Dear Fred,
during object creation, the values of the slots are not accessible by
each other for principle reasons and this is the case where a special
initialization mecahism "initfunc" comes into play. The "initfunc" gets
the raw incomplete version of the object (called object in creation) and
one has all methods to access and manipulate the slots.
See package vignette or http://www.jstatsoft.org/v22/i09 for an example.
For the "lvfred" example, different possibilities exist (see below), but
for your other problem you don't need "initfunc", just add the
parameters of the sine function to the parms vector:
parms = c( ......, Tm = 12, Ampl = 6, Per = 365, Faz <- 365/12, ....)
and call the signal in the "main" model function:
with(as.list(c(init, parms)),{
tempC <- Tm - Ampl * sin((2*pi*times / Per) - Faz)
.......
})
For more complicated cases with real data, use something like the
following, where lvfred2 with approxfun is more flexible and faster.
Hope it helps
Thomas P.
require(simecol)
lvfred <- odeModel(
main = function(time, init, parms, inputs) {
s.in <- approxTime1(inputs, time, rule = 2)["s.in"]
with(as.list(c(init, parms)),{
ds <- s.in - b*s*p + g*k
dp <- c*s*p - d*k*p
dk <- e*p*k - f*k
list(c(ds, dp, dk), s.in)
})
},
parms = c(b = 0.1, c = 0.1, d = 0.1, e = 0.1, f = 0.1, g = 0.05),
times = seq(from = 0, to = 365, by = 1),
init = c(s = 1, p = 1, k = 1), # substrate, producer, consumer
solver = "lsoda",
initfunc = function(obj) {
tmp <- as.matrix(data.frame(
time = times(obj),
s.in = c(rep(0.1,99), rep(0.2,101), rep(0.1, 166))
))
inputs(obj) <- tmp
return(obj)
}
)
##==============================================================================
lvfred2 <- odeModel(
main = function(time, init, parms, inputs) {
s.in <- inputs$signal(time)
with(as.list(c(init, parms)),{
ds <- s.in - b*s*p + g*k
dp <- c*s*p - d*k*p
dk <- e*p*k - f*k
list(c(ds, dp, dk), s.in = s.in)
})
},
parms = c(b = 0.1, c = 0.1, d = 0.1, e = 0.1, f = 0.1, g = 0.05),
times = seq(from = 0, to = 365, by = 1),
init = c(s = 1, p = 1, k = 1), # substrate, producer, consumer
solver = "lsoda",
initfunc = function(obj) {
tmp <- approxfun(times(obj),
c(rep(0.1,99), rep(0.2,101), rep(0.1, 166)))
inputs(obj) <- list(signal = tmp)
obj
}
)
system.time(plot(sim(lvfred)))
system.time(plot(sim(lvfred2)))