On 6/8/2010 2:03 PM, Ben Bolker wrote:
<cmmu_mile<at> yahoo.com> writes:
Hi,
I have used DeSolve package for my ODE problem regarding
infectious disease transmission and currently am
trying to pass lots (roughly a thousand) of model parameters
to the C compiled model (I have to use C
compiled code instead of R code purely because of the speed).
I can't go define it one by one as it gonna take ages to finish
and also quite difficult to revise. I have read
the instructions in "Writing Code in Compiled Languages", which
is very well written, but still have no
clue on how to proceed.
Please can anyone suggest the best way to go about this, and also the places
where I can find examples of
DeSolve C compiled code.
There's another example of compiled code in
http://www.jstatsoft.org/v33/i09/paper , but it probably
won't say anything the 'Writing Code' guide doesn't already
cover. I found the guide pretty complete ...
I would suggest that you pack your parameters into a single
numeric vector (or several, if that makes more sense) and pass
them that way.
What kind of infectious disease data do you have that will
allow you to fit a model with thousands of parameters ... ??
(Just curious.)
I agree in using vectors (and matrices) like recommended by Ben. In
addition, you may consider to use structures and unions instead of
#define macros:
union my_parms_vec {
struct {double foo1, foo2, bar[15];};
double value[18];
};
static my_parms_vec p;
// ...
// This structure has then to be initialized
// as vector 'value' in initmod:
/* initializer */
void initmod(void (* odeparms)(int *, double *))
{
int N=3;
odeparms(&N, p.value);
}
// so that you can use constructs like
p.foo or p.bar[7] in your model (i.e. derivs) function.
With respect of the large number of parameters you may think whether
they are really "parameters" and not something like external forcings,
for which recent versions of deSolve have separate mechanisms to deal
with. See ?forcings
Hope it helps
Thomas Petzoldt
PS: There is also a dedicated mailing list for discussions like this:
https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models
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