia

jamaas wrote:
> 
> I'm just getting to grips with using ode function and have used the 
> examples and vignettes to produce a small model of a one-pool, 
> michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate 
> into pool A is constant (fluxoa) however the rate of flux out of pool A 
> is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A 
> ))     ).  This function works fine and gives correct answers for the 
> size of the pool of quantity of substrate in pool A at all times, 
> however if possible I'd like to also extract the values of interim 
> variables at each time t.  Could anyone give me a clue of how to include 
> the value of CA at each time t, along with QA in the results?
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> 
> Thanks
> 
> Jim
> 
> R code
> =================> parameters <- c(vola = 17.3629, vmax = 4.7, mmk =
0.5435, fluxoa >                  2.389)
> state <- c(QA=9.437)
> 
> MM <- function(t, state, parameters) {
>    with(as.list(c(state, parameters)),{
>      ## concentration of substrate in pool A, quantity
>      ## divided by the volume of the solvent pool
>      CA <- QA/vola
>      ## output of substrate from pool A
>      fluxao <- vmax / (1 + (mmk/CA))
>      ## rate of change of quantity of substrate
>      ## in pool A
>      dA <- fluxoa - fluxao
>      ## return the rate of change
>      list(dA)
>    })
> }
> 
> times <- seq(0, 100, by = 5)
> library(deSolve)
> out1 <- ode(y = state, times = times, func = MM, parms = parameters)
> head(out1)
> 
See this very recent post on R-help:
http://r.789695.n4.nabble.com/deSolve-output-td3738970.html
And a reply: http://r.789695.n4.nabble.com/deSolve-output-td3740431.html

Modify your function to this

MM <- function(t, state, parameters) { 
   with(as.list(c(state, parameters)),{ 
     ## concentration of substrate in pool A, quantity 
     ## divided by the volume of the solvent pool 
     CA <- QA/vola 
     ## output of substrate from pool A 
     fluxao <- vmax / (1 + (mmk/CA)) 
     ## rate of change of quantity of substrate 
     ## in pool A 
     dA <- fluxoa - fluxao 
     ## return the rate of change 
     list(dA, CA=CA)   ### <<<=== Add stuff at the end
   }) 
} 


It is in the documentation for ode (in the description of "func")

Berend


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