[R] Fitting data with optim or nls--different time scales
spencer.graves at pdf.com
Thu Aug 10 10:40:59 CEST 2006
<see in line>
Leslie Chavez wrote:
> I have a system of ODE's I can solve with lsoda.
> #parameter definitions
> lambda=parms; beta=parms;
> d = parms; delta = parms;
> p=parms; c=parms
> xdot = lambda - (d*x)- (beta*x*x)
> xdot = (beta*x*x) - (delta*x)
> xdot = (p*x) - (c*x)
> I want to fit the output out[,4] to experimental data that is only
> available on days 0, 7, 12, 14, 17, and 20. I don't know how to set up
> optim or nls so that it takes out[,4] on the appropriate day, but still
> runs lsoda on a time scale of 0.01 day.
> Below is the function I've been using to run 'optim', at the
> course-grained time scale:
SG: What about the following:
lsodaTimes <- seq(min(times),max(times), by=0.01)
obsTimes <- (100*times-1)
Your example is not self contained, so obviously I haven't tried this
with it. However, something of this nature should work fine, I believe.
Something similar but different should also work, I believe, with
'nls'; this would give you access to many helper functions (see
"methods(class='nls')"). If 'nls' bombed on me, I'd then try 'optim' as
it is less brittle. Then I might use the output of 'optim' as initial
values for 'nls' to get confidence intervals etc.
hope this helps.
> #parms(lambda, beta, d, delta, p, c)
> s0=c(49994,8456,6.16E-8,0.012) #initial values
> Right now, lsoda is being run on too course-grained a time scale in the
> function Modelfit. Most examples of optim and nls I have found compare
> two data sets at the same times, and run lsoda on the time scale the
> data is available at, but I would like to run lsoda at a finer scale, and
> only compare the appropriate time points with the experiment. I have also
> tried using nls, but I have the same problem. Does anyone have
> Thank you very much,
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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