ode first step
Have you looked at the vignette in the deSolve package?
(deS <- vignette('compiledCode')) # opens a "pdf" file
Stangle(deS$file) # writes an R script file to "getwd()"
In spite of the name, this vignette includes an example entirely
in R. By comparing it with your code, I see that you do NOT provide a
connection between y, parms, K1, C0, m, V, K2 and q. Something like the
following might work:
kinetic.model<-function(t,y,parms){
dq.dt = parms['K1']*y['C0'] - (parms['K1']*y['m']/y['V']+ parms['K2'])*y['q']
list(dq.dt)
}
This may not be correct, but I hope the changes will help you see
how to make it work.
Bon Chance.
Spencer Graves
Benoit Boulinguiez wrote:
As I do not thoroughly understand the way 'lsoda' works, I face some
difficulties to 'get' myself into the function(), though I changed the code
as follows:
------------------------------
require(deSolve)
qm<-0.36
y0<-c(0)
parms<-c("K1","K2")
times<-seq(0,10000,1)
kinetic.model<-function(t,y,parms){
dq.dt = K1*C0 - (K1*m/V+ K2)*q
list(dq.dt)
}
foo<-lsoda(y0,times,kinetic.model,parms)
Error in func(time, state, parms, ...) : object 'K1' not found
------------------------------
'K1' and 'K2' are parameters but 'C' is not a parameter, it's a dependant
variable of the time.
I actually express it as a function of q(t) to get this new equation
dq/dt= K1*C0 - (K1*m/V+ K2)*q(t)
where K1 and K2 are the unknown but desired parameters and {C0,m,V} are
constant known values.
Nevertheless, I still get this 'Error about object 'K1' not found'.
Regards/Cordialement
Benoit Boulinguiez
-----Message d'origine-----
De : Dieter Menne [mailto:dieter.menne at menne-biomed.de]
Envoy? : jeudi 14 mai 2009 12:12
? : 'Benoit Boulinguiez'
Objet : RE: [R] ode first step
Try to hide yourself inside the function(). What would you see? No K1, for
sure, no C, no K2.
These are passed through parms, so parms["K1"] would work, but not for C,
you should add it.
-----Original Message-----
From: Benoit Boulinguiez [mailto:benoit.boulinguiez at ensc-rennes.fr]
Sent: Thursday, May 14, 2009 11:53 AM
To: 'Dieter Menne'
Subject: RE: [R] ode first step
------------------------------
qm<-0.36
y0<-c(0)
parms<-c(K1=1,K2=1)
times<-seq(0,10000,1)
kinetic.model<-function(t,y,parms){
dq.dt<- K1*C*(qm-q)-K2*q
list(dq.dt)
}
require(deSolve)
nls(foo<-lsoda(y0,times,kinetic.model,parms)
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